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Higher and Lower Density SNP platforms

Higher and Lower Density SNP platforms. Higher Density SNP Platforms. Discussions with Affymetrix and Illumina 300K to 1M SNP Need MORE SNP How should chip be designed? Informativeness across breeds Distribution across chromosomes Uniform Concentrated at QTL. Breeds to Sequence for SNP.

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Higher and Lower Density SNP platforms

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  1. Higher and Lower Density SNP platforms

  2. Higher Density SNP Platforms • Discussions with Affymetrix and Illumina • 300K to 1M SNP • Need MORE SNP • How should chip be designed? • Informativeness across breeds • Distribution across chromosomes • Uniform • Concentrated at QTL

  3. Breeds to Sequence for SNP • BFGL & Univ Missouri • Holstein, Jersey, Angus, Brahman, Nelore • Roslin Institute • N’Dama & Sahiwal • Univ Liverpool • Romagnola, Boran • Tuli, Africander, Hanwoo, Simmental

  4. Low Density • What Density is “Low” • Objectives: • Imputing higher density • Genetic prediction • Parentage verification • Determination of “G” • Animal identity/traceback

  5. Low Density • Collaboration with Illumina • 384 SNP assay using pooling • ~96 dedicated to pedigree verification/traceability • 378 for genetic prediction • Stages of development • Alpha – test of multiplex • Beta – 1-3 Groups Genotyping ~20K samples • Commercialization ~300K+/yr?!

  6. Data Sharing for Parentage • NCBI – NIH’s National Center for Biotechnology Information • Keepers of public genome databases • Genbank • Offer to maintain database • 96 parentage markers • 378 private markers • Provide parentage calculations!

  7. Implications • Obviate need for pedigree • Increase heritability of phenotypes • Corrected parentage • Accounting for Mendelian sampling • Allow BLUP in arenas where not previously possible • Gates Foundation

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