640-16-3-386-0134 AAA Whole Genome Sequencing

General Scope



The contract will begin September 2016 for one (1) twelve (12) month base period. Whole genome sequencing of Abdominal Aortic aneurysm (AAA) samples will be performed in support of the VA Palo Alto Health Care System (VAPAHCS), Research Department.

We will isolate and quantitate genomic DNA isolated from AAA specimens. These DNA samples will be diluted at or above a given concentrations. DNA submitted is 250 nanogram total per sample.



SPECIFIC TASKS/REQUIREMENTS





DNA samples extracted from 100 study participants, who are members of a family with high prevalence of AAA, are sent to Vendor for the following tasks

.

a. All samples are first to be genotyped with highly polymorphic SNPs, providing a genetic fingerprint to confirm sample identity of subsequent sequence data.

b. Samples are then sheared and optimized to a ~350-500bp size distribution.

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 Vendor HiSeq flow cell lanes to achieve the target coverage

e. Sample identity is verified using previously stored genotypes.

f. Data is aggregated per sample and delivered in BAM format including base calls, quality scores, and alignment data.

g. Metrics are generated to inform completion and quality of sequencing data.

h. VCF file will contain SNPs and indels of interest to genotype all the samples in a project or set of projects.

i. Data transported to PI via a de-multiplexed aggregated and aligned BAM files and VCF files.



This notice of intent is not a request for competitive proposals; however, any responsible source who believes they are capable of meeting the requirement may submit a capability statement to the contracting office no later than Monday, August 8, 2016 at 1:00 PM EST. Interest/capability statements may be sent to Linda Buccigrossi at linda.buccigrossi@va.gov. No telephone responses will be accepted. A determination not to compete the proposed requirement based upon the responses to this notice is solely within the discretion of the Government.



When submitting capability statement please identify in the email subject line the following:



Genome Sequencing - Palo Alto Response to Sources Sought