The Human Genetics Branch at the National Institute of Mental Health (NIMH) Intramural Research Program (IRP), at the NIH seeks a contractor to perform and analyze exome sequencing of DNA samples on an Illumina "HiSeq" platform. In order to understand the genetic basis of bipolar disorder, the Human Genetics Branch is interested in studying all genes in the human genome using Exome sequencing technology. This requirement consists of exome capture, library construction and sequencing exome data in 50 bipolar disorder cases. In order to maintain continuity of current research, sequencing analysis of exome data shall be conducted on an Illumina HiSeq machine sequencing platform. The samples will be delivered to the contractor over a 90-day period after award.

Requirements
All samples analyzed in this study shall undergo the following procedures: Quality control analysis;
Whole exome capture using Agilent V4 kit; Library construction; Paired-end sequencing 100 x 100 bases;
Primary and secondary bioinformatics analysis data (see list of Deliverables). It is estimated that 50 exome samples will be required for analysis.

Contractor shall provide results and submission of deliverables within 6-8 weeks after the last sample has undergone Quality Control. An average 50x coverage level will be required for all samples analyzed. A total of 7 samples will be sequenced per lane and a minimum of 26 million reads per sample will be anticipated.

Deliverables
Contractor shall collect and analyze data directly from the instrument, such as reads and associated quality values and various read level quality reports.

Contractor shall perform the following types of secondary analysis of data results, for delivery to the government: Align reads against hg19 Human reference sequence; Summary statistics and reports produced from the alignment; Detailed mapping information for each read in BAM (Binary SAM) formats(read position start and end, reference position start and end, directionality, etc); Reads with alignments to reference sequence should be passed into SNP and INDEL calling process; Variants (SNPs and INDELs) should be called; Variant calls and reference calls should be provided by reference sequence and position. Each should have various metrics providing some confidence in the SNP and INDEL calls; Variants annotations such as Gene ID, dbSNP ID, Coverage for each SNP & INDEL; Targeted Re-sequencing metrics and reports should be produced based on metrics such as specificity, feature coverage, etc; Extract and report the unmapped reads.

Contractor shall deliver the results of data analysis via a secure website and USB Disk in consultation with the Project Officer. Contractor shall be accessible for support by telephone, email, or in-person site visits regarding the technical details of the project.

This procurement is released on a Total Small Business set-aside basis.

The following FAR provisions shall apply to this solicitation: 52.212-1, Instructions to Offerors--Commercial Items, 52.212-2, Evaluation--Commercial Items. Offerors must include a completed copy of the provision at 52.212-3, Offeror Representations and Certifications Commercial Items, with its offer. The Clause at 52.212-4, Contract Terms and Conditions Commercial Items, applies to this acquisition and the Clause at 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders Commercial Items applies to this acquisition.

Prospective Offerors must be registered in Central Contractor Registration (CCR) at http://www.ccr.gov/ and Online Representations and Certifications (ORCA) at http://orca.bpn.gov/ prior to award. Lack of registration in the CCR and ORCA database will make an Offeror ineligible for award.

Please reference this RFQ number on all correspondence. Quotations are to be sent electronically to [email protected] prior to the closing date of this announcement.

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