Zenger, K R

Khatkar, M S

Tier, Bruce

Hobbs, M

Cavanagh, J A L

Solkner, J

Hawken, R J

Barris, W

Raadsma, H W

2007

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.

Proceedings of the Association for the Advancement of Animal Breeding and Genetics, v.17, p. 123-126

1921208139

1328-3227

https://hdl.handle.net/1959.11/4106

Association for the Advancement of Animal Breeding and Genetics (AAABG)

QC analyses of SNP array data: Experiences from a large population of dairy sires with 23.8 million data points

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