is crispr/cas 9 going to deliver on the promise of the human genome?

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ISSUE 3 May/June 2015 www.frontlinegenomics.com

A NEW REVOLUTION IN GENOMICS IS CRISPR/CAS 9 GOING TO DELIVER ON THE PROMISE OF THE HUMAN GENOME?

A HOME FOR N OF 1 TRIALS Elaine Mardis tells the story behind Molecular Case Studies.

MAKING GENOMICS WORK, TODAY AstraZeneca’s Brian Dougherty talks about life in industry and ‘just do it’.

GENOME EDITING IN FOCUS Merck’s Michele Cleary and IGI’s Jacob Corn take us through the facts about genome editing.

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WELCOME T

There’s been one story dominating the genomic landscape lately: Genome Editing. The CRISPR/Cas9 system has given us some compelling stories. The IP battle resulted in increased media exposure for the science and the people involved. As the story developed, so did some of the questions being asked around the applications of genome editing. Then the rumours started to fly around – had a group in China already tested out CRISPR in human embryos? Had George Church’s group already done it in secret? The narrative suddenly seemed more like the space race, or the nuclear arms race. It reminded us that science is big business and is worth a lot of money. Towards the end of March, we started to hear increasingly cryptic clues. Some people knew what was coming, and they would eagerly let you know that there would be “big news” in April. Then it landed at long last; ‘CRISPR/Cas9mediated gene editing in human tripronuclear zygotes’ by Liang et al. Protein & Cell, published the first reported use of a human embryo for the purposes of genome editing. The story was picked up everywhere. The general media loved it. For those working in genome editing, the ethical considerations are nothing new. There has been a lot of work on that side of things already. What the publication did was open out that conversation. Everywhere, people were debating whether editing the germline was morally ok or not. It’s a fascinating question, and it’s something that divides opinion. Where do we draw the line? One thing we can all agree on is that there is still a lot of work to be done before you can realistically use CRISPR/ Cas9 in a viable human embryo. But whether we should or not?-I don’t know. Francis Collins came out and stated the NIH position very clearly. They’re not going to fund that kind of work. You’ll be hard pressed to find too many people who come out in an official capacity contradicting his view outright. What you will find is a lot of caution and

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leaving the door open for it. So maybe there is another thing we can all agree on; it’s an interesting time in science history. Here at Front Line Genomics, we’ve been busier than usual. We’ve been hitting the road, and getting the opportunity to meet some amazing people. It’s been very gratifying to see the magazine get a good reception, but it’s been even better seeing people get excited by what we’re trying to do as an organisation. June is going to be a big month for us, as the Festival of Genomics finally takes place. It will be the culmination of a lot of hard work from a lot of people. And not just from Front Line Genomics. A small army of people have engaged on the project to help in putting together the agenda, stepping up to present on stage, and to support as a sponsor. We’re looking forward to seeing it all come to life now and making sure all that support pays off! n

Editorial Enquiries Carl Smith Ph.D. Managing Editor, Front Line Genomics E: [email protected] T: +44 (0) 207 384 7797 Advertising Enquiries Freddy White Commercial Director, Front Line Genomics E: [email protected] T: +44 (0) 207 384 8155

FOR THOSE WORKING IN GENOME EDITING, THE ETHICAL CONSIDERATIONS ARE NOTHING NEW. THERE HAS BEEN A LOT OF WORK ON THAT SIDE OF THINGS ALREADY.

About Us Our mission is to help bring the benefits of genomics to patients faster. To achieve this, we work with the smartest people and organizations to produce a series of events and a free-to-access web portal & magazine for the genomics community. Our products are designed to support scientists, clinicians, business/research leaders and officials, from academia, research institutes, industry, healthcare and government organizations.

May/June 2015 / Frontline Genomics Magazine / 1

CONTENTS May 2015 1 WELCOME

24

Managing Editor, Carl Smith, reflects on the major developments between issues and outlines key areas of focus at FLG.

4 MAKING THE MAGAZINE Find out who helped put the magazine together and who contributed to this issue.

5 GENOMIC LENS

This issue’s photo is of our ‘Firestarters’ responsible for Race The Helix, on their recent visit to Greenwood Genetic Center.

7 ROUND UP

GENOMIC RESEARCH We look at deCODE’s volley of publications on their Icelandic cohort.

9 ROUND UP

BUSINESS & FUNDING

7

Genomics England have made the first steps in establishing formal relationships with Pharma & Biotech, with the GENE Consortium.

11 ROUND UP

SCIENCE RESEARCH We take a look at Human Genome editing in light of recent publications and announcements.

13 OUR PICK FROM THE WEB

We review Neil Davies’s turn on Authors at Google, talking about his work and themes in his book ‘Biocode - The New Age Of Genomics’.

14 INTERVIEW

Building An Open Access Forum For N of 1 Studies – Molecular Case Studies, Editor-In-Chief, Elaine Mardis tells us the story behind the new journal ahead of its launch later this year.

18 COMMENT

The Next Generation Sequencing Revolution: A View From The Inside – Mayo Clinic’s David Smith, takes us through his journey with next generation sequencing. With the market opening up a little, he tells us who he thinks is well positioned to grab a bigger share.

24 COMMENT

Achieving The Genome Payoff In the Age of CRISPR/Cas9 With all the talk around genome editing focusing on the moral and ethical dilemma of germline editing, it’s easy to forget how beneficial the technology can be for drug developers. Michele Cleary gives us a run through of why CRISPR/Cas9 is going to finally fulfill the promise of the Human Genome.

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28 INTERVIEW

47

Speculative Fiction Has Been Preparing Us For This Moment. - Innovative Genomics Initiative’s Jacob Corn, talks us through where we really are with human genome editing.

33 INTERVIEW

Just Do It - Making Genomics Work, Today. AstraZeneca’s, Brian Dougherty has been riding the wave of the genomics revolution since the 90’s. Ahead of his Festival of Genomics appearance, we get a preview of what he’s going to be sharing with the crowd.

39 COMMENT

Unlocking The Potential Of Genomics In Healthcare - Ang Davies and Jan Taylor, take a critical look at the integration of genomics into healthcare. For all the benefits promised, there is still a big shortage in clinical bioinformaticians, and a lot of work to be done on the data management side.

28

42 FESTIVAL OF GENOMICS

A preview of what to expect at The Festival of Genomics this summer.

33

47 INTERVIEW

The Man Who Makes Bioinformatics Fun And Accessible For All - Keith Bradnam is one of the most recognisable names and faces to come out of the growing bioinformatics community. As one of the field’s greatest communicators, he’s almost certainly already helped you out somewhere along the way.

44 FIRESTARTER

52

Race The Helix – Greenwood Genetic Center has a reputation for going ‘above and beyond’ for the families they help. Here we have the fascinating story of how they helped the Shenal family, and how their appreciation has led to the fund raising event ‘Race The Helix’.

52 REVIEW

Are You A Replicant? – Synthetic biology and genomic tinkering are starting to show us a glimpse of what might be possible in the future. In this issue we take a look back at Blade Runner and its noir take on synthetic life.

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Sign up and become a Front Line Genomics member. It’s completely free of charge. Receive exclusive content and discounts on event registration. For full list of benefits and sign up, visit www.frontlinegenomics.com/become-member

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MAKING THE MAGAZINE T

his has been a particularly exciting issue to pull together. For the first time we faced a new challenge: how do we keep the visual impact without doubling the size of the magazine? From a content point of view, that’s an amazing problem to have! The IS CRISPR/CAS 9 GOING TO DELIVER ON THE balance was scaling PROMISE OF THE HUMAN GENOME? back on some of the supporting imaging we use. One of the things we’ve been A HOME FOR N MAKING GENOME EDITING OF 1 TRIALS GENOMICS WORK, IN FOCUS TODAY adamant about from the beginning, is that this would be a magazine about people. So we sacrificed some of the fancier images, to allow the photographs to keep their prominence. Luckily, our interviewees and contributors have done a great job in sending us in some great photos to use! ISSUE 3 May/June 2015

www.frontlinegenomics.com

A NEW REVOLUTION IN GENOMICS Elaine Mardis tells the story behind Molecular Case Studies.

AstraZeneca’s Brian Dougherty talks about life in industry and ‘just do it’.

Merck’s Michele Cleary and IGI’s Jacob Corn take us through the facts about genome editing

ADVISORY BOARD Jean-Claude Marshall Director, Clinical Pharmacogenomics Lab Pfizer

David Smith Professor of Laboratory Medicine & Pathology and Chair of Technology Assessment Committee for the Center for Individualized Medicine Mayo Clinic Gholson Lyon Assistant Professor Cold Spring Harbor Laboratory

Alka Chaubey Director, Cytogenetics Laboratory Greenwood Genetic Center

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CONTRIBUTORS Carl Smith / Managing Editor For this issue’s pick of the web, Carl reviews Neil Davies’s turn on the ‘Authors at Google’ series. The talk explains how genomics is being applied to give us a better understanding of ourselves and the systems in which we live. In this issue’s movie review, Carl considers the relevance of Blade Runner, in today’s world.

David Smith / Mayo Clinic David is one of the early adopters of Next Generation Sequencing. He recounts his own journey, realising that the technology had the potential to revolutionise research and change his lecture slides! A decade later, the technology continues to develop, but is product life cycle becoming too short to deliver value for money?

Michele Cleary / Merck & Co Back in 2010, Michele was asked why our knowledge of the human genome had not yet enabled new medicines. Five years on, she reflects on that encounter and builds a compelling case as to why the Genome is going to payoff in the age of CRISPR/Cas9.

Ang Davies / The University of Manchester & Jan Taylor / St. James Institute of Oncology Ang and Jan take a look at clinical bioinformatics. Now that the diagnostic odyssey may soon be a thing of the past, it’s time to address how the huge quantitates of genomic data need to be efficiently managed, and the shortage of skilled clinical bioinformaticians who put it to turn it into useful information.

Photo courtesy of jon holloway

The Shenal Family visited Greenwood Genetic Center this month. Take a look at our FireStarter article to find out how their relationship with GGC started and how you can ‘Race The Helix’ to support their mission.

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We never We never stop seeking. stop seeking. We are driven to know more—to relentlessly search for the answers that will advance the understanding of genomics We are driven to know more—to relentlessly search for theto improve Andthe weunderstanding realize we can’t do it alone.to answers human that willhealth. advance of genomics We’re counting the next of scientific to improve human on health. And generation we realize we can’t do minds it alone. help keep up on thethe momentum. As the leading developer We’reuscounting next generation of scientific mindsoftolife science technologies and services, accelerate genetic help us keep up the momentum. As we the help leading developer of life research and its use in the fields of cancer, hereditary disease, science technologies and services, we help accelerate genetic reproductive disease, forensics, and agriculture. research andhealth, its useinfectious in the fields of cancer, hereditary disease, Together, we’ll realize the promise of personalized medicine. reproductive health, infectious disease, forensics, and agriculture. Together, we’ll realize the promise of personalized medicine. www.Illumina.com/vision www.Illumina.com/vision

Illumina is proud to be a founding partner of Front Line Genomics. Illumina is proud to be a founding partner Front Genomics. © 2015 Illumina, Inc. All rights reserved. Illumina, the pumpkin of orange color,Line and the Genetic Energy streaming bases design are trademarks of Illumina, Inc. in the U.S. and/or other countries. © 2015 Illumina, Inc. All rights reserved. Illumina, the pumpkin orange color, and the Genetic Energy streaming bases design are trademarks of Illumina, Inc. in the U.S. and/or other countries.

GENOMICS ROUND UP

PUBLIC ATTITUDE ON GENOMIC DATA PUBLISHED The European Journal of Human Genetics published the results of the world’s largest survey of public attitudes towards genomic data. The study was led by the Wellcome Trust Sanger Institute’s Deciphering Developmental Disorders (DDD) project. This study, and its publication, is a major step forward in the on-going discussions around the reporting of incidental findings. Efforts to increase the scale of genomics, and integrate the technology into healthcare, are raising new ethical questions that need to be considered carefully. Building an adequate consent framework is amongst the most challenging. Policy should have the patient’s best interests at heart. The only way you can achieve that is by making sure that they are given a voice and an opportunity to influence these decisions. It is also important to balance empathy and the need for information with what is practical for researchers. In some cases, it may not be practical to pursue and report every incidental finding.

“BY LOOKING AT THE WIDER POPULATION, AND ‘HEALTHY’ PEOPLE, YOU CAN START TO SEE A MUCH MORE DETAILED PICTURE.”

ICELANDIC POPULATION DATA SHOWS THE WAY FOR GENOMICS RESEARCH

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here have been some big stories and big publications over the past couple of months. As far as genomic research is concerned, one can make the case that deCODE’s volley of publications in Nature Genetics was right up there with the biggest.

of the dangers of over-hype in genomics. What the group here have done, is deliver on that hype. The ability to look at gene effects in human knockouts is a mouthwatering proposition. Beyond that, they demonstrate a shift in mentality that has been coming for a while.

For those who may have missed them, the published studies are built around the most comprehensive, population-wide, tally to date of sequence variation. The four papers were: Largescale whole-genome sequencing of the Icelandic populations; Identification of a large set of rare complete human knockouts; The Y-Chromosome point mutation rate in humans; and Loss-offunction variants in ABCA7 confer risk of Alzheimer’s disease.

The majority of sequencing studies will gather a cohort based on a particular disease. This can identify variants that correlate very strongly with that particular condition, but only tell half the story. By looking at the wider population, and ‘healthy’ people, you can start to see a much more detailed picture. Where else is that variant present? Are there other variants that impact its effect? There is a lot of information to be gleaned from this kind of study that will ultimately lead to better diagnostics and much better healthcare. n

In the last issue of the magazine, we looked at some

DECODE GENETICS deCODE genetics was founded in 1996 by Kari Stefansson in Iceland. The company seeks to identify human genes associated with common diseases by the use of population studies. This information can then be used to help inform drug discovery and development.

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BUSINESS & FUNDING ROUND UP

NEWS ROUNDUP Human Longevity collaborate with Cleveland Clinic to sequence and analyse GeneBank.

Pacific Biosciences and RainDance Technologies codeveloping de novo whole genome assembly solutions. Francis Collins states “NIH will not fund any use of gene-editing technologies in human embryos”. BGI opt for PacBio RS II and upgrade their partnership with QIAGEN. Congenica raises an additional £2.2M from Amadeus Capital Partners and Cambridge Innovation Capital. $15 million investment and alliance puts WuXi NextCODE’s genome analytics on DNAnexus’s cloud platform. AstraZeneca and Montreal Heart Institute collaborate to genotype 80,000 samples from AZ’s biobank of blood and tissue samples. Evotec get a $286 million boost from Sanofi deal, to accelerate R&D.

“ONE OF THE GOALS OF THE 100,000 GENOMES PROJECT IS TO CREATE A FUNCTIONAL DATABASE THAT CAN BE USED TO HELP DEVELOP THE NEXT GENERATION OF PRECISION THERAPIES.”

GENE CONSORTIUM FORMED TO TRIAL 100,000 GENOMES PROJECT

G

enomics England announced the formation of the Genomics Expert Network for Enterprises (GENE) Consortium. This is a group of ten pharmaceutical and biotech companies that will oversee a year-long industry trial around the 100,000 Genomes Project. One of the goals of the 100,000 Genomes Project is to create a functional database that can be used to help develop the next generation of precision therapies. The formation of the consortium is the first formal step in developing this relationship. The companies involved will be working on data across cancer and rare diseases to understand how best to collaborate with clinicians and researchers. Genomics England will also be working with data analysis companies to work out some of the technical aspects of keeping data secure while making it accessible for these groups.

The 100,000 Genomes Project is going to be compared to the USA’s Precision Medicine Initiative. They both have similar goals of sequencing large cohorts, and integrating genomics into healthcare. As far as large datasets go, they will also have to compete with the 23andMe Research Portal, and any future offering from Ancestry.com. Following the FDA’s approval of 23andMe’s Bloom syndrome, the market for direct-to-consumer testing has the potential to open up again. Ancestry. com, who have already collected DNA from 850,000 customers, have stated their interest in pursuing a medical offering. They are currently exploring the idea of collecting users’ medical histories, to explore the genetic basis of disease. If they do move ahead, it will be intriguing to see if they too feel the commercial pull of drug developer interest in their database. n

GENE CONSORTIUM The ten founding companies of the GENE Consortium are: • AbbVie • GSK • Alexion Pharmaceuticals • Helomics • AstraZeneca • Roche • Biogen • Takeda • Dimension Therapeutics • UCB

May/June 2015 / Frontline Genomics Magazine / 9

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SCIENCE ROUND UP

PARALLEL SEQUENCING UNVEILED April saw Genome and Transcriptome Sequencing (G&Tseq) debut in Nature Methods. The paper itself, G&T-seq: parallel sequencing of single-cell genomes and transcriptomes, describes the method used to separate and sequence genomic DNA and full-length mRNA from single cells. This allows for an impressive level of detail when observing cells. Sequencing genomic DNA only tells you part of a story. Each cell in our body shares the same genome, but can develop in very different ways. Being able to look at not just genomic sequences but, gene expression data as well, helps give a clearer idea of the functional consequences of genetic variation. The scale up of this technology will be interesting. The published study looked at around 220 cells. To give more meaningful insights into the heterogeneity of cells in a tissue, they will need to be able to look at thousands of cells at a time. As the cost of genome sequencing continues to drop, the outlook looks very promising for G&T-seq.

“FROM A POSITIVE PERSPECTIVE, IT’S EXCITING TO THINK THAT WE ARE AT A SCIENTIFIC FRONTIER THAT COULD CHANGE THINGS SO SIGNIFICANTLY.”

EDITING THE HUMAN GENOME

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RISPR/Cas9-mediated gene editing in human tripronuclear zygotes. It was one of the worst kept secrets out there, but the much rumoured use of genome editing techniques on human embryos was finally published in April. It was quickly sensationalised in the general media, and was at the core of several ethical discussions. It should be noted that the study conformed to ethical standards of the World Medical Association’s Helsinki Declaration on the ethical principles for medical research involving human subjects. Some parties have suggested that the regulatory framework in China is a little more relaxed than in the west. However, those closer to the issue recognise the importance of ensuring policy is kept contemporary. The issue here isn’t that the study has taken place. It was all

fully consented and in-line with global ethics. The issue is – what happens next? The study shows the need to improve the fidelity and specificity of the CRISPR/ Cas9 platform before it is even considered for any clinical applications. Francis Collins has already come out and stated “…NIH will not fund any use of gene-editing technologies in human embryos.” Many view this as a line that we should never cross. From a positive perspective, it’s exciting to think that we are at a scientific frontier that could change things so significantly. Hopefully it stops short of becoming a political battleground, but for now it will be an extraordinary time to observe and be active in genome editing. It is certainly resurrecting some powerful ethical debates over the limits of mankind’s influence on its own evolution. n

IP BATTLE The CRISPR/Cas platform is also subject to an intense IP battle. The US Patent and Trademark Office, awarded the first patent for use of the system to Feng Zhang (Broad Institute of MIT). However, the IP award is being contested by Jennifer Doudna (UC Berkeley), and Emmanuelle Charpentier (Helmholtz).

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AROUND THE WEB

HOW IS GENOMICS HELPING US UNDERSTAND OURSELVES AND THE WORLD WE LIVE IN?

BIOCODE – THE NEW AGE OF GENOMICS The book describes the rapid rise of genomics, and the unprecedented possibilities it brings. It puts forward potential implications for humans: should all newborns be sequenced at birth? What is the legality around sample collection? It also recounts the latest developments moving from sequencing to the creation of new forms of life. The real meat of the book comes in showing us how genomics is revealing the scale and diversity of life on earth. Highlighting the incredible number of previously unknown viruses and bacteria. It also explores some of the possibilities for genomic observatories and biocoding the whole planet. ‘Biocode – The New Age of Genomics’ is available through Oxford University Press.

O

ur pick of the web for this issue comes from ‘Talks at Google’: Neil Davies | Biocode: The New Age of Genomics | Authors at Google (https://youtu.be/lOqHWLcDs18). Talks at Google, presents an interesting program of authors, musicians and innovators. The premise is to explore the projects that capture the popular and intellectual zeitgeist. With that context, it’s no surprise that genomics is featured in the series. This particular talk is by Neil Davies, Executive Director of UC Berkley’s Gump Station in French Polynesia, based in Moorea. He co-wrote the book Biocode, with Dawn Field from Oxford University. Davies begins by explaining that the book is homage to DNA, describing the world as DNA’s phenotype. After a quick run-through of where we are with DNA and genomic technology today, he guides our attention towards the Pacific islands of Moorea, Tetiaroa, and Tahiti. The geographical context presents an interesting natural system for study. The talk moves quickly through to biodiversity. After a nice analogy with astronomy, he introduces the audience to the concept of organisms as ecosystems. After pointing out the vast majority of our cellular and genetic matter is microbial, he asks whether it should change how we think about ourselves. In short we’re walking ecosystems. This is one of the main messages in his book. To fully understand our health, we need to understand our personal ecosystem. The rise in genomic technology, and drop in price, is helping us to find out more and more. But there are still some uncompressible costs. Although the informatics and processing is getting cheaper, there are still significant costs in collecting samples.

While Davies’s work is in ecosystems, he presents the medical approach as a useful model to adapt. Citing the P4 approach of systems biology (Predictive, Preventative, Participatory, Personalised), suggesting that a ‘genome up’ approach is more useful to answer certain questions, and then working up to a global scale. There are a lot of sequences available, but without the contextual data there is limited value. So improving genomic efforts in biodiversity is crucial to take advantage of the technology. Genomic Observatories are a great presented example of this. This is when the talk really comes into its own. Davies explains some of the opportunities out there for his field, and how it can be scaled up on existing infrastructure and mass-scale coordination. The parallels with the field of medical genomics are very clear. Both fields are making concerted efforts to scale up and contextualise and enrich information with additional layers of detail. And both fields have bioinformatic and database challenges to support that. It’s an interesting look at the application of genomics outside of healthcare. Ecologists don’t have to deal with the same level of consent issues, ethical barriers, and privacy issues. They do, however, deal with an incredibly level of interaction between organisms. Both fields are starting to take advantage of computational methods to further understanding. As these become more and more predictive, the relevance to environmental and health policy are huge. And that’s why we liked this talk so much. It’s a little off topic for us, but it does show how genomic technology is being applied and leveraged to answer other biological questions. It’s also interesting to see how other fields have been approaching similar challenges. n

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INTERVIEW

BUILDING AN OPEN ACCESS FORUM FOR N OF 1 STUDIES Elaine Mardis, Editor-In-Chief, Molecular Case Studies & Co-Director, Robert E. and Louise F. Dunn, Distinguished Professor of Medicine, McDonnell Genome Institute at Washington University

A LOT OF INDIVIDUAL SEQUENCING IS TAKING PLACE. IT’S ABOUT TIME THAT THESE ’N OF 1’ STUDIES HAD AN OPEN ACCESS HOME. ELAINE MARDIS HAS ADDED TO HER, ALREADY IMPRESSIVE, LIST OF ACHIEVEMENTS AND DONE JUST THAT CREATING A NEW JOURNAL, MOLECULAR CASE STUDIES, WITH CSHL PRESS

E

laine Mardis is one of the true ‘Rock Stars’ of genomics. But what elevates someone to that status? A big part of it is seeing the opportunity to go further with what’s available. She was at the very forefront of cancer genome sequencing in the mid 2000’s. This was a big paradigm shift at the time, and one of the major steps that has defined modern genomic practice. Having learned so much from one genome, it’s no surprise she also recognises the value of today’s N of 1 studies. We spoke with Elaine to find out how and why she came up with the concept of Molecular Case Studies - the new journal she now takes charge of as Editor In Chief. FLG: Elaine, looking through your impressive biographical notes, it seems clear you were destined for the world of science from an early age.

“I ALWAYS HAVE FELT THAT GENOMICS HAD AN ADVANTAGE OVER ENGINEERING OR PHYSICS IN THAT IT IS A RELATIVELY “NEW” DISCIPLINE AND WAS THEREFORE QUITE ATTRACTIVE TO WOMEN BECAUSE ESTABLISHED ROLES AND GENDER DOMINATION WASN’T YET A PROBLEM.”

of biochemistry and molecular biology, especially the way he taught it, that I began to visit during his office hours to discuss more. Bruce had recently taken sabbatical in Fred Sanger’s laboratory at the MRC about three years after the 1977 paper describing the Sanger dideoxy method. He was passionate about DNA sequencing and really set up one of the first labs in the US to pursue the Sanger method. I was really just one of many people trained by Bruce who have pursued DNA sequencing in their careers. Perhaps the best other example is my current “partner in crime” at the McDonnell Genome Institute at Washington University, Rick Wilson, who got his PhD a couple of years before I did. FLG: Having finished your PhD in 1989, when the notion of sequencing the human genome was just gaining traction, alongside hard work, how important a role would you say luck has played in your career – of being in the right place at the right time?

EM: I’ve always had a love of science, even from a young age. I recall finding one of my father’s textbooks from his college days, on Zoology, and seeing a picture therein of the duckbill platypus, for the first time. I was captivated by that enigmatic creature, and years later we sequenced the genome of the platypus. So, that brought me full circle, I suppose!

EM: I would say that luck has played a major role in my career! Other than knowing I wanted to be in science for my life’s work, I had no other concrete plan as to how this might be achieved. I feel like my life has been a series of incredibly lucky events and I still feel like the luckiest person in the world to get to do this for a living.

FLG: Your undergraduate degree in Zoology, and PhD in Chemistry and Biochemistry, (both obtained at the University of Oklahoma) is where your curiosity in molecular biology can be traced back to. I guess this led to you becoming interested in DNA sequencing?

FLG: In 2008, you produced your breakthrough paper in which you reported whole genome sequencing of a tumor genome. Can you take us through that journey?

EM: During my senior year at OU, I took a course in Biochemistry that was taught by Bruce Roe. I was so captivated by the notion

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EM: Absolutely. We had begun a program project funded by NCI with Tim Ley to uncover the genetic underpinnings of acute myeloid leukemias (AMLs), that involved PCR and capillary sequencing of candidate genes. After three hard years of work,

“I RECALL FINDING ONE OF MY FATHER’S TEXTBOOKS FROM HIS COLLEGE DAYS, ON ZOOLOGY, AND SEEING A PICTURE THEREIN OF THE DUCKBILL PLATYPUS, FOR THE FIRST TIME. I WAS CAPTIVATED BY THAT ENIGMATIC CREATURE, AND YEARS LATER WE SEQUENCED THE GENOME OF THE PLATYPUS.“

MOLECULAR CASE STUDIES

we hadn’t uncovered too many new genes and this was coincident with our betatesting of the Solexa 1G sequencer (that later was bought by Illumina). So, Tim, Rick and I began to discuss what it would be like to simply use the Solexa instruments we had and take an unbiased look at the AML genome—rather than trying to predict which genes we thought would be mutated, we would instead let the genome tell us what had gone wrong. So, we worked with our colleagues to devise a proposed coverage (we settled on 30-fold) that should cover the genome, and we wrote 10 genome pairs (tumor + normal) into our next five years of the project budget (2 per year). Of course, this was not reviewed favourably and we were asked to resubmit. Realizing this was much too “soon” for conventional funding, we turned to a local philanthropist, Alvin J. Siteman, and asked for the $1M we thought would give us sufficient funding to sequence one patient.

That was AML1, our first patient and the subject of our Nature 2008 manuscript. It was only a single case, but we learned so much! FLG: You’ve recently taken on the role as EDITOR-IN-CHIEF of Molecular Case Studies. Launched in the Spring of this year, the journal’s stated aim is to bring a more rapid peer-review process to publication. Can you give an overview of the fields covered and, indeed, what prompted you to become involved with the project? EM: The journal was an essential concept that I had come to, seeing how much individual sequencing was going on in so many places for different reasons, and knowing that a mechanism to communicate “N of 1” studies was going to be vital to helping these different sites stay abreast of what other sites were generating,

Cold Spring Harbor Molecular Case Studies is an open-access, peerreviewed, international journal in the field of precision medicine. Articles in the journal present genomic and molecular analyses of individuals or cohorts alongside their clinical presentations and phenotypic information. The journal’s purpose is to rapidly share insights into disease development and treatment gained by application of genomics, proteomics, metabolomics, biomarker analysis, and other approaches. The journal covers the fields of cancer, complex diseases, monogenic disorders, mitochondrial diseases, neurological conditions, orphan diseases, infectious disease, and pharmacogenomics. It has a rapid peer-review process that is based on technical evaluation of the analyses performed, not the novelty of findings, and offers a swift, clear path to publication. Article types include Research Reports that present detailed case studies of individuals and small cohorts, Research Articles that describe more extensive work using larger cohorts and/or functional analyses, and Follow-up Reports linked to previous observations published in the journal.

May/June 2015 / Frontline Genomics Magazine / 15

Elaine Mardis Editor-In-Chief Molecular Case Studies Dr Mardis joined The Genome Institute at Washington University School of Medicine in 1993. As Director of Technology Development, she helped to create methods and automation pipelines for sequencing the Human Genome. She is a Professor in the Department of Genetics, with an adjunct appointment in the Department of Molecular Microbiology. Before making her name at Washington University, she was a senior research scientist at Bio-Rad Laboratories. She completed her Ph.D. in Chemistry and Biochemistry at the University of Oklahoma. She is the Editor-In-Chief of the new peerreviewed journal, Molecular Case Studies.

to helping everyone understand new variants that were being identified, treated, and used in diagnosis. I brought the idea to several entities in the scientific publishing business, and the folks at CSHL Press did some investigational work and came back to me with the proposal to start the journal. This is not a sequencing-only journal, as we encourage other reports that utilize “omic” data to solve patient diagnoses or to uncover new treatments, etc. FLG: There is a growing weight behind the call for more open access publications. Are we finally seeing a gradual change toward this? EM: I quite agree. For MCS, open access is critical to the mission and success of the journal, allowing engagement from scientists, clinicians, and patients. All of the papers will be published continuously online and can be read by anyone, facilitating the rapid dissemination of potentially clinically relevant insights into disease and treatment options. To be clear, we are keen to publish open access n of 1 studies, but of course we must balance this with respect for patient anonymity and other legal restrictions on sharing patient data. In general, we’ve seen only positive feedback for these central tenets of our approach. FLG: With advertising and subscription revenues supporting publications, there are many who feel submission fees are unjustified. The purpose of peer reviewed publishing, is to create a critical forum for knowledge sharing, is there a risk of the commercial element working against that goal? EM: It’s a fair question, but I must point out that for MCS, there are no subscription or submission fees, and all articles are free online for anyone to read. To cover the costs associated with publication, the authors pay an Open Access fee per paper, which is on a sliding scale. Since CSHL is a not-for-profit research and educational institution, the launch of MCS is fully in-line with their mission. FLG: It’s easy to see the publisher as ‘the bad guy’ in some of

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this, but often times there is some naivety around what goes into producing a journal. Is there anything that has surprised you or that you think would surprise people about the work that goes on behind the scenes? EM: Other than it’s a lot of hard work? I guess there probably isn’t anything too surprising other than the difficulty in getting people who you really think would be good to volunteer their time for the peer review. It’s a fundamental worry that I think a lot of us have, that ensures the science being presented is rigorous and well controlled. FLG: The ultimate goal of an n-of-1 trial being to determine the optimal, or best, intervention for an individual patient using objective data-driven criteria. Now that there is a publishing home for this kind of study do you believe n-of-1 trials will have an increasing role in clinical science? EM: I think the primary impact of “N of 1” studies will initially be to generate a recognition that the pursuit of these studies can and will have clinical utility, to help patients receive appropriate therapy or diagnosis or both. Perhaps the underlying value of these studies will be to emphasize how much better the collective sharing of information can make our medical pursuit of excellence for every patient. FLG: Coordinated n-of-1 trials have the potential to radically change the way in which evidence-based and individualized medicine is pursued, how do you foresee the development of benefits going forward in terms of patient care? EM: The primary benefit will be to emphasize the clinical utility that is brought to bear on individual patients by these trials. There already are groups accruing the data and evidence to support this clinical utility. However, we are experiencing many of the same barriers to effective implementation and one hope is that open access information sharing will ease at least a few of these barriers to implementation. Here, I wish to emphasize that even negative

EM: I think the best advice I could offer is as follows: 1) be a good collaborator by having respect for the expertise others bring to bear on the problem you all care about solving, and 2) insist that they do the same regarding your contributions. Team or collaborative science can be such an amazing enterprise when everyone respects each other and everyone contributes equally, with enthusiasm and a shared set of goals. FLG: There is increasingly wider attention on female representation within the genomics field. Bioinformatics is one area in particular that is heavily male dominated. When you ask people who the most famous female in genomics is, you’re almost always the first name people think of. In contrast, people will give a list of names when asked from prominent men in the field. Is this still an artefact of slow changing social prejudices? What should we be doing to make the field a more attractive career path for women, and ensure that they get the same opportunities to take on leadership positions? EM: So, firstly that is surprising to me—there are many, many successful women in genomics besides me. I always have felt that genomics had an advantage over engineering or physics in that it is a relatively “new” discipline and was therefore quite attractive to women because established roles and gender domination wasn’t yet a problem. I am sensitive to the fact that women tend to not stay in science due to their desire to fulfil other roles such as that of primary caregiver to children (and sometimes to aging parents). I’m not sure how that can be fixed, however. It’s a complex problem.

FLG: Despite some of the discontent felt at times, Genomics is an exceptionally exciting field at the moment. Whether it is the advances in technology, the applications they open up, or the new influx of expertise from computer sciences, there’s a lot to get excited about. What is capturing your imagination most at the moment? EM: The most interesting thing to think about is how many different groups of very smart researchers are focused on the many aspects of precision medicine, and how interdisciplinary these pursuits have become. It’s an educational opportunity for those involved to learn about new areas of expertise, to share the collective intellectual pursuit of a problem, and to hopefully break new ground in how medicine is practiced. I am personally captivated by work going on that fuses genomics with cancer immunotherapy, and I think there will be dramatic advances in this area over the next few years. FLG: Thank you so much for your time. You’re reputation as not only a rock star of genomics, but also one of the nicest people around, is very well deserved. Before we wish you the best of luck with Molecular Case Studies, is there anything else you would like to say? EM: Only that the success of MCS will be due to the many contributors of research reports to our journal. I sincerely hope everyone will consider submitting their case studies, so we can achieve our mission whilst effectively, quickly and freely communicating the results. n

results that could be informative to others are of interest at MCS.

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FLG: With your work with Washington University continuing to help refine the completion of the human genome, in close collaboration with the NCBI [National Center for Biotechnology Information], how do you perceive the next steps in the sequencing project’s future?

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EM: The continued improvement of the reference genome, and the generation of additional high quality reference genomes should tell us collectively what we miss by alignment of short read data to a fixed reference. I think future-forward that our large-scale studies will be accelerated by these genome-to-genome comparison data and will help us think of new and accelerated analysis paradigms. It’s much like high-energy physics, which has a penchant for only keeping data from new, never documented events that occur in the superconducting supercollider, and throwing out the events that already were seen. At some point, this might be our approach to genomics as well. FLG: Do you have any advice for young scientists embarking along a career path in respect of technological development and its applications in translational research?

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COMMENT

DAVID I SMITH, PH.D. Professor, Department of Laboratory Medicine and Pathology Chairman of the Technology Assessment Group Center for Individualized Medicine MAYO CLINIC

DAVID SMITH, IS MAYO CLINIC’S RESIDENT NGS EXPERT. WHEN NOT RESEARCHING INTO OROPHARYNGEAL CANCER, HE’S ON THE LOOK OUT FOR THE LATEST TECHNOLOGY AND APPLICATIONS.

THE NEXT GENERATION SEQUENCING REVOLUTION:

A VIEW FROM THE INSIDE

THERE IS AN ALMOST INCREDIBLE AMOUNT OF DISCOVERY, INNOVATION, AND APPLICATION TAKING PLACE IN THE FIELD OF GENOMICS TODAY. THIS HAS BEEN A DIRECT RESULT OF THE THE RISE OF NEXT GENERATION SEQUENCING TECHNOLOGY. IS IT TIME TO LOOK AT WHICH TECHNOLOGIES ARE GOING TO TAKE US EVEN FURTHER?

I

n this article I am going to describe my own personal experiences which would completely transform how we did research and more with the excitement that is the next generation sequencing importantly how this could be rapidly translated into clinical practice. revolution. My name is David I Smith and I am a Professor in the What I could not imagine was how rapidly advances would occur with Department of Laboratory Medicine and Pathology at the Mayo massively parallel sequencing. Clinic. For a ten year period I was the Chairman of the Research Core I went to visit 454 in Connecticut several times in 2007 and 2008 Oversight Committee at the Mayo Clinic and for the past several years and saw their advancements that led to increases in sequence output I have been the Chairman of the Technology Assessment Committee of the Genome Sequencer from 20 to eventually 500 Mbs. However, for the Mayo Clinic Center for Individualized Medicine. In this capacity it became obvious that there were a number of key limitations to this I have had the pleasure to not only review the exciting revolutions platform. While I originally thought that these were the cumbersome in DNA sequencing but to also visit the major suppliers of these and messy procedure of emulsion PCR and the limitations of using technologies and to go to many of the centers that are leading the way unblocked nucleotides (the homopolymer problem), the real issue with this revolution. Finally I have been to many with this platform was its’ inability to increase of the next generation sequencing meetings sequence output beyond 500 Mbs. In spite including multiple years at what is clearly the of this, this platform was able to dramatically Academy Awards of sequencing meetings, the reduce the cost of whole genome sequencing Advances in Genome Biology and Technology and they sequenced the second named meetings in Marco Island. individual (James Watson) for a cost of one My first exposure to this revolution occurred million dollars. in 2006 when I attended a seminar given at the The second commercially available NGS Mayo Clinic by 454 where they were talking machine was originally produced by Solexa “CURRENTLY THE SEQUENCING about the Genome Sequencer 20 (GS20). which eventually became Illumina. I went LANDSCAPE FOR BOTH RESEARCH It was capable of 20 megabases (Mbs) of with a number of Mayo colleagues and visited AND ITS CLINICAL TRANSLATION IS sequencing per run of the machine. This was Illumina several times and we were impressed COMPLETELY DOMINATED BY THE astounding at the time. My impression was with a platform that had solved many of the two-fold. First I realized that the slides that I 454 problems including the use of bridge ILLUMINA PLATFORM AND THIS had been presenting to students every year amplification to amplify DNA fragments on DECIDED LACK OF COMPETITION about Sanger sequencing were now completely a flow-cell and blocked fluorescently labeled DOES NOT BENEFIT THE END outdated and the second was that massively nucleotides. The original Illumina Genome parallel sequencing was going to be a huge deal Analyzer was capable of 1 gigabase (Gb) of DNA USERS.”

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COMMENT

“THE PAST 15 YEARS HAS SEEN DRAMATIC IMPROVEMENTS IN SEQUENCING TECHNOLOGIES AND THE CURRENT COST FOR WHOLE GENOME SEQUENCING IS QUICKLY APPROACHING THE $1,000 MARK.”

sequence output which was accomplished by very short sequencing (31 base pairs) of 48 million amplified DNA fragments. The very short DNA fragments were a severe limitation for sequence assembly and the accuracy of the last few bases only increased this problem. However, the major key strength of this platform was the incredible headroom that it had for dramatic increases in sequence output. I was able to obtain funding for a partnership between the Mayo Clinic and the University of Minnesota so that Mayo could obtain their first NGS machine in 2008, the Genome Analyzer (GA), and this was placed in the DNA sequencing Core at the Mayo Clinic to support our researchers. A year later we obtained out second GA (the GA II). When the HiSeq instrument came out we began to purchase these with their considerably greater sequence output. The Genome Sequencing Core of the Mayo Clinic heavily invested in the Illumina sequencing platform and they currently have seven of the different HiSeq instruments. We also have several MiSeq instruments within that research core laboratory. The technological advances on the Illumina platform have been astounding and now the major problem with this platform have been solved due to dramatic increases in obtainable sequence length (which really solved the alignment problems). They

$1000 $1 00 $100 have also had dramatic increases in the number of simultaneous sequences obtained. The increase in sequence output from one Gb to over 1 terrabase in such a short time period on this platform have been absolutely astounding and truly herald in the age of NGS especially for clinical practice. A new problem, however, is that the newest Illumina machines utilize patterned flow cell technology which will quickly make the HiSeq 2000s and 2500s obsolete. Thus, the Mayo Genome Sequencing Core, and other places with large investments in those platforms realize that their multi-million dollar investment quickly becomes obsolete. This is a problem with this entire technology, however perhaps with the patterned flow cell technology there is the capability for slightly longer instrument life cycle, by merely increasing the number of patterned sequencing centers. The third commercially available sequencing platform utilized sequencing by ligatation (the SOLID system). I went to Life Technologies in 2009 and obtained training for to run that machine. Life Technologies also provided me and the Mayo Clinic with a SOLID machine but they never provided any funds for the running of that machine thus we had a machine for over a year but never got to kick its tires in house.

David I Smith, Ph.D. The laboratory of David Smith, uses the most cuttingedge genomic technologies to better understand the molecular alterations that underlie Oropharyngeal cancer development. He is also studying long noncoding RNA. In particular one transcript that appears to be stress-responsive, and is suppressed in most breast cancers studied.

May/June 2015 / Frontline Genomics Magazine / 19

COMMENT

Fortunately Life Technologies did run some of our tumor samples on their platform and we were able to obtain RNAseq data on a number of our tumors which they then analyzed. There were a number of strengths to the SOLID platform. It too utilised blocked nucleotides and because it utilized two-base encoding offered the capabilities of higher sequence accuracy than the Illumina platform. Unfortunately it still utilised emulsion PCR, had a very cumbersome and slow sequencing by ligation strategy, and was very limited in the number of bases it could sequence from any amplified fragment. The biggest problem, however, is that it tried, and failed to play catch-up to the Illumina sequencing platform and this eventually spelled its doom. Life Technologies invested heavily in the Ion Torrent sequencing platform and eventually dropped the SOLID platform. There were a number of advantages to this platform including the utilisation of computer chip manufacturing to produce the sequencing chips, its utilisation of simple unmodified nucleotides, and much faster run times than the Illumina sequencers. Another key advantage of this platform is the ability to start with lower amounts of input DNA for library

“I WENT TO VISIT 454 IN CONNECTICUT SEVERAL TIMES IN 2007 AND 2008 AND SAW THEIR ADVANCEMENTS THAT LED TO INCREASES IN SEQUENCE OUTPUT OF THE GENOME SEQUENCER FROM 20 TO EVENTUALLY 500 MBS.”

2006

20

MEGABASES (MBS)

500 2008

MEGABASES (MBS)

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construction prior to sequencing. However, this platform still utilises emulsion PCR to amplify DNA fragments on beads, and the naked nucleotides suffer from the same homopolymer problem that plagued the 454 platform. The low cost of the PGM machine made it a very easy machine to purchase and many of these machines were sold. However, it has become clear that most of these machines sit idle and that we exist in a world where the vast majority of sequencing is done on the Illumina platform. There have been some dramatic increases in sequence output on the Ion Torrent platform and suggestions that it could provide greater sequence accuracy than the Illumina platform. Unfortunately the promise of continued increases in sequence output has not kept up with expectations and currently this platform offers considerably less sequence output than the Illumina platform. One of the key limitations to both the Illumina and Ion Torrent platforms is relatively short read lengths hence the next generation of NGS machines are those based upon single molecule sequencing. These offer a number of advantages including removing the need for any PCR amplification of DNA fragments and the capabilities of extremely long read lengths. The first viable single molecule sequencer was the Pacific Biosciences machines. Unfortunately sequence accuracy on this platform has and is been one of its major problems (producing only 85% accurate sequencing). A potential solution for this is provided by the utilisation of “smart-bells” so that DNA fragments are sequenced multiple times which produces much more accurate consensus sequences, but dramatically decreases overall sequence output. The past several years has seen increases in sequence output on this machine and the ability to sequence considerably longer DNA fragments (currently in the 10-50 Kb range). However, the promise of a $100 genome in 2014 (originally promised by Dr. Stephen Turner at AGBT in 2009) is little more than a pipe dream. A promising single molecule sequencer is the Oxford Nanopore sequencing platform and this produced considerable buzz when presented at AGBT several years ago. The Minion sequencer is now being provided to a large number of laboratories but the first sequences obtained on this platform were highly inaccurate. There have been some considerable improvements on this platform and the promise of a very large number of nanopores on the GridION system suggest that this platform could in the future produce sufficient sequence to start to overcome the limitations of sequence accuracy upon first pass sequencing. As part of my role in the Technology Assessment Committee, I also visited a number of other companies that are working to develop NGS-based technologies. This includes GnuBio which is developing a fully integrated droplet-based DNA sequencing technology. They were recently acquired by Bio-Rad and offer the capability of sequencing small gene panels with high accuracy. I also visited NabSys which using solid-state nanodetectors to analyze single DNA molecules. While not technically a DNA sequencer it could be useful for the analysis of DNA structural variation and genome mapping. There is also a new sequencing by synthesis platform being developed by Qiagen. One of the strengths is that Qiagen is working on developing an integrated NGS platform with everything from sample prep, automated library construction as well data analysis on the Ingenuity platform. The weakness is apparently their sequencing platform which appears to not be ready for primetime. The current NGS landscape is pretty much defined by the Illumina sequencing platform. They produce a group of machines from low output MiSeq instruments of various flavors to the highest output HiSeq X Ten machines. On the HiSeq X Ten machines you can sequence the human genome below the mythical $1,000 mark. However, this

COMMENT

does not factor two very important things into generate the assembled sequences for you. the equation which are the cost of sequence In addition, it currently is only viable for whole assembly and analysis and perhaps the greater genome and whole exome sequencing. The cost of storing all that information. Hence, is this data generated is also not available for further truly a $1,000 genome? Unfortunately it is not! manipulation. There are rumors that BGI will be In October 2014 I was fortunate to be invited making selling the CGI platform for purchase so “I WENT WITH A NUMBER OF to speak at a BGI Conference in Shenzhen. As that Centers can generate their own sequences part of this Conference I was taken on a tour in house, but these remain rumors at this point MAYO COLLEAGUES AND VISITED of their facilities and shown the Complete in time. ILLUMINA SEVERAL TIMES AND Genomics sequencing platform (they purchased In conclusion the past 15 years has seen WE WERE IMPRESSED WITH A CGI a year earlier). The CGI sequencing platform dramatic improvements in sequencing utilizes DNA nanoballs which are packed tightly technologies and the current cost for whole PLATFORM THAT HAD SOLVED on a silicon chip. They then utilize combinatorial genome sequencing is quickly approaching the MANY OF THE 454 PROBLEMS probe-anchor ligation to sequence the DNA $1,000 mark. These technological improvements INCLUDING THE USE OF BRIDGE within the packed nanoballs. There are a have made these technologies viable for the AMPLIFICATION TO AMPLIFY DNA number of features of this platform that are total and complete transformation of clinical very attractive. The most attractive feature is practice, a subject for its own discussion. FRAGMENTS ON A FLOW-CELL that they have considerable bioinformatics Currently the sequencing landscape for both AND BLOCKED FLUORESCENTLY expertise provided by BGI thus for a single price research and its clinical translation is completely LABELED NUCLEOTIDES.” can generate a complete human sequence dominated by the Illumina platform and this and assemble and annotate that sequence decided lack of competition does not benefit the with high accuracy. It is projected that price will be at the $1,000 mark end users. There are a number of new technologies being developed sometime in 2015. A second attractive feature is that there appears to but many of them are a considerable way from having any impact be considerable headroom for further increases in sequence output. A on the sequencing landscape. However, the complete CGI platform third is that they can also generate phased sequenced genomes with provided by BGI does offer an alternative sequencing solution and their long fragment read technology. However, there are some key the potential competition between those two platforms should limitations to this platform including the fact that they do not currently offer further improvements in these technologies and even cheaper sell their platform but instead you send your DNA to them and they sequencing in the future. n

May/June 2015 / Frontline Genomics Magazine / 21

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I

n 2010, for the 10th anniversary of the completion of the first genomic changes that are causal for disease. The targets on our draft of the human genome, I was asked by a reporter for a lists that gained the most enthusiasm were those for which there prominent newspaper why our knowledge of the human genome was already literature support, putting in question the value of had not yet enabled new medicines. At the time, our team was looking for novel genes in the first place. using RNA interference (RNAi) to identify new drug targets across In the years to follow, the genomic and genetic information diverse disease areas. Informed by genomic sequence information, available to scientists has burgeoned substantially. There has we had built a world class genome-scale RNAi screening platform. also been a surge in additional ‘omics and clinical data that can The reporter asked if any new drugs had been facilitated by our be intersected with genome data to empower hypotheses about approach. I replied that it was still early days, disease biology and potential novel drug and that we would see the fruits of this type targets. Until recently, however, rigorous of genomics-based drug discovery in years experimental follow up and validation of to come. The reporter scoffed and used my these remained elusive due to a sustained statement as support for his thesis that the dearth of precise and effective tools to get at investment in the human genome had not the heart of gene function. really paid off. Over the past few years, a breakthrough for I often reflected afterwards on my target validation has been realized in the area “OUR CURRENT RESEARCH IS disappointing response. As a post-genome of genome editing. Technologies involving DEDICATED TO PROVIDING drug discovery scientist, genomic information engineered zinc finger nucleases and TALENs FUNCTIONAL VALIDATION OF was woven into every research plan that my debuted as options for creating genome teams pursued. At the time of the interview, modifications that could inform on gene POTENTIAL NEW DRUG TARGETS we had already conducted many successful function. But for reasons both technical and THAT ARE IDENTIFIED THROUGH screens and assembled comprehensive lists practical, the adoption of these approaches HUMAN GENETICS. IN ESSENCE, WE of potential new targets. Unfortunately, this has been somewhat limited (for review, see ALLOW THE GENETIC CRAPSHOOT was usually as far as we could go. While we Sander and Joung 2014). In 2013, adaptation could confirm our screening hits in additional of the bacterial CRISPR/Cas9 system emerged OF HUMAN REPRODUCTION TO DO assays by re-targeting those genes via for genome editing in mammalian cells, THE TARGET IDENTIFICATION FOR RNAi, we lacked tools that were free from and, since then, it has been evolving at an US (SOMETIMES REFERRED TO AS appreciable off-target effects and that could unprecedented pace (for review, see Hsu, et more precisely mimic in relevant models al. 2014). EXPERIMENTS OF NATURE).”

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COMMENT

“OUR LAB WORKFORCE IS ONE OF OUR MOST LIMITED RESOURCES. WE HAVE A MODEST-SIZED TEAM WITH GENOMESIZED GOALS. WHEREVER WE ARE ABLE TO DO SO, WE OUTSOURCE TO ENHANCE PRODUCTIVITY. “

Michele Cleary – Michele Cleary is a scientific director with over 20 years of experience in molecular and cellular biology and 13 years of experience managing laboratory efforts in a pharmaceutical industry setting. She is co-author of more than 50 primary research papers in the fields of drug target biology, RNA interference, microRNAs, cell cycle, biomarkers, genomics and oncology. Currently, she leads the Target & Pathway Biology group within MRL’s Genetics and Pharmacogenomics department. The mission of this global laboratory effort is to enhance MRL’s early-stage drug discovery pipeline by providing functional validation for novel drug targets anchored in human genetics.

CRISPR/Cas9 has many advantages including impressive efficiency, overall flexibility in generating gene knockouts or sequence substitutions, and easily designed and synthesized reagents, which allow for iteration and optimization. The ease and efficiency of CRISPR/Cas9 also enables the engineering of changes at multiple genomic loci simultaneously. Most importantly, however, researchers can use it to mimic disease-relevant human genetic alterations more precisely in cellbased and animal models. To say that the CRISPR/Cas9 technology has revolutionised drug discovery is an overstatement. There are still some limitations to robust target validation. But CRISPR/Cas9 has enabled the pursuit of those novel targets that typically got left by the wayside after comprehensive target identification campaigns due to the lack of tools for probing the associated biology in depth. Perhaps the biggest advantage, however, is that its speed and ease of use allow for rapid experimental iteration in a wide variety of biological systems. It is this characteristic of CRISPR that has started a new era of functional genomics, in which forward genetic screens benefit from high throughput gene knockouts at the DNA level and a potential to pursue modulation (repression and

activation) of RNA transcription (for review, see Shalem et al. 2015). Our current research is dedicated to providing functional validation of potential new drug targets that are identified through human genetics. In essence, we allow the genetic crapshoot of human reproduction to do the target identification for us (sometimes referred to as experiments of nature). By sifting through genotypes of large numbers of patients and controls, or looking at families with a high incidence of a disease, we arrive at hypotheses about genome alterations that cause pathologies as well as those that may be protective. With information in hand and the robust genome engineering afforded by CRISPR/ Cas9, we can study the biological significance of these events in multiple ways. A first step in following up on genetic findings is to determine whether perturbations in a gene impact phenotypes relevant to a disease. Achieving this goal requires an assay or panel of assays that are translatable. In other words, with such assays there is a high level of confidence that the knowledge gleaned is truly meaningful with respect to the pathophysiology observed in humans. CRISPR/Cas9 can offer a very quick view into the potential impact of a gene in an assay through a direct knockout of that gene.

May/June 2015 / Frontline Genomics Magazine / 25

COMMENT

If a change in phenotype results, the gene could distant future, engineered cells can be made likely be important from a pathway perspective. externally in less than 2 months, allowing these If there is no change, however, the gene isn’t tools to keep up with the pace of our science. necessarily irrelevant. More work just needs to Another application with room for be done. improvement is CRISPR/Cas9 for sequence “THE TARGETS ON OUR LISTS Genetic variations can have multiple impacts substitution. CRISPR results in gene knockouts THAT GAINED THE MOST on the genes with which they are associated. If through the non-homologous end joining a single nucleotide polymorphism in a coding (NHEJ) process. NHEJ is a DNA repair process ENTHUSIASM WERE THOSE FOR region results in a synonymous change, the that responds to the double-stranded breaks WHICH THERE WAS ALREADY encoded amino acid remains the same and the that CRISPR/Cas9 enzymatic activity induces. LITERATURE SUPPORT, PUTTING impact on protein sequence will be negligible. The repair is error-prone and coupled with IN QUESTION THE VALUE OF Missense variants resulting in amino acid chewing back of the broken DNA strands. When sequence alteration can change the folding of the chewed back sequence is then ligated, LOOKING FOR NOVEL GENES IN a protein, its function or its ability to bind other sequence deletions result and some will cause THE FIRST PLACE.” molecules in a cell. Nonsense mutations can frameshift mutations in coding sequence that result in loss of function when the “business could lead to early stop codons and protein end” of a protein is deleted. Getting at the heart truncation. CRISPR also induces homologyof these changes biologically is best done by directed repair (HDR), which requires a template recreating them in a normal cell or correcting with considerable homology to the site of the the variant back to wild-type in a cell from a double strand breaks. NHEJ competes with HDR genetic carrier. It is toward this goal that CRISPR/ and is much more efficient (upwards of 50% Cas9 genome engineering offers a significant success versus HDR’s rate of 100 KB) and we into our target validation work flow, we have uncovered several have concerns that making the necessary substitutions to replace their deficiencies that could benefit from optimization. For our research, an animal counterparts may be too challenging. The rapid advancement of important limitation is in the commoditization of CRISPR engineered CRISPR/Cas9 and the intense focus of many excellent thought leaders cell line generation. Our lab workforce is one of our most limited make us optimistic that breakthroughs for this application will be just resources. We have a modest-sized team with genome-sized goals. around the bend. Wherever we are able to do so, we outsource to enhance productivity. In 2020, I hope to have the opportunity to redeem the investments Lulled by the hype that CRISPR engineering is fast, efficient, and easy, that have been made to amass genomic information and fine tune our we mistakenly viewed it as an established commodity. Unfortunately, tools. If I am so privileged to once again address the question asked of our experience with outsourcing cell line generation has been me in 2010, I anticipate reciting a list of new drugs empowered by our disappointing as the turnaround times for delivery of homozygous knowledge of the genome so lengthy that the payoff for human health knockout clones have been lengthy. It is our hope that in the not too is clearly a no-brainer. n

Acknowledgments Many thanks to Galya Vassileva, Joel Klappenbach, Myung Shin, and Richard Chen for helpful suggestions for this commentary.

References Sander, J.D. and Joung, J.K. 2014. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32:347-355. Hsu, P.D., Lander, E.S., and Zhang, F. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 157:1262-1278

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Shalem, O., Sanjana, N.E., and Zhang, F. 2015. High-throughput functional genomics using CRISPR-Cas9. Nat. Rev. Genet. 16:299-311 Maruyama, T., Dougan, S.K., Truttmann, M.C., Bilate, A.M., Ingram, J.R., and Pleogh, H.L. 2015. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by

inhibition of nonhomologous end joining. Nat. Biotechnol. Published online March 23, 2015. Chu, V.T., Weber, T., Wefers, B., Wurst, W., Sander, S., Rajewsky, K., and Kuhn, R. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. Published online March 24, 2015.

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INTERVIEW

SPECULATIVE FICTION HAS BEEN PREPARING US FOR THIS MOMENT Jacob Corn, Managing Director & Scientific Director, Innovative Genomics Initiative

GENOME EDITING COULD GIVE DOCTORS THE ABILITY TO CURE THE INCURABLE. THE POTENTIAL IS VERY APPEALING, DESPITE THE ETHICAL ISSUES THAT STILL NEED TO BE WORKED THROUGH. WE’RE AT THE BEGINNING OF AN EXCITING JOURNEY, BUT THERE IS STILL A LONG WAY TO GO.

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enome editing isn’t new. We’ve been doing it for years in various different systems. The concept of editing the human genome isn’t that new either. It’s a topic that has been subject of serious debate and fiction for years. So what’s changed? The concept of editing a human genome is no longer just a concept. It’s not in the realm of the possible yet, but is now very firmly in the realm of the plausible. And that’s what makes this such an exciting time. While the general media speculates, there is an incredible amount of activity behind the scenes to make sure that progress isn’t reckless. Through his work at the Innovative Genomics Initiative, Jacob Corn, is one of the key figures in making sure genome editing delivers on its bright promise

“SCI-FI MAY ACTUALLY BE AN APT COMPARISON AND OFFERS A FEW POSITIVE EXAMPLES OF SUCCESSFUL PROGNOSTICATION: EDWARD BELLAMY PREDICTED CREDIT CARDS IN 1888 AND ARTHUR C. CLARKE DESCRIBED COMMUNICATIONS SATELLITES IN 1945.”

FLG: The CRISPR/Cas9 system has many advantages over zinc finger nucelases and TALENs based approaches to genome editing. It feels like genome editing is gathering the same kind of excitement as sequencing did when NGS began to offer practicality. These days, everything and anything is getting sequenced – how far away from a similar genome editing boom are we? JC: Even though it feels like genome editing is everywhere, I think we’re still in the early stages of the boom. Labs all over the world are starting to use genome editing for their research, and many are having great success. But others are still trying to get started. In some cases this is the Paradox of Choice: since there are so many great reagents now for genome editing, some feel paralyzed about where to start. Hence, the IGI is offering a course this summer on Cas9-based editing for both human cells and model organisms (https://innovativegenomics.org/crispr-workshop/). Other labs follow

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the biology to difficult systems where genome editing is less well explored, but I think these areas become more tractable with time and work. As more labs become comfortable with genome editing for basic research, we’ll see applications in the clinic and elsewhere rapidly follow. See a blog post I made recently for some speculation about where things might be going in the future: https:// innovativegenomics.org/blog/three-timescales-ofimpact-for-next-gen-genome-editing/ FLG: Genome editing is starting to make its way across to the general public media. It’s always encouraging when a field captures the imagination, but it can take on a life of its own as misconceptions grow. How do you explain what genome editing actually is and why it’s practically beneficial to a lay audience?

JC: I find that lay audiences are already well acquainted with the general idea behind genome editing. Speculative fiction has been preparing us for this moment for decades. I’ve talked about the topic people from all walks of life; everyone gets it right away. You don’t need to know a thing about Cas9 or mechanisms of DNA break repair to understand. Most people very quickly get that genome editing means giving doctors the ability to repair genetic disorders that are currently an incurable luck of the draw for patients, and they see how much good that could do. But everyone also sees how much harm might come if we’re reckless and how much care should be taken. In the long term, the most concrete (and speculative) benefit is that our relationship with genetic diseases could fundamentally change. I’m not necessarily talking about germline editing, since one might have the same benefit with the ability to replace affected tissues with edited tissues. There is the opportunity for real and permanent cures for terrible diseases in which people currently just make do.

INNOVATIVE GENOMICS INITIATIVE The Innovative Genomics Initiative (IGI) was established at the Li Ka Shing Center for Genomic Engineering in early 2014 through a generous gift from the Li Ka Shing Foundation. The gift also created an affiliated faculty chair, the Li Ka Shing Chancellor’s Chair in Biomedical and Health Sciences, which is currently held by executive director Jennifer Doudna. Li Ka-Shing, a Hong Kong-based, self-made businessman and philanthropist, had also provided a cornerstone gift of US$40 million to establish the Li Ka Shing Center for Biomedical and Health Sciences, which opened its doors in 2012. The IGI Lab is composed of branch laboratories at UC Berkeley and UCSF which address the IGI’s main flagship research project portfolio, including drug discovery, regulatory variation and improving treatments for pediatric disease, as well as core basic research on CRISPR/Cas9 biology. As of 2015, the IGI and its affiliated laboratories are actively participating in collaborations with academic and industrial research partners worldwide. Support from private donors, foundations and industrial collaborations continues to support IGI science on a global scale.

That’s powerful stuff. But it’s a long road, and while some major technical roadblocks have been cleared, it’s still a long journey. FLG: The need for public trust is something that can’t be ignored in today’s day and age. Is this a product of the new technologies that uncover and interact with what makes us individuals, such as NGS and CRIPSR, or are we just living in a media rich and information hungry age? JC: I don’t think the need for public trust is anything new, and is just as important now as it has been for decades. Disruptive change is always nerve-racking: there were books about computersgone-rogue long before the internet age, and people were frightened of being unable to breathe at high speeds on the first major steam train line. As humans, we become used to the way things are, and it’s scary when things dramatically change in our lifetimes. But thanks to one of these disruptive technologies, the internet, media has become so democratised that there is a great opportunity to develop public trust. Anyone can meet and interact with researchers via things like Youtube, blogs, and video chats. At the IGI we’re dedicated to public outreach opportunities and have been busily making several videos to explain Cas9 technology. For example, https://innovativegenomics.org/genome-engineeringwith-crispr-cas9-birth-of-a-breakthrough-technology/ and https:// innovativegenomics.org/igi-future-of-genomics-research-video/and https://innovativegenomics.org/introduction-to-genome-editingusing-crisprcas9/. We’re looking forward to continuing to engage with both scientists and the public about this new era of genome editing in the near future. FLG: You have a great perspective on how various stakeholders interact around research. You had a spell at Genentech, and now you’re at the Innovative Genomics Initiative. With so much innovation coming out of the academic field, what do researchers need to do to give their work the best opportunity of translating into a viable healthcare application?

JC: I think this question is best addressed via an outlook, rather than a how-to list for turning your research into a drug, since fortune favors the prepared mind. The most important thing is learning to consider problems in multiple ways and at multiple scales of time and purpose. Academia is outstanding at breakthrough science that takes the long view: where are the blank spots in our understanding and how do we fill them in? Industry excels at the difficult job of understanding immediate needs in the real world and turning basic research into commodities that people come to depend upon. Both spheres are critically important, and both are hard, backbreaking work. I think much comes down to better communication between academia and industry. Not so long ago there was some frustration and even stigma associated with academia and industry working together. More recently, I think researchers on both sides very much want to learn from each other to have the best chance of making a positive difference in the world. And that’s the key – learning from each other. Let’s start with baby steps: next time you’re at a conference, whether you’re from academia or industry, find someone in the opposite camp and have lunch with them. Most times you’ll find all of the academics eating at one table and all of the industry folks at another table. Ask people at the table what they’ve been working on and why it’s hard. Really listen. Think about how your work might have some kind of impact on those difficulties, either in the next few years or the next few decades. For those interested in a few more words on this topic, I wrote a bit about better communication between academia and industry in a recent blog post: https://innovativegenomics.org/blog/two-way-radios/. FLG: In January, AstraZeneca announced their push into utilising CRISPR-Cas9. Part of this is collaboration with you guys at the Innovative Genomics Initiative. What kind of work will you be doing together? JC: Our collaboration is aimed at using Cas9-based transcriptional regulators for basic research in many disease areas (oncology,

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Jacob Corn Managing Director & Scientific Director Innovative Genomics Initiative Jacob Corn is the Scientific Director of the Innovative Genomics Initiative (IGI) and faculty at UC Berkeley in the department of Molecular and Cell Biology. For several years he was a group and project team leader at Genentech in the department of Early Discovery Biochemistry, leading multidisciplinary teams. Jacob’s research bridges reductionist mechanism with cell biology, with the overarching goal of understanding how biophysical properties interact within the cellular environment to shape signalling behaviour and how disease arises when these properties go awry. As director of the IGI, Jacob is pushing the boundaries of next-generation genome editing for transformative insights into fundamental biologies and to laying the groundwork for clinical and commercial applications of the technology.

cardiovascular, metabolic, respiratory, autoimmune and inflammatory diseases and regenerative medicine). We’re working together to identify and validate gene targets relative to several diseases and to understand how these factors go awry in disease. This collaboration is a two-way-street, with close communication and sharing of research data between AZ and IGI, with the goal of positively impacting drug discovery and development to hasten treatments to patients.

research settings: fundamental discoveries that will accelerate and broaden our understanding of the world around us.

Medium: Within five years true gene editing (surgically replacing one sequence with a defined replacement) will have matured and be as easy in human cells and model organisms as plasmid mutation currently is bacteria. We’re already starting to see some hints of this on the horizon, so maybe this should even be in the “short” bin. But I think a lot of current work is focused on very low FLG: We talked at the top of the interview about the speed at hanging fruit (important though it is), and there’s still no clear path which genome editing is developing. One of the things you’re towards quickly and robustly engineering silent or deleterious passionate about at the Innovative Genomics Initiative, is thinking variants, for example mutants with a fitness disadvantage. So this ahead to applications and really considering where this is all one goes into “medium term”. Surgical introduction of mutation heading. What’s the short term and long term outlook for CRISPRwould be huge for any number of basic biologies, since it would Cas9? enable one to readily ask reductionist and mechanistic questions in the context of a living cell or organism without confounding JC: I think this is best summarized in a blog post I recently made factors. On the translational front, in the medium term gene about short/medium/long term impacts of genome editing will totally change the way preclinical editing on human health: research is carried out. Custom-designed safety models (e.g. humanized rats), highly engineered Short: In the next few years I think we’ll see cell lines to meld target and phenotypic greater adoption of genome editing in many labs, screening, synthetic biology for enhanced both academic and industrial. This will mostly be drug production, and so on. People have been what I call “RNAi v2.0″ — disruption of genes in a wanting to do these things for a long while very fast and easy mode (either via CRISPRcutting or and they might take a little longer to achieve “I DON’T THINK THE CRISPRinhibition). This will extend to both human cells in industry only because the focus will include NEED FOR PUBLIC and model organisms, but the scope accessible for robustness of the systems rather than purely TRUST IS ANYTHING reverse genetics will be greatly expanded. Now that speed, but they’re coming. More relevant to the NEW, AND IS JUST AS more and more genomes are sequenced, we’ll finally general public, in the medium term we’ll start IMPORTANT NOW have a way to figure out what biologies underly all of to see the widespread clinical emergence of AS IT HAS BEEN FOR those great annotations in those organisms (reverse ex vivo therapies that take advantage of gene DECADES. DISRUPTIVE genetics) or screen for which genes are responsible editing, especially in the hematopoietic system. CHANGE IS ALWAYS for incredible phenotypes (forward genetics). How do Clinical research and trials are already ongoing NERVE-RACKING: salamanders regenerate limbs? How do some fungi here (e.g. Sangamo’s work with ZFN knockout THERE WERE BOOKS turn insects into zombies? What are the roles of genes of CCR5 for HIV), but now I’m talking about ABOUT COMPUTERSexpressed during Plasmodium infection? Does ablating FDA approval and widespread use of an edited gene X slow tumor progression in this model system? product as a therapeutic. The trial data has so GONE-ROGUE LONG Are all of these genes really necessary for epithelial far been very impressive on many fronts, but BEFORE THE INTERNET differentiation in the gut? These kinds of questions will time will tell and the finish line is always further AGE.” be broadly answerable in both academic and industrial away than you think.

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and DNA damage. Third, we are committed to Long: Since the likelihood of anyone accurately the short-term application of genome editing predicting at this timescale is quite low, rather for impact in hematopoietic disease, both in than make any specific predictions I’ll instead discovering novel causative disease variants and wax philosophic. Here we’re starting to talk about working towards therapies to reverse disorders. disruptive science fiction entering our lives in a real way. Things like in vivo editing in adult or postmitotic FLG: Research is just part of what you do, “EVEN THOUGH tissues. Sci-fi may actually be an apt comparison though. You also put in a considerable amount of IT FEELS LIKE and offers a few positive examples of successful work into building new models for collaboration GENOME EDITING IS prognostication: Edward Bellamy predicted credit between academia and industry, helping to EVERYWHERE, I THINK cards in 1888 and Arthur C. Clarke described promote entrepreneurship. How did that become WE’RE STILL IN THE communications satellites in 1945. And in a way, an area of focus for you? EARLY STAGES OF media of all kinds has been preparing us for genome THE BOOM. LABS ALL editing for decades. I was recently asked how I JC: When I began working as a group leader at explain what genome editing is and why it’s practically OVER THE WORLD Genentech, I was humbled by how little I knew ARE STARTING TO USE beneficial. But the thing is, I actually don’t need to do about modern drug discovery and development. I GENOME EDITING FOR much explaining. I’ve talked about genome editing had been a grad student and postdoc in top labs at with taxi drivers, hair dressers, graphic designers, major research and was taught well so had good THEIR RESEARCH, AND high school students, and Hollywood actresses. handle on the biology, but research leadership is MANY ARE HAVING Everyone gets it right away. You don’t need to know about much more than just science and there was GREAT SUCCESS. a thing about Cas9 or mechanisms of DNA break still a steep learning curve. I’m very grateful to all BUT OTHERS ARE repair to understand genome editing. Most people of my Genentech colleagues who took time show STILL TRYING TO GET very quickly understand what genome editing is and me the ropes. Now I want to help expose graduate STARTED.” they see how much good it could do. But everyone students and postdocs to different styles of research also sees how much harm might come if we’re during their training, and if they’re interested to help reckless and how much care should be taken. So in the long term, them to help them understand the business side of their research. I our relationship with genetic diseases will fundamentally change. think universities currently do an excellent job of training graduate I’m not necessarily talking about germline editing, since one might students and postdocs how to think logically and critically about have the same outcome with the ability to replace affected tissues scientific problems, but we typically teach a very academic style with edited tissues. There is the opportunity for real and permanent of management. I’d like to not just teach people about academic cures for terrible diseases in which people currently just make do. or industry approaches, but broadly help them understand how That’s powerful stuff. But it’s a long road, and there’s a lot left to be various approaches are different and might be appropriate in various done. situations. How do you know when to move on from a project? How do you maintain a research group or a large multidisciplinary FLG: Innovative Genomics Initiative is going to play a major role in team? How do you obtain operational support for your ideas? driving this. How did IGI form? These questions have wildly different answers if you’re in academia, an established company, or starting your own entrepreneurial JC: The IGI was catalysed to bring together Bay Area expertise in adventure. I want to provide information and training that’s genome editing and regulation by Jennifer Doudna (Berkeley) and appropriate for career goals, as well as encourage more dynamic Jonathan Weissman (UCSF), as well as Mike Botchan (Berkeley). After roles at the interface of academia, industry, and entrepreneurship. Jennifer’s work developing Cas9 as a programmable DNA nuclease This will not only better prepare people for their own futures, but will and Jonathan’s work repurposing it as a programmable regulator lead to exciting new discoveries, technologies, and companies. of transcription, they recognized that this technology would quickly become bigger than any one lab could handle. Marsha Fenner was FLG: Are there any groups out there that you’re really excited about? first recruited as the IGI Program Director and I was soon afterwards recruited to be the Scientific Director and Managing Director. Since JC: One of the most exciting things about the genome editing then we’ve built stellar foundational labs at Berkeley and UCSF to revolution is that incredible work seems to pop up every week push the boundaries of genome editing and regulation, as well as from the most unexpected places. This makes it very hard for me developed a wonderful group of IGI Affiliates throughout the Bay to single out any one group! Cas9’s extreme democratisation of Area. More information on the foundational labs and the affiliates genome editing for basic research is incredibly inclusive, and I love are available at https://innovativegenomics.org/about-igi/ seeing the creative ways everyone is using it to answer their own biological questions. FLG: You’ll have a very big role to play personally, as Managing Director and Scientific Director. What’s the focus of your research at FLG: Thank you for speaking with us. Is there anything else you the moment? want to mention? JC: We currently have three main thrusts. First is developing next-generation tools that push genome editing and regulation even further and enable exciting new discoveries. Second, we are using those new technologies for basic biological research, to better understand how complex cellular signalling networks are maintained. Ubiquitin-mediated signalling is one focus, but there are also on-going projects in areas such as transcriptional regulation

JC: It’s my pleasure. The field of genome editing is moving incredibly quickly, and I’m excited about the IGI’s role in bringing about fundamental change in biological and biomedical research by enabling scientists to read and write in genomes with equal ease. Genome editing is already changing the research world and it’s just a matter of time before benefits are apparent in our day-to-day lives. n

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INTERVIEW

JUST DO IT - MAKING GENOMICS WORK, TODAY Brian Dougherty, Translational Genomics Lead - Oncology, AstraZeneca R&D

A QUICKLY GROWING FIELD, LIKE GENOMICS, CONSTANTLY THROWS UP NEW CHALLENGES. BUT HOW DO YOU INCORPORATE NEW TECHNOLOGIES? HOW DO YOU MAKE SURE YOU’RE AHEAD OF THE GAME? SIMPLE- SET THE BAR HIGH, TRUST YOUR TEAM, AND GO FOR IT. YOU’LL BE AMAZED BY WHAT YOU CAN ACHIEVE.

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rug development has been one of the areas most changed by genomics in the last 15 years. Brian Dougherty went into the industry just at the point when it was looking for people with that sequencing expertise. He’s seen some big changes take place in that time. Today he’s AstraZeneca’s Translational Genomics Lead in Oncology and is overseeing some remarkable projects. We caught up with him at AACR to find out how he got to where he is today, and how to start moving across to the cloud. We also get a preview into the projects he’s currently working on and what he’ll be sharing with the crowd at the Festival of Genomics next month. FLG: You’ve been involved in and around genomics since the early 90’s. What started you off down that particular path?

FLG: That’s a great motto to have. Is that something you’ve taken on yourself in your current role at AZ?

“A LOT OF SCIENTISTS, BUT BIOLOGISTS IN PARTICULAR, ARE USED TO WORKING ON THEIR OWN. THERE WAS A GOOD QUOTE BACK IN THE FIRST ERA OF GENOMICS THAT ‘BIOLOGISTS WOULD RATHER SHARE A TOOTHBRUSH THAN A GENE NAME’”.

BD: It was kind of an offshoot of molecular biology. Back in the 80’s, molecular was the big, hot, marketable field. People were recruiting professors into departments because they were ‘Gene Jockeys’. I got into molecular biology early. Then, all of a sudden, the next marketable thing was genomics. When I went to Ham Smith’s lab for my Postdoc at Hopkins, one thing led to another – he collaborated with Craig Venter while Craig was finishing up the EST sequencing. As that was winding down he had the sequencing infrastructure and algorithms to consider ‘Just Do It’. That was always Craig’s motto, to just sequence the genome – “don’t sit around and wait for ten years for the cost to theoretically come down, just get going with today’s technology and see what happens”. So it was a much more bottom up approach. With Ham we used a bacterium that he had studied for decades, Haemaophilus influenzae,, as a model organism for the human genome and worked out the techniques there. Slowly over time people went through larger and larger model organisms and worked their way up to the human genome.

BD: Yes! Many of us have “JDI” written at our desks, though often with an extra letter added to the acronym - reminding us to ‘just get it done’ when we meet up with challenges. So we definitely try to keep that same attitude. FLG: Going into industry is something that a lot of young scientists are wary of. There’s a certain element of caution knowing you’ll be in a situation where your research is dictated, not so much by scientific curiosity, but business case. Are there ever times when you miss the academic lifestyle?

BD: Yeah, I was told by Professors “It’s so great to stay in academics”, but I’m watching them pulling their hair out trying to write grants. And a lot of time, you still have to deliver to the grant. So there is a level of freedom in academia, but not as much as I would have thought. What I liked about industry, was that it’s a bit more team oriented and you don’t have to do as much writing to get the funding for your research. It’s provided for you, and you discuss what you need to deliver, and then you need to deliver. I’ve found, personally, that I’ve still had a lot of freedom and resources to still do exciting research and cool science. One of the big trends in pharma R&D, at the moment, is realising that the productivity isn’t what it was in the past, though things are beginning to improve again. They’re encouraging innovation and writing up blue sky ideas and seeing if we can get funding for them internally. We might not have as many seminars as in a university, but there’s still a lot of creativity, and we are trying to encourage that internally and tap into it. The downside is that there’s politics everywhere. We sit through

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ASTRAZENECA AstraAB was founded in 1913 and headquartered in Södertälje, Sweden. Astra was an international pharmaceutical group engaged in the research, development, manufacture and marketing of pharmaceutical products. Zeneca Group PLC was founded in 1993 when Imperial Chemical Industries (ICI, founded in 1926) demerged three of its businesses (Pharmaceuticals, Agrochemicals and Specialties) to form a separate company. Headquartered in London, Zeneca was a major international bioscience group engaged in the research, development, manufacture and marketing of pharmaceuticals. AstraZeneca, formed in 1999, is a global, science led biopharmaceutical business, employing over 57,000 people worldwide and with a primary focus is on three important areas of healthcare: Cardiovascular and Metabolic disease (CVMD); Oncology; and Respiratory, Inflammation and Autoimmunity (RIA). More information can be found at http://www.astrazeneca.com.

a lot of meetings. But there’s a lot of diversity out there beyond academia, from big pharma, smaller pharma, biotechs, not-forprofits, government – each with their different advantages. FLG: It sounds like a lot of companies are finding ways to encourage blue sky thinking to see where it might go. Is that something you implement at AstraZeneca? BD: Yes, it’s something I always encourage in my own teams. Even simple things like reserving 10-20% of your time to try out an idea – it might not always work, but if there is that freedom to innovate and you are encouraged to take chances, good things will eventually happen. It’s kind of what brought me into industry – I went from academics to TIGR – but then eventually I found myself doing the same thing over and over. We kept finding exciting things and thought of cool applications and follow-up experiments, but we weren’t going to do them at a place primarily focused on the sequencing. At that point the timing just worked out – I was working in genomics in one of the premier places and there were departments opening up in the pharmaceutical industry looking for people who knew how to bring in this new technology. And that’s what really started me at Bristol-Myers Squibb, wanting to do research that would more directly help patients. It kind of makes sense now that I look back, but at the time you just didn’t know if you were making the right choice for your career.. FLG: As you said, you’re big start in industry was at Bristol-Myers Squibb, working in Applied Genomics. This was still very much in the Human Genome Project era in ‘98. Now you’re Translational Genomics Lead in Oncology for AstraZeneca. What would you say have been the big changes you’ve seen take place in the field in that time? BD: In the pharmaceutical industry, some fields get more or less funding and it changes over time. Companies are looking at where the unmet medical need is and investing their research dollars in that area – and if it eventually pays off that money is

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re-invested back into research for other unmet medical needs. More and more it’s been pushing towards fields like oncology and Alzheimer’s. But when a company de-emphasizes one area of research to focus on another, it can be hard for a researcher specifically focused on, say, antibiotic research, to now become a cancer researcher. I’ve been focused more on the technology that is always needed in all of these research areas, and then work really hard to understand the biology and the problems that these teams are trying to solve. So for me the big changes have been in the genomic technologies, especially sequencing. In the first days of genomics, it was higher and higher throughput in Sanger sequencing. But that could only scale so far. In that decreasing cost of sequencing hyper-Moore’s plot, you can see the inflection point when 454 sequencing began to have a big impact, it had its dominance for a moment in time, and since then it’s been primarily Illumina sequencing technology that is driving down commodity sequencing costs, particularly pushing the cost of a human genome towards the $1000 price point. So in terms of what’s changed, it’s definitely the scale. I was sitting back in my graduate research days thinking “You know…a generation from now graduate students will just go to some online database and pick their research”. But it happened a lot faster, and within 5 years we were sequencing the first free living organism’s genome and putting the data online. And within a year or two of that, there were PhD students working on sequencing a bacterial genome as their thesis project. The scale has changed such that now a single person, rather than an entire centre, can performing the sequencing portion of decoding a human genome in one day. FLG: Predicting the long term future seems easier some times. Why is it so tough to predict short term changes like that? BD: As Yogi Berra famously said, “It’s tough to make predictions, especially about the future”. But seriously, I don’t know that I have an answer for that. I think you just need to learn to change as the science

and technology evolves. Thinking back to my time in academia, there were some professors they were bringing in doing exciting new work, and helped drive the department forward. There were other professors who had been working in yesterday’s hot field but continued to stay with the old ways and were never looking for the next big thing or ways to do something new more. It’s one of those “evolve or die” situations. FLG: For better or for worse, genomics has been quite heavily linked and, at times, driven by politics. How much do you feel that influence in industry? BD: I think it’s important, more because scientists aren’t too good at educating the public of their country about the value is of what they are doing and why there should be more money going into their research. They just know it’s true, and want to focus on the science. But sometimes it takes politicians to highlight it, or help form some big initiative, for people to say “Wow! This is going on, and these are the potential benefits!?” On the downside, there was a lot of promise to the Human Genome Project. It did deliver value, but not quite in the way that people thought that it would. This time around, the pace at which we’re leveraging genetics to find the basis of disease and response to therapies is staggering – that’s where genomics can really help us stay ahead of the curve. So I’m very interested to see how things turn out with the new big human genome projects like 100,000 genomes in the case of Genomics England or a million person cohort for the US Precision Medicine Initiative. FLG: There’s a growing acknowledgement that inconsistencies in accuracy is a mounting problem. Either results are reported differently, or there is a lack of consistency in hardware and software being used, or a whole host of other variables. For guys like you looking to translate this into the clinic, it must be even more problematic. From a commercial perspective, taking anything into the clinic is going to require a significant investment, but more importantly – you’re asking patients to be involved. So the issue of accuracy is possibly felt most intensely by you guys in the translational space. How do you go about untangling some of these sources of variation and solve the accuracy problem? BD: A lot of scientists, but biologists in particular, are used to working on their own. There was a good quote back in the first era of genomics that “Biologists would rather share a toothbrush than a gene name”. When it comes to a number of NGS analysis algorithms and workflows that are being used as well, it’s similar. There are some good bestpractice workflows out there – like those from the Broad Institute and Sanger Centre – but they are really just a starting point. We need to refine and optimise then work towards standardization. At AstraZeneca we have a head of our production informatics group, Justin Johnson, who was a leader

Brian Dougherty Translational Genomics Lead Oncology AstraZeneca R&D Brian’s responsibilities at AZ include coordinating the delivery of genetic / genomic technologies, including Next-Gen sequencing, for Oncology translational /clinical teams with the goal of developing DNA-based biomarkers, patient selection strategies, and identifying new geneticsbased cancer targets. At previous companies (TIGR, Bristol-Myers Squibb, Pfizer, and Amgen), Brian has managed sequencing and functional genomics labs, applying technologies to enable the discovery and development of medicines for cancer, infectious diseases, and Alzheimer’s.

“BACK IN THE 80’S, MOLECULAR WAS THE BIG, HOT, MARKETABLE FIELD. PEOPLE WERE RECRUITING PROFESSORS INTO DEPARTMENTS BECAUSE THEY WERE ‘GENE JOCKEYS’. I GOT INTO MOLECULAR BIOLOGY EARLY. THEN, ALL OF A SUDDEN, THE NEXT MARKETABLE THING WAS GENOMICS.”

in the Genome in a Bottle initiative, as well as the Archon Genomics XPRIZE work that was set up in order to determine what “truth” is in variant calling. The XPRIZE was set up to judge the winner of a contest to sequence 100 human genomes in 100 days - how would they judge them and say that they were finished and they were right? They realised they needed to use reference DNA and standards and benchmark upon that. We’ve taken that to heart in our sequencing projects internally. We sequence the NA12878 Coriell DNA used as a benchmark now for human genetics, though for cancer there isn’t really an agreed upon standard so we use several. There are also a number of Dream challenges and initiatives where people are pushing the edge of what’s possible. For example, one of the things that we found quite early on from sequencing our tumours is that we needed to develop a lot of our own algorithms to deal with the volume of data we were producing. One of our AZ colleagues, Zhongwu Lai, was involved in the Dream challenge with one of his variant calling algorithms, and it did really well, particularly when calling indels, dealing with high sequencing coverage, and accurately calling somatic variants in the absence of a matched normal sample. So even today, when you try to compare between labs and really dig into the data, it’s quite difficult. I liken it a bit to the early days of microarray work where nobody really agreed on algorithms, and there were multiple technologies being used. Eventually there were platform and reference standards plus standard practices that were followed and brought about more uniformity and the ability to have consistency and accuracy. FLG: It’s difficult to have a genomics conversation these days without bringing up NGS and Data. With regard to the amount of data being produced at the moment, I’ve heard our current understanding of it described as “trying to crack hieroglyphics without the Rosetta Stone”. Pharma and healthcare is notoriously conservative. When you’re dealing with huge investments and patients’ wellbeing, you can’t afford not to be. But is there a danger of stunting progress by not being nimble enough when it comes to cloud computing and IT in general? BD: That’s a great point. I saw the data deluge problem in 2007 at Pfizer, where we’d done a project to really test 454 – we sent them about 30 samples and had them do a pooled-amplicon next gen experiment, and it just about broke their system, which was the largest next-gen sequencing centre in the world at the time. Nowadays a PCR amplicon study like this would be one of the first techniques to cut your teeth on in a Next Gen lab. But the other thing I learned from that experience was our lack of infrastructure to store and analyze the data when we got it back. Way too many rows to fit into an Excel file and our traditional PC based tools just couldn’t handle it – plus we did not have enough bioinformatics support lined up to help us mine the data.

May/June 2015 / Frontline Genomics Magazine / 35

So you need infrastructure (storage, compute power, fast data transfer) and bioinformaticians, and ultimately the biologists need to learn to use these analysis tools to perform more of the analysis and allow bioinformaticians to develop more advanced techniques for them. So about cloud - you typically have high performance computing ‘in house’ where your data is stored, though with cloud computing that’s starting to change. We feel a local-hybrid solution is the ideal solution, so we’ll need to maintain some level of internal infrastructure as well as develop the cloud capability further. Putting sequencing data into the cloud is a big challenge presenting itself to big pharma right now, mostly around learning how to do it right and dealing with potential security concerns. I don’t quite get it… there’s lots of other areas within our industry where we put our sales data and e-mail in the cloud. Obviously nobody in industry is being cavalier with human sequencing data, but we’re trying to figure out measured approaches to getting to the cloud more quickly.

problem. It’s a really challenging thing even with ten samples, let alone tens of thousands. And it’s not just one data point. You’ll be harvesting and cleaning up electronic health records and monitoring each patient longitudinally. So it’s an “COMPANIES ARE incredibly big challenge, but also bringing a lot of LOOKING AT WHERE computational and IT experts into the field who are looking to meet the challenge. THE UNMET MEDICAL People who are thinking about getting into NEED IS AND Biology always ask “what should I study?” Now INVESTING THEIR RESEARCH DOLLARS IN you just tell them “Computers!” Science is datadriven, and we are generating huge volumes of THAT AREA – AND IF IT data now – it’s not like the brochures we see with a EVENTUALLY PAYS OFF scientist in a white lab coat holding one test tube! THAT MONEY IS REThese days we’re running experiments that give INVESTED BACK INTO people the kind of data that they can work on for RESEARCH FOR OTHER months and years. So you need computers and UNMET MEDICAL software and the people who know how to use NEEDS.” them. For example, our work with Bina: they’ve brought in experts from Silicon Valley who have solved some of these Big Data problems at Internet and social media companies. We’re working with these experts to build problems to solve our problems in biology, and we give them FLG: Is there a fundamental misconception around what the feedback on what we’d like to be able to do - and they do it, plus cloud actually is? As you said, we’re already using it in everyday life more. It’s very satisfying to work and improve things in that way. and business, but there seems to be considerable hesitation around So yes, absolutely. The data integration challenge is one that using it for this kind of stuff. is going to be with us for a long time. Here at AACR for example there’s a session on mutation actionability. Just because you’ve BD: Exactly. Cloud just means you’re using somebody else’s found a mutation against a reference human genome (which in computers, they’re not near you, and the meter is running. It itself is an imperfect construct), you still need to answer whether presents a lot of challenges for sure. I’d say that it’s better to be or not it actually matters. From the thousands of variations you working with a company that is dealing with security issues 24/7. It’s find per sample, very few of them will drive a diseaseresponse or their business and they continue to figure out how to keep the bad drug resistance. So that’s information that you really need to get guys out. We just need to get people comfortable with the idea of out of people’s heads and into a computer program so that you can data outside our firewall, and then in a few years we’ll be wondering automatically filter with that data in and make sense of what comes what the fuss was all about. out of a sequencer. FLG: Is it just uncertainty when introducing a third party? BD: Well Amazon Web Services provide security and services, but there’s other work that’s incumbent on the end-users. So there are the companies like DNAnexus, SevenBridges, Cycle Computing, NextBio and Bina that we are talking to in order to help us get our NGS data out to the cloud, to be able to share with collaborators, and to have the tools and apps to work with it and get optimal performance from the cloud environment. FLG: A lot of the large-scale sequencing projects are looking at addressing a lot of the integration issues around genomics. It’s one of the missions of the Precision Medicine Initiative and The 100,000 Genomes Project in the UK. AstraZeneca are one of the first ten companies to sign up to the GENE Consortium. What is the biggest practical benefit of these large scale projects? BD: We talked earlier about the need to leverage the price point of whole genome sequencing more and more. So the 100,000 Genomes Project illustrates that point quite nicely. I think you need these big initiatives to make a big splash and challenge people. You want to set an audacious goal to get scientists to think “Oh my god, we can’t do this right now. How do we even come close to doing it?” – and then they eventually figure out how to do it at a very large scale. A big part of that will be figuring out the data integration

36 / Frontline Genomics Magazine / May/June 2015

FLG: This summer you’re speaking at our Festival of Genomics in Boston. You’re stepping up on the Cancer Genomics stage to speak on ‘Biomarker-defined trials in Oncology: Recent NGS Advances, Challenges and Opportunities’. You’ve been involved in a number of patient stratification efforts for AstraZeneca lately. What are you going to be sharing with the crowd from your work at AZ? BD: I still need to finalise that! But there are two important studies we’ve done recently, that I think I’ll be drawing upon. In one case study, we had a nice patient stratification example where we had patients responding to a PARP inhibitor and we had to understand the genetic basis of that response. So by sequencing patient tumours, we confirmed what was known – that BRCA1 and BRCA2 mutants were driving that response. But when we looked at the responses, we could see that there was a signal that was beyond BRCA1 and BRCA2. These were lower penetrance genes, but could potentially be 5-10% of the patient response. If we could figure out what those genes are, then that’s another 5 or 10% of patients that may be helped. So that’s the kind of work we’re doing right now. In the case of BRCA mutations, there are about 20-35% of the overall BRCA mutations that occur spontaneously in the tumour. We are presenting evidence at AACR that supports the concept that these somatic BRCA mutations that arise spontaneously in the tumour can drive response in a manner similar to germline mutations that are inherited. It’s some exciting initial data and, as usual, more research is warranted.

The second example is that we’re taking plasma samples from our clinical trials – liquid biopsies in near real time - to monitor tumour DNA levels in the blood. The work shows that the patient derives benefit from treatment for a while, but then, unfortunately, as with nearly every targeted cancer drug the cancer eventually comes back and the tumour DNA levels go back up. Within samples at those late treatment time points you’ll also find, within that collection of mutations, one or more resistance mutations occurring. So we’re collecting more and more of these plasma samples, as it has several benefits over working with tissue, in particular that longitudinal aspect it gives to a study. This exploratory translational biomarker study should be published soon. So going back to the data integration issue, it gets even more complex as you start to look back across all the sample time points. We are seeing for our compounds, not just which patients are benefiting, but also figuring out how tumours are eventually going to evolve resistance to a drug, then we “back-translate” to our preclinical stage research to come up with new molecules that will deal with that resistance mechanism and get those new and improved drugs into the pipeline. FLG: Liquid biopsies are proving very popular right now. Apart from the kind of data it allows you to generate, it’s also a lot less invasive from the patient perspective as well. BD: Absolutely. But it does take some work to refine lab and analysis techniques since there are a number of challenges as you’re sequencing through the normal DNA to find the tumour DNA with the mutations. Plus the DNA is very dilute and sheared up, but we’ve adapted the techniques to deal with these challenges. We have some nice examples of where we’ve had a tiny sample from a patient’s blood, and we’ve been able to stitch together an entire whole genome sequence of the tumour from baseline and later time points to figure out what’s different as the tumour becomes resistant. I think we’re relearning some of the important lessons that the virology field determined decades ago. They were dealing with highly mutagenic strains of viruses such as HIV, and realised they had to take a combination approach to therapy to deal with the emergence of resistance. We’re realising that too in oncology, but it’s an even bigger challenge with tumours. One of the good things about sequencing technology is that we’re able to predict which mechanisms to test to limit the number of possible drug combinations and focus on combining two targeted therapies where we know what the escape mechanisms will be FLG: Can you give us a preview of some of the challenges and opportunities you’ll be discussing in your talk? BD: Some of the things we’ve touched on really. The strengths and weaknesses of doing things externally versus internally, both for sequencing and analysis, as well as and how to distil all the data generated into actionable drug response information. FLG: What are you hoping people will come away from the talk with? Are there any questions or areas of feedback you hope people will have for you? BD: I mentioned before that a lot of the work we’re doing is in collaboration with people who are experts in their respective fields with computer-based approaches. So one place where I’d value the

feedback, in addition to likeminded lab scientists trading ideas and recipes, is somebody from computational experts in a completely different field who can help us solve problems based on analogous approaches they’ve taken. FLG: What made you want to get involved with the festival in the first place? BD: When I heard that there was a genomics meeting that was coming up in Boston, I thought it was already a pretty crowded field. There are a lot of academic meetings, commercial meetings, NGSfocused technical meetings, yet hearing about some of the guiding principles behind the festival and of what it was trying to accomplish – it sounded like a really exciting opportunity to have a broad cross section of different people and different approaches. Plus the TED-style talks make it a little more dynamic than some of the more traditional meetings. These are the kinds of meetings we need to get to, to hear what other people are doing out there since the technologies, particularly in sequencing, are changing very quickly, so the cross-pollination and networking aspects of the Festival of Genomics is really important to us. We are hoping to get our whole team to attend. FLG: Who are you looking forward to seeing present? BD: There are a lot of great speakers and it’s a nice diversity and cross section of the field. But if I had to pick one… that’s probably Craig Venter. And that’s because he was a real leader in the first era of genomics. Everybody was waiting for him to get back into the game after his Celera days – people would just sit there and anticipate “what’s going to bring him back”, and then pretty soon they started to settle down and think “maybe he’s all set…maybe he’s not coming back.” But once the Illumina HiSeq X10 sequencer came out, he decided not to buy just one set of ten instruments but two for his company (go big or go home, right?)… That’s going to be very interesting to see what gets delivered, and see how commodity human whole genome sequencing will impact our research. In the infection area, in particular, no one does enrichment of genes anymore – they just sequence entire genomes. But for us, with human genomes being 1000 times larger, there’s always going to be some place for enrichment approaches, but as the cost drops more and more for whole genome sequencing it’s will be a game changer. And long read technologies like PacBio or synthetic long reads like 10X Genomics will play a more important role as we look to understand structural variation and consider de novo genome assembly. FLG: Is there anything else you’d like to say to the readers? BD: To my point earlier about industry being much more team orientated – all of this I’ve talked about isn’t just my work, its part of a much larger team of talented people. There’s no way to take on some of these projects and be successful without having teams bringing our different skills and perspectives together. I saw that early on at Craig Venter’s TIGR and JCVI organizations – you’d look around and you’d realize what an incredibly diverse set of backgrounds was in the room, with everyone having their own particular strength that complemented those of the others. By all working together you accomplished something that you didn’t realise you’d be able to do, and really nail it. That’s a very satisfying kind of work to be a part of, and I’m privileged to be doing it again in Carl Barrett’s Translational Science Oncology group at AstraZeneca. n

May/June 2015 / Frontline Genomics Magazine / 37

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COMMENT

JAN TAYLOR Clinical Scientist Bioinformatics ST. JAMES INSTITUTE OF ONCOLOGY

ANG DAVIES Lecturer in Healthcare Sciences THE UNIVERSITY OF MANCHESTER

UNLOCKING THE POTENTIAL OF GENOMICS IN HEALTHCARE

INTEGRATING GENOMICS INTO HEALTHCARE IS A MONUMENTAL TASK THAT NEEDS TO BE BROKEN DOWN. HERE, DR DAVIES AND DR TAYLOR, USE THEIR COMBINED EXPERTISE TO EXPLORE THE CHALLENGES FACED BY CLINICAL BIOINFORMATICIANS IN THE NHS. IT’S AN EXCITING TIME AT THE COALFACE, AND THERE’S STILL A LOT OF WORK TO BE DONE.

G

enomics is beginning to have a significant impact on areas of differences between the training and role of an eye surgeon to a heart medicine other than clinical genetics, including cancer, cardiology, surgeon. The use of programming languages that a bioinformatician microbiology and ophthalmology to name but a few. The might use in their work is a good example of this, varying from Python, realisation that we can now very quickly and relatively cheaply sequence to Perl, to Java and so on. a number of genes simultaneously that will influence a treatment In the UK, Modernising Scientific Careers led by Health Education regime, provide a diagnosis or even exclude certain diseases/conditions England has gone some way to addressing the requirement for training means that clinicians are opting for this route rather than conducting focused on clinical need, leading the development of a new Scientist a sequential genetic testing which can be time-consuming and often Training Programme in Clinical Bioinformatics. This training comprises does not lead to a diagnosis – often referred to 3 years of work-based training and a partas the diagnostic odyssey. What has not been time masters programme undertaken at The addressed to date is the efficient management University of Manchester, enabling them to apply of huge quantities of complex genomic data for clinical registration through the Health and that sequencing technologies produce and the Care Professions Council. Unfortunately however shortage of skilled clinical bioinformaticians to the first cohort will not finish until July 2016, in the analyse and interpret this data. meantime there will be the opportunity for those There is a small cohort of clinical currently practising as clinical bioinformaticians “AT THIS MOMENT IT IS UNLIKELY FOR bioinformaticians working within the NHS in the to undergo a process of equivalence to this THE BIOINFORMATICIAN TO DIRECTLY UK, who come from diverse backgrounds. Many programme to also become registered scientists SEE A PATIENT BUT CERTAINLY IN have come from a biological or computer science and therefore also progress to Consultant Clinical research or translational research background, Bioinformaticians. These leadership roles will be THE LARGER CENTRES THEY WILL whilst others were trained as a clinical scientists vital in years to come if we are to truly benefit TAKE PART IN MULTI-DISCIPLINARY and have developed their own bioinformatics from this genomic revolution. MEETINGS WITH CLINICIANS, SENIOR skills within their clinical centres. Bioinformatics So what is the situation really like at the CLINICAL LABORATORY SCIENTISTS is a broad discipline, covering a wide range of coalface for current bioinformaticians managing, specialisms and current clinical bioinformaticians analysing and interpreting all of this genomic data AND ALSO GENETIC COUNSELLORS, have very different backgrounds which impacts in the healthcare setting? WHERE THEY WILL BE HELPING TO on their mode of practice. This could be likened INFORM A CLINICAL DIAGNOSIS OR to a surgeon for example, whilst they might all be described as surgeons clearly there are vast TREATMENT REGIME.”

May/June 2015 / Frontline Genomics Magazine / 39

COMMENT

Jan Taylor, Clinical Scientist Bioinformatics, St. James Institute of Oncology Jan is a clincial bioinformatician working in the Haematological Maligancy Diagnosis Service, Leeds Cancer Centre, St James Hospital, Leeds, UK. After gaining a PhD in Computational Biology, She built a research career in bioinformatics, working on varied projects applying machine learning algorithms to large data sets, in plant science, agriculture, then transitioning to human cancer research. After spending a year developing and delivering professional training courses in Bioinformatics to clinical scientists and healthcare researchers, she moved to clinical bioinformatics, currently developing NGS pipelines for delivery of new molecular diagnostic tests in the NHS. She is an honorary lecturer at the University of Manchester, teaching on the MSc Clinical Bioinformatics.

“CLINICAL BIOINFORMATICS IS A NEWLY RECOGNISED HEALTHCARE PROFESSION, AND AS SUCH THERE IS A LOT OF WORK TO DO TO INCREASE ITS REPUTATION IN THE HEALTHCARE SETTING. FOR THOSE OF US WORKING AT THIS FRONTIER, IT’S A TIME FOR BUILDING A COMMUNITY OF BEST PRACTICE, SHARING A DIVERSE SET OF SKILLS AND EXPERIENCES, AND EMBEDDING BIOINFORMATICIANS AS INTEGRAL MEMBERS OF THE MULTI-DISCIPLINARY CARE TEAM.”

40 / Frontline Genomics Magazine / May/June 2015

In practice the experience is vastly different, varying from Trust to Trust, and even between departments of the same Trust. Roles vary from being part of a team (3-4 people), or a single role embedded in a clinical department. In an ideal world one might imagine a team of bioinformaticians made up of a system administrator, programmers, and web developers, although most centres are a long way from this currently. However with the introduction of bench-top Next Generation Sequencing instruments most centres, be they large or small, do have access to the technology and so most likely will be analysing some kind of genomic data requiring the development and implementation of a bioinformatics ‘workflow’ to analyse this data. This workflow will enable the signal generated from the sequencer, to be converted into sequence, reassembled and mapped back to a reference genome and then analysed for differences which are then further analysed using specialised tools and databases. This might be done using bespoke ‘in-house’ bioinformatics workflows, commercially sourced workflows, or a hybrid of the two. The workflow choices depend on many factors; choice of sequencing machine, DNA capture method, sample type, available computing infrastructure, and previous bioinformatic experience. This makes clear the difficulty in standardisation of standard operating procedures and protocols between laboratories currently and this is unlikely to change, as departments have different priorities for procuring NGS capabilities (budget likely being the overriding influence). This therefore places the emphasis and importance on the need for validation against test data sets and adherence to appropriate recording of programming code and version control, and databases and tools that are used in the bioinformatics analysis. Pressure is being brought to bear in this regard with the introduction of ISO standards that bioinformatics workflows that will need to be adhered to for clinical laboratories to retain accreditation. Provision of the appropriate IT infrastructure required to store and analyse genomic data is also an issue which needs to be addressed. As with sequencing technologies, the available computing power to a bioinformatician varies greatly, from a single standard workstation, a linux server through to a managed HPC facility, depending on the centre, and sometimes the available links to University research computing facilities. The landscape of IT provision in the NHS is complex and each hospital Trust is likely to be different, therefore the bioinformatician has to communicate with many stakeholders to ensure this functions as required: this includes data storage; health informatics and governance, who may have important information that links to part of a patients records; clinical colleagues – this will be discussed in more detail; data communications - that look after the networks through which these large quantities of data are moved around the hospitals; IT services; and also research IT services – sometimes it is easier for hospitals to collaborate with universities to analyse this kind of data as they already have the systems in place; and the other important route of communication is with other bioinformaticians to try to establish best practice in this developing discipline. Dealing with these complex structures requires tenacity, perseverance, leadership and strong communication skills. It is important for the bioinformatician not to lose focus of the fact that there is a patient, with most probably additional family members in the case of inherited diseases for which the outcome of their work could have a huge impact. At this moment it is unlikely for the bioinformatician to directly see a patient but certainly in the larger centres they will take part in multi-disciplinary meetings with clinicians, senior clinical laboratory scientists and also genetic counsellors, where they will be helping to inform a clinical diagnosis or treatment regime. Therefore they have a really important part to play in educating their clinical colleagues such that the workflows and bioinformatics steps are more transparent and stand up to the necessary rigour that other laboratory processes are required

COMMENT

to achieve. One of the most important roles that the bioinformatician needs to undertake is to ensure that patient data, including symptoms and phenotype are captured by clinical colleagues and linked with associated genotype. Achieving this on a much larger scale with National/ International databases such that more data and information can be shared subject to patient consent within the clinical genomic community means that the patients particularly with rare conditions and diseases will benefit more quickly from advances in genomic sequencing. It also fundamental that the bioinformatician is informed of any changes to laboratory protocols such as the addition of additional genes or changes to protocols that will impact on the bioinformatic workflow such that these can be planned for, validated and tested prior to being relied to inform clinical diagnoses and decisions. Clinical bioinformatics is a newly recognised healthcare profession, and as such there is a lot of work to do to increase its reputation in the healthcare setting. For those of us working at this frontier, it’s a time for building a community of best practice, sharing a diverse set of skills and experiences, and embedding bioinformaticians as integral members of the multi-disciplinary care team. n

Ang Davies, Lecturer in Healthcare Sciences, The University of Manchester In addition to Lecturing, Ang is also Programme Director for Masters Programmes in Clinical Bioinformatics and also Genomic Medicine. She is also Academic Lead for Continuing Professional Development (CPD) for the Faculty of Medical and Human Sciences. Ang Davies graduated with a BSc in Biochemistry from the University of Bath, before completing a PhD in Molecular Biology at the University of Warwick, later completing a postdoctoral research fellowship at AstraZeneca and then moved to Renovo in Manchester as a Principal Scientist. For 5 years she then managed the Education and Training Team at Nowgen, a partnership between Central Manchester University Hospitals NHS Foundation Trust and The University of Manchester.

“THE REALISATION THAT WE CAN NOW VERY QUICKLY AND RELATIVELY CHEAPLY SEQUENCE A NUMBER OF GENES SIMULTANEOUSLY THAT WILL INFLUENCE A TREATMENT REGIME, PROVIDE A DIAGNOSIS OR EVEN EXCLUDE CERTAIN DISEASES/CONDITIONS MEANS THAT CLINICIANS ARE OPTING FOR THIS ROUTE RATHER THAN CONDUCTING A SEQUENTIAL GENETIC TESTING WHICH CAN BE TIMECONSUMING AND OFTEN DOES NOT LEAD TO A DIAGNOSIS.”

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www.maverixbio.com May/June 2015 / Frontline Genomics Magazine / 41

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DON’T MISS PLENARY SESSIONS BY THESE INDUSTRY LEADERS

George M. Church

Professor of Genetics Harvard Medical School

Eric D. Green

Director National Human Genome Research Institute

Heidi Rehm

Chief Laboratory Director Partners Healthcare

Jonathan Bingham Product Manager Google Genomics

Robert C. Green

Associate Professor of Medicine Harvard Medical School

J. Craig Venter

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Ting Wu

Professor of Genetics Harvard Medical School

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SAVING LIVES WITH COMPASSIONATE CARE AND CONTEMPORARY TECHNOLOGY THE LIST OF CASES WHERE GENOMICS HAS HELPED PATIENTS IS GROWING. HERE WE LOOK AT THE REMARKABLE EXPERIENCE THE SHENAL FAMILY HAD WITH GREENWOOD GENETIC CENTER, AND HOW THEIR RELATIONSHIP CONTINUES TODAY.

S 5K Run A N D 1 Mile Run/Walk

tephen and Jodi Shenal of Stevenson and Taylor found Greenwood, South Carolina support in the medical community are passionate advocates for a of Greenwood, SC. Inspired by the cause that is near and dear to their vision laid out by these two men, the family. In 2010, excitedly expecting business community including local their second child, prenatal businessman and philanthropist, Jim “THE PRIORITY ultrasounds revealed abnormalities Self, and the state of South Carolina FOR THE CENTER’S in the Shenal’s unborn daughter. all became involved in making this TEAM WAS TO Her prognosis was uncertain. vision a reality. The Greenwood Shortly after Ryleigh was born, Genetic Center became the first FIND AN ANSWER the Greenwood Genetic Center independent genetics institution FOR THE SHENALS was called in to assist in her care. in the United States to provide AND PROVIDE Although her initial karyotype was comprehensive genetics services. COMPASSIONATE normal, Center Director and Senior The compassionate and innovative CARE FOR THIS Clinical Geneticist, Steve Skinner, vision of the Greenwood Genetic YOUNG FAMILY.” evaluated Ryleigh and recommended Center continues today, as does the RACE THE HELIX a microarray to look for even smaller combination of public and private • Race the Helix brings cytogenetic changes. Through the microarray, the support from institutions such as the Self Family together competitive Greenwood Genetic Center’s laboratory discovered Foundation and the SC Department of Disabilities runners, GGC employees, a microdeletion in chromosome 1, too small to and Special Needs. The vision of the center has community supporters, be appreciated through routine karyotyping. At expanded with a focus on the development families and children the time there were only 50 documented cases and delivery of genetic services and expanding for a 5K race and a 1 worldwide. The Shenals now had an answer, a treatments to patients and families impacted by mile run/walk on the community, and most importantly, hope. birth defects, intellectual disabilities and autism. GGC’s home campus in Today, four years after her diagnosis, Ryleigh Today, this small town experiment is a trusted Greenwood, SC faces challenges, but her progress is steady and her international leader in the field of genetics and • The first Race The Helix future is brighter because of the compassionate genomics and is recognized for the manner in was held just shy of care she received from the Greenwood Genetic which they treat their patients – as family, getting Ryleigh’s first birthday Center. The priority for the Center’s team was the best they have to offer. and raised over $3,600 to find an answer for the Shenals and provide Stephen and Jodi Shenal found themselves so • Last year’s Race raised compassionate care for this young family through a grateful for the care they received that before over $10,000 thanks to very difficult and trying period in their lives. Ryleigh’s first birthday, they organized ‘Race growth of the event and The Shenals exceptional experience at the the Helix’, an 5K race and 1 mile walk to raise generous sponsors Greenwood Genetic Center is not unique, nor awareness for those living with genetic disorders • Funds raised through did it happen by chance. This center, located and to raise funds for the Greenwood Genetic ‘Race the Helix’ have in a small town in South Carolina, was founded Center Foundation. The 5th annual ‘Race the Helix’ supported research, on two principles- providing all patients with will take place this fall in Greenwood. The event has 7:00 am – 7:45 am equipment purchases compassionate care and making sure they all have grown in each year through increasing community access to contemporary technology. Without both and industry support. All funds raised through 8:00 am and genetics services for families who can’t afford pieces of the puzzle, the Shenals may not have ‘Race the Helix’ support the overall mission of the Greenwood Genetic Center to pay had their answer and certainly would not have the Greenwood Genetic Center and provide advancing • 2014 saw the launch of gratitude for GGC that they have today. technologies and care for families who may have Race finish will be up the hill on Helix Road ‘Race The Helix-Upstate’ The Greenwood Genetic Center was founded trouble affording it. n $20 for 5K in Greenville, SC four decades ago through an unlikely series of HOW TO GET INVOLVED events. Two genetics fellows, Roger Stevenson, $15 for 1 Mile Run/Walk MD and Hal Taylor, PhD, developed the idea of Please make checks payable to GGC Foundation. For the latest news and to get involved, keep a genetics center that was different from any checking www.GGC.org and the ‘Race The Helix’ other inby existence – different in philosophy T-Shirts guaranteed to entries received Thursday, September 10and facebook page. in structure. Armed with genetics expertise and a 12 and under, 13-19, 20-29, 30-39,passionate 40-49, 50-59, 60+ vision of and helping patients and families,

GREENWOOD

e Helix Greenwood y, October 3, 2015

HI N E!

Top male and female finishers, and top male and female 44 / Frontline Genomics Magazine / May/June 2015 in each age group

GREENWOOD

5K Run AND 1 Mile Run/Walk

Race the Helix Greenwood Saturday, October 3, 2015 RAIN OR SHINE! RE GI S TR ATI ON : 7:00 am – 7:45 am STA R T TI M E :

8:00 am

LO C ATI ON :

Greenwood Genetic Center Race finish will be up the hill on Helix Road

EN TR Y F E E S :

$20 for 5K $15 for 1 Mile Run/Walk Please make checks payable to GGC Foundation.

D E A DL I N E :

T-Shirts guaranteed to entries received by Thursday, September 10

AGE GR OUP S :

12 and under, 13-19, 20-29, 30-39, 40-49, 50-59, and 60+

AWA R DS :

Top male and female finishers, and top male and female in each age group

BE N E F I TTI N G:

#RaceTheHelix Race The Helix

QU EST IONS O R N E E D M O R E IN F O R M ATION? Contact the Greenwood Genetic Center Foundation at 864.388.1813. TO R E G I S T E R , PL E AS E VI S I T W W W. G G C. OR G May/June 2015 / Frontline Genomics Magazine / 45

INTERVIEW

THE MAN WHO MAKES BIOINFORMATICS FUN AND ACCESSIBLE FOR ALL Keith Bradnam, Associate Project Scientists, UC Davis Genome Center

GENOMICS IS A TECHNOLOGY DRIVEN FIELD. PRODUCING DATA IS ONE THING, BUT THE ABILITY TO APPLY COMPUTATIONAL SKILLS IS WHAT IS TURNING IT INTO APPLICABLE INFORMATION. YOU MIGHT RECOGNISE KEITH BRADNAM’S NAME. HE’S PROBABLY HELPED YOU DEVELOP THOSE VERY SKILLS YOURSELF.

T

echnology has enabled a lot of what genomics is achieving today. As amazing as it can be, it is still people who are applying it. To get the most out of the tools available, people need to be able to educate themselves and really understand how to apply them. That makes people like Keith Bradnam, invaluable to the genomics community. He writes text books, organises events, expertly maintains his blog, is one of the people to follow on twitter… You’d be forgiven for thinking that science communication was his full time job. He’s also an integral part of the UC Davis Genome Center. In a rare moment of free time, we caught up with Keith to find out how it all began and what he’s working on at the moment…

“THERE IS A LOT OF TALK THESE DAYS OF THE ‘$1,000 GENOME SEQUENCE’, BUT THIS IS A LITTLE MISLEADING. YOU MAY BE ABLE TO BUY $1,000 WORTH OF SEQUENCING DATA, BUT THE RAW OUTPUT OF MOST OF THE LATEST SEQUENCING MACHINES IS TYPICALLY A VERY LARGE SET OF INCREDIBLY SHORT DNA SEQUENCES.”

FLG: You do a tremendous amount for the field of Bioinformatics. Outside of your own research projects and mentoring students, you do a fantastic job of raising the profile of bioinformatics and making it much easier to understand. You’re one of the people to follow on twitter in genomics, you have a fantastic blog (www. acgt.me), you cowrote ‘Unix and Perl to the Rescue!’, and you put together the Assemblathon. It all started for you back in 1993 when you became one of Europe’s first Bioinformatics MSc students. What made you move from ecology to bioinformatics? KB: One of the main reasons that I chose ecology was that I was interested in evolution, and ecology deals with this at the ‘big end’ of the scale (e.g. evolution of species and ecosystems). Bioinformatics offers just as many opportunities to study evolution, but now you

are looking at the other end of the scale (e.g. evolution of genes and genomes). One thing that bioinformatics lacks, however, is the ability to hike about on windy hillsides and throw quadrats around. FLG: The Internet has developed considerably since the early 90’s, as has IT in general. We were also a long way off from the kind of sequencing data we have today. What kind of work were you being taught to do back then?

KB: No matter what the year, there are some things that always seem to hold true for bioinformatics research. Some of the things that I had to deal with back in 1993 remain issues today. Namely: 1. The amount of CPU power, memory, and bandwidth that your computer has will always struggle to keep up with the ever-growing size of the sequence files that you want to download and process. 2. You will spend more time than you had planned converting files from one bioinformatics file format into another. 3. At some critical juncture in your research, you will struggle to satisfactorily complete a task because of the incompleteness – or total lack – of documentation for a particular piece of bioinformatics software that you need to use. But thinking back to my MSc course, it is important to note that the Internet was a very different place back then. The World Wide Web had only just begun to develop and there was very little content on it that was useful to the field of bioinformatics. If you wanted to download interesting data sets, you needed to be conversant with tools such as Gopher, not to mention Veronica and Archie of course! So some of the teaching had to cover how to use these tools (along with telnet and FTP) so you could find some data to work with.

May/June 2015 / Frontline Genomics Magazine / 47

“ONE OF THE MAIN REASONS THAT I CHOSE ECOLOGY WAS THAT I WAS INTERESTED IN EVOLUTION, AND ECOLOGY DEALS WITH THIS AT THE ‘BIG END’ OF THE SCALE (E.G. EVOLUTION OF SPECIES AND ECOSYSTEMS).”

SCIENTIST COMMUNICATOR WRITER Keith was first nominated as one of Next Gen Seek’s ‘Top Genome Scientists To Follow on Twitter’ in 2013. As well as actively tweeting through @kbradnam and @ assemblathon, Keith maintains a series of blogs: FLG: The course clearly set you up for a very successful career as a bioinformatician. At the time, there wasn’t quite the same demand for that skill set as there is today. Was doing a PhD the only viable route to apply those skills, or was there ever any thought of leaving academia? KB: In late 1994, when I finished my MSc, there were very few ‘career paths’ in bioinformatics outside of academia. Biotech companies were just in the process of developing bioinformatics research groups and job opportunities in the private sector were few and far between. In my early attempts to find a job in the private sector I sometimes found myself competing for jobs with other graduates from my MSc (there were only 12 of us as I recall)! So despite being promised that ‘bioinformatics is going to be huge’, I actually found myself – for the first time in my life – unemployed after finishing

my MSc. I realised that I wanted to consider an academic path instead and worked for a small software company in Cambridge for a year or so during which I took the time to find a place where I could work on something that interested me. Ultimately that led me to the University of Nottingham where I started my PhD in 1996. I seem to recall that even in academia, there didn’t seem to be many groups that specialised in bioinformatics research, so there were not many suitable places to apply to. FLG: You’ve been developing genome databases ever since you completed the PhD. How did you end up enjoying life in California at UC Davis? KB: While I was working at the Wellcome Trust Sanger Institute, I shared some office space with Ian Korf who was a visiting postdoc at the time. That was his last position

48 / Frontline Genomics Magazine / May/June 2015

ACGT: A frequently updated blog, giving Keith’s thoughts on biology, genomics and ‘the ongoing threat to humanity from the bogus use of bioinformatics acronyms. Scared of Heights: Posts of thoughts and observations relating to technology (including a useful tip if you want to listen to videos in the background on an iOS device). The Bradnam Blog: Keith’s personal blog for topics not relating to science or technology (including a detailed breakdown of why a Japanese restaurant’s sign is unfit for purpose). The Molluskan Zodiac: Easily one of the stranger things you’ll come across online. The Molluskan Zodiac- The world’s only nautical-themed set of horoscopes that are automatically generated by a Perl script.

Keith Bradnam Associate Project Scientists UC Davis Genome Center Keith began his academic career with a B.Sc. in Ecology at University of Leeds. His life in bioinformatics began by completing an M.Sc. in Bioinformatics at University of Manchester. He studied eukaryotic genome evolution for his Ph.D. at University of Nottingham, before working on the WormBase database at the Wellcome Trust Sanger Institute. This is where he first met Ian Korf, whom he would follow to California and the UC Davis Genome Center where he is a pillar of the burgeoning bioinformatics scene.

“The amount of CPU power, memory, and bandwidth that your computer has will always struggle to keep up with the ever-growing size of the sequence files that you want to download and process. “

before he moved to Davis to set up his own lab. Within a few months of moving to California, he heard that I might be interested in a career change and encouraged me to apply for a post-doc position in his lab. So I became the first person to join his group back in 2005, and since then I have been failing spectacularly at my ongoing plan to stay for ‘just a year or two’.

FLG: You’re passion for science communication seems to have really flourished while at UC Davis. Is there anything in particular that encouraged you to develop that side of things?

KB: On the one hand, the rise of social media – not to mention the increasing ease-ofuse of many blogging platforms – means that it is easier than ever to reach out to others. Twitter has proven to FLG: What kind of projects are you working on at the moment? be such an incredibly useful tool for academics, both to disseminate information and also to find out about the latest research in your KB: The main thing that I am working on is a new collaboration with particular field. In particular, the live tweeting of conference talks Danielle Lemay who is a Faculty member here at the UC Davis Genome (when permitted) really helps ensure that everyone can benefit from Center. Danielle is the guru of all things to do with milk genomics and the results of publicly funded scientific research being shared in an I’m providing bioinformatics support to help characterize genomic ele open manner. I’ve been using twitter since 2008 and I think this was ments that may be involved with mammary gland function in cows. the spark that started me on the the path to writing regularly on my I’m also wrapping up two other collaborative projects ACGT blog. Sometimes I encounter things in my that primarily involve genome data from Arabidopsis day-to-day life as a scientist that surprise, delight, thaliana. One project is helping to characterize the or annoy me. These can all be good things to blog about. Although it may seem that I spend a lot of patterns of ‘genome catastrophe’ in some specific lines of time criticizing poorly chosen scientific acronyms, A. thaliana; these plants have an extra copy of one of their I really prefer writing pieces that hopefully help chromosomes which becomes highly scrambled (similar others to better understand a subject. There is a things happen in human cancer genomes). The other “AT SOME CRITICAL lot of ‘accepted bioinformatics wisdom’ that can project involves developing tools that can computationally be hard for newcomers to the field to get their predict how much certain plant introns might enhance JUNCTURE IN YOUR heads around, so occasionally I like to explain gene expression. There is good experimental evidence RESEARCH, YOU concepts in a way that even your grandparents that some introns in A. thaliana can increase expression WILL STRUGGLE TO could (hopefully) understand. Analogies can be up to 10x (compared to when intron of interest is SATISFACTORILY good for this. The other big motivator for me to removed), but these wet-lab experiments can take up to COMPLETE A TASK develop science communication skills is because a year to do properly. In contrast, our software tool does BECAUSE OF THE I’ve found so many scientific presentations to be a good job at predicting the boost in expression in just INCOMPLETENESS – confusing, unfocused, and often tedious. Most seconds! As well as beginning some preliminary work OR TOTAL LACK – OF talks are informative, but when you have talks that regarding a possible Assemblathon 3 contest, I manage DOCUMENTATION FOR are informative without being memorable then it and update the Genome Center’s website and twitter A PARTICULAR PIECE is often a waste of time for all involved. account, act as system administrator for our lab, mentor OF BIOINFORMATICS I want all of the students from our lab to give students, and continue to deal with a surprisingly large presentations that are informative as well as being number of emails about the CEGMA tool that our lab SOFTWARE THAT YOU memorable, and (hopefully) entertaining. developed a long time ago. NEED TO USE.”

May/June 2015 / Frontline Genomics Magazine / 49

Too many people seem to give presentations that fail to address the #1 question that all talks should aim to address – why should the audience care about this? This can usually be addressed by making your talk tell a story. I.e. it should have a beginning, middle, and end. The most common problem in talks from early career scientists is ‘too much middle’ (lots of results) without first setting the scene or clarifying what all those results mean. FLG: As part of your ‘101 Questions’ series on your blog, you’ve interviewed a who’s who of bioinformaticians. Are you finding any trends emerging in what people enjoy or don’t enjoy about current bioinformatics research? KB: I’ve noticed that bioinformaticians like the diversity of the research experience that can occur. Sometimes this is driven by rapid changes in underlying technologies, such as sequencing, that opens new doors to researchers, but sometimes it just comes about from the many collaborations that emerge in the field. If you are skilled at slicing and dicing genome data, you may find yourself sometimes switching projects to work on completely different species, with different biological challenges, but all of which are underpinned by genome data written in the same language.

that there is a lot of room for improvement in the field of genome assembly. However, the technology is moving so fast that this situation will hopefully improve in the near future.

“ALTHOUGH IT MAY SEEM THAT I SPEND A LOT OF TIME CRITICIZING POORLY CHOSEN SCIENTIFIC ACRONYMS, I REALLY PREFER WRITING PIECES THAT HOPEFULLY HELP OTHERS TO BETTER UNDERSTAND A SUBJECT. THERE IS A LOT OF ‘ACCEPTED BIOINFORMATICS WISDOM’ THAT CAN BE HARD FOR NEWCOMERS TO THE FIELD TO GET THEIR HEADS AROUND”

FLG: We thought you might enjoy the 101 Q experience yourself… KB: Sorry, I reserve the right to interview myself on my blog at a later date! FLG: As we mentioned at the start of the interview, you’re also one of the guys behind the Assemblathon. Could you explain what the Assemblathon is for our non-bioinformatician readers? KB: There is a lot of talk these days of the ‘$1,000 genome sequence’, but this is a little misleading. You may be able to buy $1,000 worth of sequencing data, but the raw output of most of the latest sequencing machines is typically a very large set of incredibly short DNA sequences. They only have utility once they are assembled into much longer sequences. This problem can be likened to trying to solve an extremely large jigsaw puzzle. However, in the field of genome assembly your puzzle box may contain up to 100 copies of most of the pieces, no copies at all of some of the pieces, and quite a few pieces will be from a completely different puzzle. Furthermore, you may be missing the lid to the puzzle box so you might not know what the puzzle is meant to look like (or how big it should be). If it wasn’t obvious by now, genome assembly is not an easy problem to solve! In trying to tackle this issue, scientists have developed many different software tools that try to perform the task of putting a genome together from all of the constituent pieces. However it is far from clear which tools are the best. This is not a simple problem because you can define ‘best’ in many different ways, and while researchers may hope for a resulting genome assembly that is the best however it is defined, this doesn’t yet seem possible with today’s tools. So the Assemblathon contests were an idea to test a bunch of different genome assemblers to a) see how they differ and b) see whether we can judge any of them as being consistently better than others. The results from the first two Assemblathons suggest

50 / Frontline Genomics Magazine / May/June 2015

FLG: Any plans to follow the success of Assemblathon 2 with Assemblathon 3? KB: Many plans, but nothing formalized just yet. This may change in the coming weeks though…stay tuned! FLG: We spoke briefly about Bioinformatics in the 1990’s. The role has changed considerably since then. At what point does that skill set become a core competency for researchers in general?

KB: Bioinformatics has become quite a sprawling field which can involve many different facets of biology, computing, mathematics, and statistics. I like to think of ‘classic bioinformatics’ as the ability to run command-line programs against some biological data and use Unix commands and (relatively) simple scripting languages to slice and dice that data. If you accept my definition of ‘classic bioinformatics’, then I feel that this skill set is becoming more prevalent, but the pace of change is still too slow. I feel that the real change needs to happen before students even start at university. Coding and data processing skills should be a required part of all educational curriculums. My experience from helping high school students in the annual Young Scholars Program that UC Davis organizes tells me that such students are not only capable of learning to code, but they are often excited and enthusiastic to learn such skills. FLG: Will there ever come a point where you make a conscious decision to move full time into a communications or writing career? KB: Very possibly! It seems that I spend an increasing amount of my time writing for websites and social media, both personally and professionally. This is an avenue I’m keen to explore (also see answer to last question). FLG: Do you have plans to expand on the mythology of the Molluskan Zodiac? KB: The Molluskan Zodiac already plays an important guiding role in the lives of many people. Never before has a horoscope been based on the lives of marine invertebrates, and never before has a system of divination been implemented through use of a Perl script. Aside from one early issue that arose, there have no been no recent upheavals in Molluskan Zodiac mythology and there are no plans for any further changes. FLG: Thank you very much for sharing your thoughts with us. Is there anything else you’d like to say to our readers? KB: I’m finally planning to moving back to the UK (or possibly western Europe) in early 2016 and would love to talk to anyone who knows of opportunities that might be a good fit for me. I’m interested in a position relating to bioinformatics/genomics which involves outreach/communication and/or training/teaching. n

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BLADE RUNNER - THE FINAL CUT, IS ENJOYING A CINEMATIC RE-RELEASE AT THE MOMENT. ARE ITS PHILOSOPHICAL QUESTIONS STILL VALID?

B

lade Runner consistently sits at the top of almost every ‘best sci-fi movie’ list you’ll find. Its achieved a rare status of being one of those movies that you can’t admit to not having seen. Whether or not you actually enjoy it, seems almost irrelevant these days. But if anyone asks just tell them you think Deckard is a replicant… For modern viewers, it’s important to approach the film with the proper context. It is loosely based on a book from 1968 (P.K. Dick’s ‘Do Androids Dream Of Electric Sheep?’) saw its original release in 1982, and is set in the 2019. We knew a lot less about the world back then. And the effects-driven movies weren’t anywhere near as technically advanced as they are today. So what makes it perennially intriguing? Is it the synth-heavy score by Vangelis? Is it the blend of American and Oriental cultures? Maybe. For some, the style is irresistible. Personally, I’m not sure it’s for me. Blade Runner serves as an interesting retrospective look at man’s imagination. Most sci-fi fans will be quick to tell you that the genre consistently influences the direction of scientific research. In recent times, we’ve heard Professor Stephen Hawking share his concerns about artificial intelligence; seen the rise of synthetic biology; made enormous advances in our understanding of genetics; and managed amazing progress in our understanding of the planets around us. All of a sudden, Blade Runner doesn’t quite seem so science fiction anymore. That being said, the script still throws up some interesting ‘movie biology/genetics’ to keep you laughing! Fortunately it’s not the science that drives the plot. This is really a movie about what makes us human. And that’s what makes it so relevant now. Primarily the film, and the book, explore life and humanity. What are the key ingredients that mark

VERDICT: OK

us out as part of the human race? Is it the raw materials? Or is it belief and a human experience? These are some of the ethical questions we’re asking ourselves right now. Genome editing is a great example of this. The potential benefit of being able to repair a gene, or remove a faulty gene from the mix, is clear. But we’re challenging the moral and ethical framework that we’ve held for so long. Add to that, Craig Venter’s group is doing some amazing stuff working on creating synthetic life. So where does that leave us? Will confused synthetic humans be knocking on the door at the JCVI to meet their maker? Probably not any time soon. But we do find ourselves in a very exciting period of scientific discovery. We’ve come far enough that we are being faced with some very complicated ethical questions with big implications. The decisions made today, will almost certainly shape tomorrow’s human experience. n

“WILL CONFUSED SYNTHETIC HUMANS BE KNOCKING ON THE DOOR AT THE JCVI TO MEET THEIR MAKER?”

PROS

For new generations, Blade Runner looks and feels dated. It still has a lot to offer as an important slice of sci-fi movie history. That being said, its themes seem more relevant today than when it was first released.

52 / Frontline Genomics Magazine / May/June 2015

Presents interesting philosophical questions Rutger Hauer portrays a compelling villain/hero as the angry and confused replicant, Roy Batty

CONS

Time is starting to tell. The once spectacular effects are looking very dated. The themes of what makes us human aren’t explored anywhere near as well as in the book on which the script is based.

RATING

6.5

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