REQ__5012580-S.O.W._FOR_MACROGEN_CLINICAL_LABORATORY-1.docx

Statement of Work for Whole Genome Sequencing services in Macrogen

BACKGROUND: The research goal of Mechanisms of Genome Dynamics Group (MGDG) of NIEHS is to understand molecular mechanisms underlying somatic genome instability in humans. Genomic DNA derived from blood and from clones of somatic cells will be whole-genome sequenced at high coverage (50-60x) (n=15). Somatic point mutations, insertions/deletions, and copy number alterations will be identified by comparing reads from blood with reads from somatic clone from the same individual. The MGDG has conducted and published in PLOS Genetics 2016 a study in two human subjects showing feasibility of the approach with requested coverage.

OBJECTIVE: The research goal of Mechanisms of Genome Dynamics Group (MGDG) of NIEHS is to understand molecular mechanisms underlying somatic genome instability in humans. The purpose of this project is to assess genetic changes found in somatic cells of human individuals identified through NIEHS Environmental Polymorphisms Registry. Whole Genome Sequencing will be performed on DNA from blood serving as a surrogate for germline and on DNA from clones of skin fibroblasts isolated from biopsies by NIEHS Clinical Research Unit (CRU).

SCOPE: This will encompass whole genome sequencing. Fifteen (15) samples of double stranded genomic DNA will be sequenced by Illumina HiSeq X platform. The estimated output is 200 gb sequenced corresponding to coverage approximately 60x. Reports will be delivered as FASTQ files.

REQUIREMENTS:

The Contractor shall:

Generate a sequencing library for each sample. Perform whole-genome sequencing of human genomic DNA with 50X - 60X coverage for each sample. Sample output needed will be specified for each sample individually.

Reports - The Government will receive regular updates including QC reports and sequencing metrics.

QUALITY ASSURANCE:

Contractor Quality Requirements

Tests - Contractor shall use existing knowledge of acceptable libraries and sequencing output to verify that quality is maintained.

GOVERNMENT QUALITY ASSURANCE

Inspection Criteria - The Government will download FASTQ files by NIEHS secure FTP protocol.

Acceptance Criteria - The Government will perform sequence alignment and contamination checks to verify that the sequence reads are genuine and authentic. The Government will assess data delivery to determine that specified sequencing output (in gb) is delivered for each sample as required.

PLACE OF PERFORMANCE: At the Contractor's Facility.

PERIOD OF PERFORMANCE: 12-months from date of award.

REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE

All deliverables will be sent to the NIEHS Technical Point of Contact.

Deliverables: The contractor shall provide Quality reports and FASTQ files. The contractor shall provide one or more pairs of FASTQ files for each sample to be sequenced. FASTQ file pairs will contain 180 – 220 gb of sequencing output, as indicated for each sample submitted. Deliverables are due within six weeks after samples pass Microgen Quality Control (QC).