technologies to provide a single point of contact from your initial inquiry ... To learn more about working with NYGC co
GENOMICS SERVICES
T H E N E W YO R K G E N O M E C E N T E R NYGC is an independent non-profit implementing advanced genomic research to improve diagnosis and treatment of serious diseases. $PMMBCPSBUJOHXJUI QIZTJDJBOTDJFOUJTUT XFVTFGJSTUJODMBTT UFDIOPMPHJFTBOEIJHIMZFYQFSJFODFEQFSTPOOFMUP PGGFSTVQFSJPSJOUFHSBUFEHFOPNJDT capabilities.
N E X T- G E N E R AT I O N R E S E A R C H A N D C L I N I C A L S E Q U E N C I N G FA C I L I T Y •
10 Illumina HiSeq X instruments to enable sequencing of up to 18,000 30x human whole genomes or 4,500 tumor/normal pairs at 80x/40x each year.
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12 Illumina HiSeq 2500s to allow annual sequencing of tens of thousands of whole exome, RNA, methylation, or custom samples.
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High-throughput processes and rapid turnaround times are achievedVTJOH extensive automation GSPN wet-lab robotics UP highly parallelized analysis pipelines. This, coupled with the highly experienced scientific staff, yields IJHI quality data.
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NYGC has a CLIA certified clinical lab that satisfies New York State CLEP regulations.
T E C H N O L O GY I N N O VAT I O N L A B O R AT O R Y •
Composed of engineers, molecular biologists and chemists working together to develop cutting-edge technologies to optimize genomics research and clinical applications.
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Expertise in: single-cell sequencing, microfluidics, molecular biology, current and future next-generation sequencing technologies, chemical synthesis, and surface chemistry.
ABOUT NEW YORK GENOME CENTER JULY 2015
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HIGH-PERFOR M ANCE COMPUTING INFR ASTRUCTURE •
Efficient and highly parallelized analysis of large-scale data sets achieved using a high-performance compute infrastructure containing 4,200 cores of computing power and 11Pb of storage.
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Secure 2N storage facility provides a high level of protection against failure of any component.
D E D I C AT E D P R O J E C T M A N A G E R S •
Each project will be assigned to a dedicated project manager with expertise in genomics and genomic technologies to provide a single point of contact from your initial inquiry through data delivery.
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Project managers provide updates as samples pass through NYGC to give you up-to-date information on the progress of your project.
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Your project manager will communicate and address questions that are generated once data is provided.
B I O I N F O R M AT I C S E X P E R T I S E •
Expert bioinformaticians answer a wide range of biological questions by combining streamlined pipelines and varied technical approaches. Typical service includes standard pipeline analysis of sequencing data (e.g., through variant annotation or transcript quantif i cation); in addition bioinformatics support is available for advanced analysis either on a fee-for-service or a collaborative basis.
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Automated pipelines identify diverse types of variants from a multitude of sample types. This includes, somatic analysis of tumor and matched-normal samples, familial analysis to identify inherited and de novo variation in individuals, metagenomic analysis, epigenetic analysis, and differential expression analysis.
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Additional areas of expertise include variant curation through literature review, pathway analysis, cell-type specific biology, extended pedigree analysis, Mendelian and complex disease studies, pathogen identification and interpretation, integration of patients’ DNA and RNA data, and fusion transcript detection.
To learn more about working with NYGC contact us at
[email protected].
ABOUT NEW YORK GENOME CENTER
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NEW YORK GENOME CENTER
SERVICES
WHOLE GENOME SEQUENCING Hum an WGS •
NYGC’s whole genome service provides investigators with high quality whole genome data at a competitive rate.
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NYGC has completed sequencing of thousands of whole genomes on Illumina’s HiSeq X sequencing platform.
COV E R AGE OP T IONS:
Minimum of 30x
L I B R A R Y P R E PA R A T I O N :
Illumina TruSeq Nano DNA or Illumina TruSeq PCR-Free DNA
T U R N A R O U N D T I M E 1:
10 weeks
Hum an WGS Q ualit y Co ntro l •
Samples sequenced at NYGC are subject to an array of rigorous in-line quality assurance protocols
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Contamination checks (software and chips): up-front analysis for sample contamination assures the correct sample type is present throughout.
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Concordance checking against the Illumina genotyping chip. Net results geared toward delivering a high level of accuracy and assurance of sample identif i cation. Can be used to check familial relationships and sample duplication.
N o n-hum an WGS •
NYGC’s non-human whole genome service can be customized to your organism of interest. Past projects have included mouse, rat, bacteria, virus and other non-model organisms.
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NYGC has 12 HiSeq 2500s and capacity to support very large projects.
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De novo assembly is available as an additional service for genomes without a reference.
L I B R A R Y P R E PA R A T I O N :
Illumina TruSeq Nano DNA or Illumina TruSeq PCR-Free DNA
T U R N A R O U N D T I M E 1:
10 weeks
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W H O L E E XO M E S E Q U E N C I N G Human WES •
The Agilent SureSelect capture kit provides optimal coverage and targets about 21,000 genes.
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NYGC runs large-scale exome projects and has processed tens of thousands of exomes.
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Whole exome sequencing plus 3’ and 5’ untranslated regions is also available and allows interrogation of some regulatory regions.
L I B R A R Y P R E PA R A T I O N :
Agilent SureSelect XT v5, 51Mb (exon) or 71Mb (exon + UTR) Low input Library Preparation options also available.
T U R N A R O U N D T I M E 1:
weeks
M ouse WES •
NYGC has workflows to perform mouse specific alignment, variant calling, and annotation.
L I B R A R Y P R E PA R A T I O N :
Agilent SureSelect Mouse Exome
T U R N A R O U N D T I M E 1:
weeks
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RNA SEQUENCING mRNA •
NYGC uses oligo-dT beads to enrich the polyadenylated RNA molecules in the sample.
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Read lengths available are paired-end 50bp and 125bp.
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Current library preparation protocols preserve the strand information.
L I B R A R Y P R E PA R A T I O N :
Illumina TruSeq Stranded mRNA
T U R N A R O U N D T I M E 1:
8 weeks
To t a l R N A •
Total RNA allows the study of protein coding RNA as well as long non-coding RNAs.
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Read lengths available are paired-end 50bp and 125bp.
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Ribosomal depletion in library preparation minimizes the presence rRNA.
L I B R A R Y P R E PA R A T I O N :
KAPA Stranded RNA-Seq with RiboErase
T U R N A R O U N D T I M E 1:
8 weeks
Small RNA •
Provides the ability to study RNA molecules 17-37 molecules long.
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This includes a wide variety of classes of regulatory RNAs.
L I B R A R Y P R E PA R A T I O N :
Illumina TruSeq Small RNA
T U R N A R O U N D T I M E 1:
8 weeks
4&37*$&015*0/4 /:($SFDPHOJ[FTUIBUPOFTJ[FEPFTOUGJUBMMQSPKFDUs. ThisDBUBMPHJTEFTJHOFEUPCFBOPWFSWJFXPG TUBOEBSE/:($PGGFSJOHs'PSRVJDLUVSOBSPVOEUJNF MPXJOQVUPQUJPOTPSPUIFSTFSWJDFTOPUMJTUFE QMFBTFJORVJSFGPSNPSFEFUBJMT.
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LANE SEQUENCING NYGC Lane Sequencing Services refers to sequencing of investigator-prepared specialized libraries. Lane Sequencing can be used for any library preparation protocol not supported by NYGC highthroughput services. NYGC has designed its Lane Sequencing offering to be flexible and support the diverse application needs of the community while maintaining high quality results.
Example Uses of Lane Sequencing •
Custom targeted enrichment panels
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Single cell sequencing
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MetagenomicT
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ChIP-seq
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HITS-CLIP
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ddRAD-seq
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shRNA screen libraries
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16S libraries
Ty pe of Ser vice
Tur naround Time 1
Q u a li t y Co n t r o l 2
N Y G C Wa r r a n t y
Standard
2 weeks
Investigator performs QC2 and specifies loading concentration
NYGC will provide re-runs only if sequencer failure occurs
Full Service
4 weeks
NYGC performs QC2
NYGC will re-run if sequencer failure occurs and will troubleshoot samples returning low quality sequencing data
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Turnaround times are calculated based on when a sample passes NYGC's initial sample quality control.
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Library QC with Bioanalyzer, Qubit or Picogreen, and qPCR.
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LANE SEQUENCING OPTIONS HiS e q ® 250 0 High Out put R u n Type
M ax imum yi e ld p e r la n e ( g ig ab a s e s ) 3
M i n i mu m S ub mi s s i o n
1x50bp
11
8 lanes
1x100bp
23
8 lanes
1x125bp
28
8 lanes
2x50bp
23
1 lane
2x100bp
45
8 lanes
2x125bp
56
1 lane
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Illumina TruSeq SBS Kit v4 reagents are used to provide maximal sequence output per lane.
HiS e q 250 0 ® Rapid Run
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R u n Ty pe
M aximu m yi e ld p er la n e ( g ig aba s e s ) 4
M i n i mu m S u b mi s s i o n
1x50bp
6
2 lanes
1x100bp
13
2 lanes
1x125bp
16
2 lanes
1x150bp
38
2 lanes
1x250bp
63
2 lanes
2x50bp
13
2 lanes
2x100bp
25
2 lanes
2x125bp
31
2 lanes
2x150bp
75
2 lanes
2x250bp
125
2 lanes
Illumina TruSeq Rapid SBS Kit v2 reagents are used to provide rapid turnaround.
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NEW YORK GENOME CENTER
ADDITIONAL SERVICES
B I O I N F O R M AT I C S •
NYGC currently runs 12 application-specific fully automated analysis pipelines that process data from instrument through automated annotation.
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Importantly, these pipeline components have been geared toward reducing time for data generation.
Constitutional Whole Genome and Whole E xome Analysis •
Alignment (Standard)
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SNV and Indel Calling (Standard)
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Structural Variant Calling (Whole Genome only) (Standard) •
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Includes: copy number variants, translocations, inversions, and other complex variants
Extended Familial Analysis (Extra)
Cancer Whole Genome and Whole E xome Analysis •
Alignment (Standard)
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SNV and Indel Calling 4UBOEBSE
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Structural Variant Calling (WGS only)
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PDX Sample Analysis (Extra)
RNA Se quencing Analysis •
Alignment (Standard)
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(FOF2VBOUJGJDBUJPO 4UBOEBSE
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Differential Expression Analysis (Standard)
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Functional Annotation (Extra)
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Fusion Gene Discovery (Standard)
M i t o c h o n d r i a l 4 F R V F O D J O H a n d F u n c t i o n a l A n a l y s i s Microbiome Se quencing Analysis Epigenetics Analysis Pipelines
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D ATA D E L I V E R Y, S T O R A G E , A N D C O M P U T E Data Deliver y Options •
NYGC has designed a full service solution to work with and store your data following sequencing and analysis.
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SFTP/SCP: Access data via your own FTP client software, or SCP/SFTP from a command line.
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Aspera: High speed data delivery via a simple graphical browser-plugin with the option of using a command client.
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Other options also available
Data Storage Data is delivered via NYGC’s data delivery portal and stored for three months. Additional data storage is available for a OPNJOBMmonthly fee.
Compute After NYGC has produced raw data or performed initial analysis, investigators may wish to complete their own additional analysis. Investigators have the opportunity to use NYGC’s high-performance computing cluster to analyze large data sets that require capacity beyond what is locally available.
For more information, please visit nygenome.org
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