Q301--Human DNA Exome chip Intent to Sole Source.

The Veteran s Administration (VA) Office of Research and Development, Regional Procurement Office East in Pittsburgh, PA intends to negotiate on a sole source basis with Akesogen, Inc., based in Norcross, GA. The requirement is to provide continued DNA quality checks and reports on DNA quality data for VA approval before genotyping the samples on a Human Exome Chip on either illumine or Affymetrix platforms. The chips are being used for a VA ongoing medical study. The contents of human exome chips used should have at the minimum 600,000-1 million markers, and include the contents derived by the Exome Chip Design Consortium (http://genome.sph.umich.edu/wiki/Exome Chip Design), at least 300,000 tag SNP s from previous GWAS hits and ancestry markers besides custom contents to be derived by the VA. The custom contents for VA would include but not limited to previously validated GWAS hits for diseases like Schizophrenia, Bipolar, PTSD, Hypertension, cardiovascular diseases, diabetes, Rheumatoid Arthritis, Prostate cancer and breast cancer, besides enriching for Latino and African-American ancestry markers. The VA specific custom content will be decided in discussion with the VA PM. The study has already processed the samples of over 800,000 veteran participants, which contained 700,000 genotyping samples, 32,000 methylation samples and 2,000 metabolite sample analysis. The data is currently being actively used by over 31 research teams to investigate various diseases including PTSD, Gulf War Syndrome, Cardiovascular disease, Ageralated macular eye disease, tinnitus, Kidney disease, diabetics, multiple myeloma, Suicidality, Dementia, Schizophernia & biopolar and many others. The continued success of the study necessitates continuity in processes and protocols. The specific work to be performed includes: Continuity with current DNA quality checks, and Exome Chip genotyping on either the illumine or Affymetrix platforms. Headquarters and laboratory facilities where all the services are performed in full or in parts should be located within the Continental United States. Ability to manufacture or purchase and process human genome genotyping chip on at least one of two VA approved genotyping platforms (Illumina or Affymetrix). Analytical lab shall demonstrate the capacity to process up to 5000 VA samples per month. Ability to conduct high-throughput genotyping of VA human DNA samples at >97% genotyping call rate and >99% reproducibility. Ability for Sample tracking and management utilizing bar coding to ensure security & traceability of VA samples. Ability to produce documentation of sample handling and processing attributes/audit trail, etc. that would address sample mixing and sample error tracking. Documented evidence of contractor staff experience in performing high throughput sample and data QC on comparable projects. Documented evidence of project staff experience with providing bioinformatics support for building customized contents for genotyping chips including evaluation and selection of markers based on factors like MAF, disease associations, GWAS hits, and other SNP performances criteria. Contractors shall be required to submit for a NACI low level background investigation and security clearance in accordance with the VA IT Security Clause and complete the required training and procedures to comply with these requirements. All the QA/QC metrics and threshold developed in the project previously shall be strictly followed and adhered to. No deviations are permitted unless approved in writing by the VA PM. The contractor shall run all controls as previously agreed upon. Controls shall be added or changed only with mutually agreed upon sign-off documentation. Ability to propose project staff with minimum qualifications & skillsets in performing high throughput assays on the VA approved platform and bioinformatics experience with data QA/QC, GWAS, SNP and other relevant analysis. The requirement will take place at the contractor s facility. The sole source is pursuant to FAR 6.302-1 Only One Responsible Source and No Other Supplies or Services Will Satisfy Agency Requirements. This notice of intent 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 and supporting documentation to the contracting office no later than Thursday, Feb 27, 2020 (10:00 AM, EST). Interest/capability statements may be sent to Michael Haydo at contact@example.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.