Higher and Lower Density SNP platforms
This document discusses the comparative analysis of higher and lower density SNP platforms, including insights from Affymetrix and Illumina. It covers the need for increased SNP density, design considerations, and the role of SNP distribution across breeds and chromosomes. We address the objectives of genetic prediction, parentage verification, and animal tracing, detailing collaborations with institutions such as NCBI and the Gates Foundation. The aim is to improve heritability of phenotypes and enable genetic evaluations through advanced SNP technologies.
Higher and Lower Density SNP platforms
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Presentation Transcript
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 • BFGL & Univ Missouri • Holstein, Jersey, Angus, Brahman, Nelore • Roslin Institute • N’Dama & Sahiwal • Univ Liverpool • Romagnola, Boran • Tuli, Africander, Hanwoo, Simmental
Low Density • What Density is “Low” • Objectives: • Imputing higher density • Genetic prediction • Parentage verification • Determination of “G” • Animal identity/traceback
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?!
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!
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
