Bioinformatics Analysis of Livestock Genomics

The Food and Drug Administration's Center for Veterinary Medicine seeks bioinformatics analysis of livestock genomics—specifically visual validation of swine variants and generation of CRISPRme input files for cattle, chicken, and swine—with quotations due June 29, 2026, and questions due June 18, 2026. This procurement is a total small business set-aside using simplified acquisition procedures.

Place of performance is Rockville, Maryland. The contract period runs from July 15, 2026, through July 14, 2027, with no option years. Work comprises two primary tasks: visual validation of approximately 2,000 genomic variants from 73 swine samples (70 cases, 3 controls) with 20–70X sequencing coverage, and generation of breed-specific variant call files compatible with CRISPRme software for a minimum of two breeds per species (cattle, chicken, swine). Deliverables include validated variant datasets with supporting evidence, CRISPRme-ready VCF files, executable scripts and workflows with documentation, and comprehensive final reports. All data transfers must occur through precisionFDA, and all scripts and workflows must be executable on Linux systems with dependency management via Docker or Conda.

Contractor personnel must possess demonstrated expertise in whole-genome sequencing analysis, variant validation, structural variants, VCF formats, and preferably CRISPR/Cas9 technologies and swine genomics. The Government will furnish BAM alignment files, filtered VCF files, sample metadata, and reference genomes from Ensembl. Award evaluation applies a trade-off method considering technical approach, facilities and capabilities, and price, with emphasis on personnel qualifications and understanding of SOW requirements. The NAICS code is 518210, Computing Infrastructure Providers, Data Processing, Web Hosting, and Related Services. PSC is AJ11, General Science and Technology R&D Services.