NYGC is now accepting samples for sequencing. During its initial rollout phase, NYGC is offering a limited menu of standard sequencing services. This menu will expand over time.

If you have a requirement that is not specified here, please contact us to discuss ways that we might collaborate:  

service@nygenome.org or 888.415.6942 x1

Note: Sequencing and bioinformatics services are available on a priority basis to NYGC members and collaborators.

Current Services

NYGC offers an integrated genomics solution that includes:

• Initial consultation with wet lab and bioinformatics scientists
• Next-generation sequencing
• Bioinformatics analysis using standard pipeline
• Data storage
• Access to NYGC high-performance computational infrastructure

Scientists from NYGC work with researchers to ensure adequate sample quality, assist in evaluating experimental design options, and aid researchers in selecting optimal analysis modalities. Project pricing, estimated timelines, and a precise definition of deliverables also are provided. Following order completion and sample receipt, NYGC performs sample QC, library preparation, next-generation sequencing, and bioinformatics analysis. Standard pricing includes data storage for 24 months on NYGC servers, as well as access to a high-performance computing infrastructure for customer analysis.

NYGC is currently offering three standard sequencing services: 

1. Human Whole Genome Sequencing

• TruSeq library preparation
• 2x100bp paired-end reads
• 30x, 60x or 90x mean coverage

2. Human Whole Exome Sequencing 

• Sequence capture with Illumina TruSeq, Agilent SureSelect, or Nimblegen SeqCap EZ
• Pre- or post-capture pooling
• 2x100bp paired-end reads 

3. Human mRNA  Sequencing

• TruSeq mRNA library preparation
• 2x50bp paired-end reads

For exome sequencing and mRNAseq, different multiplexing levels (with corresponding read depths and target coverage) are available. Different read-lengths can also be selected for mRNAseq.

Other non-standard sequencing service options may also be available after consultation with NYGC sequencing program managers. If you have a requirement that is not specified here, please contact us to discuss ways that we might collaborate:

service@nygenome.org or 888.415.6942 x1

Bioinformatics

As an integral part of the standard service offering, NYGC provides:

• All pass filter reads and quality scores (including reads that did not align to the reference genome) in an archival BAM format file, suitable for visualization and downstream analysis

• Reads aligned to the NCBI genome build 37. (FASTQ file format can be extracted from the provided BAM files but are not delivered)

• For whole genome and exome sequencing: SNP calls, insertions, deletions and structural variants with respect to the reference sequence, as well as an allele calls and confidence score for every covered position in the reference in a text format. Text files contain SNP calls for all dbSNPs for which sufficient coverage has been achieved

• For mRNAseq: reads aligned to NCBI genome build 37 using an aligner that allows spliced reads (Tophat). The default transcript list will be derived from Refseq, but alternate sources of transcript annotation are available

• Expression table obtained from an algorithm able to discriminate various isoforms (Cufflinks)

Data Storage and HPC Access

NYGC has developed an innovative IT infrastructure that will serve as a valuable resource for the Institutional Founding Members. Standard sequencing services include data storage on NYGC servers for 24 months. Prolonged storage is available for an additional fee. In addition, NYGC will provide access to a high-performance computing environment to allow researchers to perform custom analysis.

Future Services

Over the course of the next year, NYGC will expand the menu of sequencing applications to include:

Terms and Conditions 

NYGC Terms and Conditions can be found here.

Service Requests

For more information or to arrange a consultation, please contact us at service@nygenome.org or 888.415.6942 x1. Include your name, institution name, and contact details, along with your requirements (e.g., project goals, sample size, desired services, timeline).

Note: Sequencing and bioinformatics services are available on a priority basis to NYGC members and collaborators.

Sample Submission Guidelines (PDF format):

• Human Whole Genome Sequencing
• Human Whole Exome Sequencing
• Human mRNASequencing
• All Guidelines (ZIP file)