GENOMICSSERVICES

NYGC is an independent non-profit implementing advanced genomic research to improve diagnosis and treatment of serious diseases.

capabilities.

THE NEW YORK GENOME CENTER

NEXT-GENER ATION RESEARCH AND CL IN ICAL SEQUENCING FAC I L IT 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.

• 12 Illumina HiSeq 2500s to allow annual sequencing of tens of thousands of whole exome, RNA,

methylation, or custom samples.

• High-throughput processes and rapid turnaround times are achieved extensive automation

wet-lab robotics highly parallelized analysis pipelines. This, coupled with the highly

experienced scientific staff, yields quality data.

• NYGC has a CLIA certified clinical lab that satisfies New York State CLEP regulations.

TECHNOLOGY INNOVATION L ABOR ATORY

• Composed of engineers, molecular biologists and chemists working together to develop cutting-edge

technologies to optimize genomics research and clinical applications.

• Expertise in: single-cell sequencing, microfluidics, molecular biology, current and future next-generation

sequencing technologies, chemical synthesis, and surface chemistry.

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HIGH-PERFOR MANCE 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.

• Secure 2N storage facility provides a high level of protection against failure of any component.

DEDICATED PROJECT MANAGERS

• 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.

• Project managers provide updates as samples pass through NYGC to give you up-to-date

information on the progress of your project.

• Your project manager will communicate and address questions that are generated once data is provided.

BIOINFORMATICS EXPERT ISE

• 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 quanti f i cation); in addition

bioinformatics support is available for advanced analysis either on a fee-for-service or a collaborative

basis.

• 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.

• 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 service@nygenome.org.

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N E W Y O R K G E N O M E C E N T E R

SERVICES

WHOLE GENOME SEQUENCING

Human WGS

• NYGC’s whole genome service provides investigators with high quality whole genome data at a

competitive rate.

• NYGC has completed sequencing of thousands of whole genomes on Illumina’s HiSeq X sequencing platform.

C OV E R AG E O P T I O N S: Minimum of 30x

L I B R A R Y P R E PA R AT 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

Human WGS Q ua l i t y Con t ro l

• Samples sequenced at NYGC are subject to an array of rigorous in-line quality assurance protocols

• Contamination checks (software and chips): up-front analysis for sample contamination assures thecorrect sample type is present throughout.

• Concordance checking against the Illumina genotyping chip. Net results geared toward delivering

a high level of accuracy and assurance of sample identi f i cation. Can be used to check familial

relationships and sample duplication.

N on-human 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.

• NYGC has 12 HiSeq 2500s and capacity to support very large projects.

• 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 AT 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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WHOLE EXOME SEQUENCING

Human WES

• The Agilent SureSelect capture kit provides optimal coverage and targets about 21,000 genes.

• NYGC runs large-scale exome projects and has processed tens of thousands of exomes.

• 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 AT 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 AT 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.

• Read lengths available are paired-end 50bp and 125bp.

• Current library preparation protocols preserve the strand information.

L I B R A R Y P R E PA R AT 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 RNA

• Total RNA allows the study of protein coding RNA as well as long non-coding RNAs.

• Read lengths available are paired-end 50bp and 125bp.

• Ribosomal depletion in library preparation minimizes the presence rRNA.

L I B R A R Y P R E PA R AT 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

Sma l l RNA

• Provides the ability to study RNA molecules 17-37 molecules long.

• This includes a wide variety of classes of regulatory RNAs.

L I B R A R Y P R E PA R AT I O N: Illumina TruSeq Small RNA

T U R N A R O U N D T I M E 1: 8 weeks

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L ANE 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 high-

throughput 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.

E xamp l e Use s o f L ane S e que nc ing

• Custom targeted enrichment panels

• Single cell sequencing

• Metagenomic

• ChIP-seq

• HITS-CLIP

• ddRAD-seq

• shRNA screen libraries

• 16S libraries

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Type of Ser vice Turnaround Time1 Qual i ty Control2 NYGC Warranty

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

1 Turnaround times are calculated based on when a sample passes NYGC's initial sample quality control.

2 Library QC with Bioanalyzer, Qubit or Picogreen, and qPCR.

L ANE SEQUENCING OPTIONS

HiS e q ® 250 0 H igh Ou t pu t

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Minimum Submiss ion

1x50bp 11 8 lanes

1x100bp 23 8 lanes

1x125bp 28 8 lanes

2x50bp 23 1 lane

2x100bp 45 8 lanes

2x125bp 56 1 lane

3 Illumina TruSeq SBS Kit v4 reagents are used to provide maximal sequence output per lane.

HiS e q 250 0 ® Rap id Run

Run Type Maximum yie ld per lane (gigabases)4 Minimum Submiss ion

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

4 Illumina TruSeq Rapid SBS Kit v2 reagents are used to provide rapid turnaround.

Run Type Maximum yie ld per lane(gigabases)3

N E W Y O R K G E N O M E C E N T E R

ADDITIONAL SERVICES

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BIOINFORMATICS

• NYGC currently runs 12 application-specific fully automated analysis pipelines that process data from

instrument through automated annotation.

• Importantly, these pipeline components have been geared toward reducing time for data generation.

Cons t i t u t i o na l Who l e G e nome and Who l e E xome Ana l y s i s

• Alignment (Standard)

• SNV and Indel Calling (Standard)

• Structural Variant Calling (Whole Genome only) (Standard)

• Includes: copy number variants, translocations, inversions, and other complex variants

• Extended Familial Analysis (Extra)

Cance r Who l e G e nome and Who l e E xome Ana l y s i s

• SNV and Indel Calling

• Structural Variant Calling (WGS only)

• PDX Sample Analysis (Extra)

RNA S e que nc ing Ana l y s i s

• Differential Expression Analysis (Standard)

• Functional Annotation (Extra)

• Fusion Gene Discovery (Standard)

Mi t o chond r ia l and Func t i ona l Ana l y s i s

M ic ro b iome S e que nc ing Ana l y s i s

Ep ig e ne t i c s Ana l y s i s P ip e l in e s

• Alignment (Standard)

• Alignment (Standard)

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DATA DEL IVERY, STOR AGE, AND COMPUTE

Da t a De l i ve r y O p t ions

• NYGC has designed a full service solution to work with and store your data following sequencing

and analysis.

• SFTP/SCP: Access data via your own FTP client software, or SCP/SFTP from a command line.

• Aspera: High speed data delivery via a simple graphical browser-plugin with the option of using

a command client.

• Other options also available

Da t a S t o ra ge

Data is delivered via NYGC’s data delivery portal and stored for three months. Additional data storage is available for a monthly fee.

Compu t e

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