The Genome in a Bottle Consortium is a public-private-academic consortium hosted by NIST to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome sequencing to clinical practice. The priority of GIAB is authoritative characterization of human genomes for use in analytical validation and technology development, optimization, and demonstration.
GIAB has currently characterized a pilot genome (NA12878/HG001) from the HapMap project, and two son/father/mother trios of Ashkenazi Jewish and Chinese ancestry from the Personal Genome Project (which, unlike the pilot genome, are consented for commercial redistribution). These samples and their IDs from NIST, Coriell, and PGP are in this table.
Benchmark (or "High-confidence") variant calls and regions:
We developed an integration pipeline to utilize sequencing data generated by multiple technologies to generate variant calls and regions for use in benchmarking and validating variant calling pipelines. Currently, benchmark VCF and BED files for small variants are available for GRCh37 and GRCh38 under each genome at ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/
Draft benchmark structural variant calls and regions:
Currently available for HG002 on GRCh37
Benchmarking best practices:
To establish best practices for using GIAB genomes for benchmarking, we have worked with the Global Alliance for Genomics and Health Benchmarking Team:
Benchmarking tools, Manuscript, GitHub
Data and analyses from most short, linked, and long read sequencing methods are publicly available without publication embargo (data indexed in GIAB GitHub and FTP).
GIAB 2016 Scientific Data publication
NCBI GIAB Bioproject
NCBI SRA Run Selector
Amazon AWS S3 bucket: s3://giab
Ongoing and Future work:
Current work in the GIAB Analysis Team is focused on establishing benchmark large indel and structural variant calls, as well as calls in difficult genomic contexts (e.g., homopolymers/tandem repeats and difficult-to-map regions like pseudogenes and segmental duplications). GIAB is also exploring expanding to additional samples consented for release of WGS and redistribution of commercial products: increasing the diversity of germline reference samples and developing paired tumor-normal cell lines.
The consortium was initiated in a set of meetings in 2011 and 2012, and the consortium holds open, public workshops typically annually at Stanford University in Palo Alto, CA or at NIST in Gaithersburg, MD. Slides from workshops and conferences are available here. The next workshop is planned for March 28-29, 2019 at Stanford University (agenda). The consortium and workshops are open and new participants are welcome.
Publications by GIAB:
Benchmark small variants for 7 GIAB genomes (in press in Nature Biotechnology)
Older benchmark small variants for pilot genome
GIAB data collected through 2016
GA4GH Best practices for benchmarking germline small variants (in press in Nature Biotechnology)
Posters and Presentations by GIAB
Publications using GIAB:
All google scholar publications mentioning GIAB and NIST