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Genomic Database Update

Genomic Database Update. Genotyped Holstein by run. * Animals with traditional evaluation ** Animals with no traditional evaluation. Genotyped Jersey by run. * Animals with traditional evaluation ** Animals with no traditional evaluation. Genotyped Brown Swiss by run.

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Genomic Database Update

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  1. Genomic Database Update

  2. Genotyped Holstein by run * Animals with traditional evaluation ** Animals with no traditional evaluation

  3. Genotyped Jersey by run * Animals with traditional evaluation ** Animals with no traditional evaluation

  4. Genotyped Brown Swiss by run * Animals with traditional evaluation ** Animals with no traditional evaluation

  5. Data & Evaluation Flow AI organizations, breed associations nominations samples evaluations ??? Animal Improvement Programs Laboratory, USDA Dairy producers samples samples genotypes DNA laboratories

  6. Genotype Processing • 2,000 New Genotypes a month • Four labs • GeneSeek • Genetic Visions • DNA LandMarks • GIVF

  7. Genotype Processing: Nomination • All animals should be nominated by the time sample reaches lab • Goal: Parents and Grandparents on every genotyped animal • Minimum: Valid ID

  8. Genotype Processing: Edits • 62 edits that the genotypes must pass to be added to the database • Most common reasons a genotype fails • Low call rate • Parent / Progeny conflict • Possible split embryo / twin • Wrong gender • Breed Check • Switched samples

  9. Continuous Updates • Pedigree changes update genotype usability daily • Harmonization with breed association important to maintain usability • Blanking a genotyped dam will make the genotype unusable • No automatic receipt of foreign pedigree updates

  10. Low call rate • 80% on X chromosome • 90% on autosomal chromosomes (43,382) • Labs generally do not send genotypes with low call rates

  11. Parent Progeny Conflict • Sire / Dam conflict • > 200 SNP conflicts • Sire / dam proposed if genotyped • Sire conflict - young animals from mixed flush • Sire conflicts represent $50,000 genotype cost

  12. split embryo / identical twin / clone • <1000 SNP differences considered identical • 98% similar, accounts for genotyping errors • Stored in clone table if valid • Animals registered as ETS or ETN (automatic) • Otherwise verification must come from requester

  13. Wrong Gender • > 50 heterozygous SNP on X (not male) • < 50 heterozygous SNP on X (not female) • Homozygous X female • Common ancestor (source of X)

  14. Source of X Bellwood BW Marshall Mara Elegant Patron Tanya Mary Jeff Mark Sam Sue Erin Patron 12144058 14860763

  15. Breed Check • 622 SNP • Nearly monomorphic in 1 breed and have fewer than 30% of animals homozygous for that allele in another breed • An error when a higher number of conflicts for the reported breed than for another breed • > 10 SNP conflicts reported to requester, but remains usable • Higher conflicts for foreign animals

  16. Switched Samples • Sample pair with reversed parents • Switched at the lab (rare) • Switched at the farm

  17. Conflicts to Requester • Genotype conflicts reported to the requester immediately • Genotype remains stored in AIPL database as an unusable genotype until conflict is resolved • 2-3 days to fix conflicts before cutoff • Once a month all conflicts remaining in the system are sent to requesters

  18. Lab QC • SNP that have call rate <90% • SNP that have high parent-progeny conflicts • SNP that deviate from HW equilibrium • Labs have the opportunity to recluster genotypes

  19. Closing thoughts • Currently 477 animals with failed or conflicted genotypes • Big increase in volume when 3K becomes available

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