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

Zenger, K.R., Khatkar, M.S., Tier, B., Hobbs, M., Cavanagh, J.A.L., Solkner, J., Hawken, R.J., Barris, W., and Raadsma, H.W. (2007) QC analyses of SNP array data: experience from a large population of dairy sires with 23.8 million data points. In: Proceedings of the AAABG 17th Conference 2007 (17) pp. 123-126. From: 17th AAABG Conference 2007, 23-26 September 2007, Armidale, NSW, Australia.

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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.

Item ID: 10140
Item Type: Conference Item (Research - E1)
ISBN: 978-1-921208-13-3
ISSN: 1328-3227
Keywords: quantitative genetics; dairy cattle; selective breeding; genetics; QTL; genomics
Additional Information:

Conference theme "Genetic Improvement - Making it Happen"

Date Deposited: 20 Jul 2010 03:44
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 90%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics) @ 10%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970107 Expanding Knowledge in the Agricultural and Veterinary Sciences @ 100%
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