A--Whole genome sequencing of (synchronous) human breast cancer Portland VA

Portland VA Medical Center has a requirement to purchase whole genome sequencing services of (synchronous) human breast cancer specimens and their associated axillary nodes or distant metastatic sites to understand the clonal relationship between synchronous bilateral breast cancers and in the case of clonally related events, the molecular changes acquired when a primary breast cancer metastasizes to the contralateral site will be identified and characterized- these will include nucleotide sequences changes, copy number variation and/or translocations. Specific Tasks Required of Vendor Whole genome sequencing of human breast cancer specimens to an average depth of 30X in a CLIA (Clinical Laboratory Improvement Amendment) and CAP (College of American Pathologists) certified facility. Vendor should have extensive experience performing whole genome sequencing for human samples. All samples are first to be genotyped with highly polymorphic SNPs, providing a genetic fingerprint to confirm sample identity of subsequent sequence data. a. Samples are then sheared to a ~350-500bp size distribution. b. Samples are end-repaired, adapter ligated, and PCR'd according to a "With Bead" protocol c. Samples are quality controlled throughout the process through a number of assays including 1) DNA quantitation after adapter ligation, 2) qPCR after library construction to assess the number of properly adapted fragments. d. Final libraries are quantitated by qPCR and loaded across the appropriate number of Illumina HiSeq flow cell lanes to achieve the target coverage e. Initial Data Alignment: Reads are extracted from sequencing instruments and aligned using BWA (http://picard.sourceforge.net/). f. Duplicate Read Marking: Duplicate reads are marked for downstream interpretation by analysis pipelines. g. Local realignment: Reads around known indels are realigned to produce higher quality alignments. h. Quality scores are recalibrated using the GATK base quality score recalibrator to increase the accuracy of reported base quality scores. i. Sample identity is verified using previously stored fingerprint genotypes. j. Data is aggregated per sample and delivered in BAM format including base calls, quality scores, and alignment data. k. Metrics are generated to inform completion and quality of sequencing data. l. VCF file will contain SNPs and indels of interest to genotype all the samples in a project or set of projects. m. Data transported to PI via a de-multiplexed aggregated and aligned BAM file delivered via an Aspera site. The purpose of this synopsis is to gain knowledge of potential qualified sources and their size classification (large business, small business, 8(a), SDVOSB, etc.), relative to NAICS code 541711 (size standard of 1000 employees). Responses to this synopsis will be used by the Government to make appropriate acquisition decisions. Based on responses to this synopsis, the Government may issue a RFQ. Performance Period: Base of one year, plus two option periods. Type of Contract: Firm Fixed Price This notice is not a request for competitive proposals, however; any responsible source who believes it is capable of meeting the requirement may submit a capability statement to the contracting office no later than Thursday, May 26, 2016, 12:00 Noon, EST. Interest/capability statements may be sent to Elaine DiBucci at contact@example.gov and should include company name, address, point of contact, business size, and product information. No telephone responses will be accepted. This notice is to assist the Government in determining sources only. A solicitation is not currently available. If a solicitation is issued, all interested parties must respond to that solicitation announcement separately from the responses to this announcement.