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Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle

Research output: Contribution to conferencePosterResearch

  • Md Mesbah-Uddin, Animal Genetics and Integrative Biology, UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
  • ,
  • Bernt Guldbrandtsen
  • ,
  • Mogens Sandø Lund
  • Goutam Sahana
We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all the bi-allelic variants within a given deletion locus, and fitted a Gaussian mixture model to the observed RD. We validated our method on brachyspina associated deletion of chromosome 21 (Chr21:21,184,869-21,188,202), which was segregating in our deletion-discovery population of Holstein cattle. We analysed the RD data of 55 progeny tested Holstein bulls with published recessive code for brachyspina (8 carriers and 47 non-carriers) along with 5 carriers from the discovery population (confirmed by assembling the breakpoint sequences). Using our approach we were able to genotype the carriers and non-carriers with 95% accuracy, and a false discovery rate of 18.8%.
Original languageEnglish
Publication yearFeb 2018
Publication statusPublished - Feb 2018
EventThe 11th World Congress on Genetics Applied to Livestock Production - Aotea Centre, Auckland 1010, Auckland, New Zealand
Duration: 11 Feb 201816 Feb 2018
Conference number: 11

Conference

ConferenceThe 11th World Congress on Genetics Applied to Livestock Production
Number11
LocationAotea Centre, Auckland 1010
CountryNew Zealand
CityAuckland
Period11/02/201816/02/2018

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