Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/4106
Title: QC analyses of SNP array data: Experiences from a large population of dairy sires with 23.8 million data points
Contributor(s): Zenger, K R (author); Khatkar, M S (author); Tier, Bruce  (author); Hobbs, M (author); Cavanagh, J A L (author); Solkner, J (author); Hawken, R J (author); Barris, W (author); Raadsma, H W (author)
Publication Date: 2007
Handle Link: https://hdl.handle.net/1959.11/4106
Abstract: The use of a high throughput SNP genotyping platform with 15,380 bovine SNP assays, across 1546 dairy bulls resulted in a data set of approximately 23.8 M SNP data points. Stringent control measures based around low polymorphic content, sample failure, deviation from HWE, low call rate, non-Mendelian inheritance, tri-allelic SNP, and incompatible clustering of data, resulted in removal of 4321 SNPs. The majority (2973) were due to low polymorphic content (MAF<0.01), with the remaining features consistent with assay quality. Despite the need for removal of some SNP, repeatability of SNP call rate was extremely high (>99%) across repeat samples, and between platforms. SNP technology has now matured where comprehensive genome-wide analyses can be conducted in cattle with a high degree of robustness.
Publication Type: Conference Publication
Conference Details: AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics, Armidale, Australia, 23rd - 26th September, 2007
Source of Publication: Proceedings of the Association for the Advancement of Animal Breeding and Genetics, v.17, p. 123-126
Publisher: Association for the Advancement of Animal Breeding and Genetics (AAABG)
Place of Publication: Armidale, Australia
ISSN: 1328-3227
Fields of Research (FoR) 2008: 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics)
Socio-Economic Objective (SEO) 2008: 830302 Dairy Cattle
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
Publisher/associated links: http://trove.nla.gov.au/work/35062558?selectedversion=NBD42373479
http://www.aaabg.org/livestocklibrary/2007/zenger123.pdf
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Conference Publication

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