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Why graph genome storage and updating wakes me up at 4 am

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Genome Reference Consortium
Genome Reference Consortium

Presentation at PanGenomics in the Cloud Hackathon, run by NCBI at UCSC (https://ncbiinsights.ncbi.nlm.nih.gov/2019/02/06/pangenomics-cloud-hackathon-march-2019/). Presents points to consider about the adoption of a pangenome reference, emphasizing aspects for long-term data management and wide-spread adoption.

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Why Graph Genome Storage and Updating Wakes Me Up at 4 am Valerie Schneider NCBI/GRC
GRCh38 Curation • Spoiler alert: GRCh38 isn’t perfect! • >300 unresolved issues remain • Incorrectly assembled seg dups • Catch-22: Constant coordinates vs. correct sequence? • Patch releases to date (GRCh38.p13): • 72 novel patches (future alt loci) • 113 fix patches! • Gap closures/extensions • Path updates (replacements, rearrangements) • There are other updates that can’t be released as patches • Sequence removal (including alt loci) chromosome novel patch scaffold fix patch scaffold
More genome assemblies • Managing updates: incremental or full rebuilds? • Impact of assembly quality on the pan-genome? • 7.7 billion people: 300 genomes (99% of MAF 1%) • Intra-population diversity • Under-representation from Africa, middle East and Oceanic populations
Pan-genome reference data definition • What does the reference become? • Collection of assemblies • Graph representation • A “golden” path • Specific representations • Data representation • Identifier for the pan-genome (e.g. GCA_000001405.$$) • Versioning: what changes trigger an update? • Distributed data: what authority manages updates? • File formats: sequence = FASTA; graph = ? Graph-based annotations = VCF, BED, GFF, ?? • Metadata • Assembly quality (old: finishing status, alignment criteria) Today’s reference assembly does not represent: 1. The most common allele/haplotype 2. The longest allele/haplotype 3. The ancestral allele/haplotype
Diverse users, diverse needs • Mapping reads • Coordinate system • Annotations • Relating samples to one another • Visualization (as a means for analysis) • Clinical reporting • Regulations for reporting on a graph? • Truth sets, documented changes essential • Clinical tools lag by at least 1 year • And the tools to support these things…

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Why graph genome storage and updating wakes me up at 4 am

  • 1. Why Graph Genome Storage and Updating Wakes Me Up at 4 am Valerie Schneider NCBI/GRC
  • 2. GRCh38 Curation • Spoiler alert: GRCh38 isn’t perfect! • >300 unresolved issues remain • Incorrectly assembled seg dups • Catch-22: Constant coordinates vs. correct sequence? • Patch releases to date (GRCh38.p13): • 72 novel patches (future alt loci) • 113 fix patches! • Gap closures/extensions • Path updates (replacements, rearrangements) • There are other updates that can’t be released as patches • Sequence removal (including alt loci) chromosome novel patch scaffold fix patch scaffold
  • 3. More genome assemblies • Managing updates: incremental or full rebuilds? • Impact of assembly quality on the pan-genome? • 7.7 billion people: 300 genomes (99% of MAF 1%) • Intra-population diversity • Under-representation from Africa, middle East and Oceanic populations
  • 4. Pan-genome reference data definition • What does the reference become? • Collection of assemblies • Graph representation • A “golden” path • Specific representations • Data representation • Identifier for the pan-genome (e.g. GCA_000001405.$$) • Versioning: what changes trigger an update? • Distributed data: what authority manages updates? • File formats: sequence = FASTA; graph = ? Graph-based annotations = VCF, BED, GFF, ?? • Metadata • Assembly quality (old: finishing status, alignment criteria) Today’s reference assembly does not represent: 1. The most common allele/haplotype 2. The longest allele/haplotype 3. The ancestral allele/haplotype
  • 5. Diverse users, diverse needs • Mapping reads • Coordinate system • Annotations • Relating samples to one another • Visualization (as a means for analysis) • Clinical reporting • Regulations for reporting on a graph? • Truth sets, documented changes essential • Clinical tools lag by at least 1 year • And the tools to support these things…