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

K R Zenger; M S Khatkar; Bruce Tier; M Hobbs; J A L Cavanagh; J Solkner; R J Hawken; W Barris; H W Raadsma

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

K R Zenger
, M S Khatkar
, Bruce Tier
, M Hobbs
, J A L Cavanagh
, J Solkner
, R J Hawken
, W Barris
, H W Raadsma

Animal Genetics and Breeding Unit

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	AAABG: Association for the Advancement of Animal Breeding, Genetics
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	123-126
Volume	17
ISBN (Print)	1921208139
Publication status	Published - 2007
Event	AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics - University of New England, Armidale, Australia Duration: 23 Sept 2007 → 26 Sept 2007

Conference

Conference	AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Armidale, Australia
Period	23/09/07 → 26/09/07

Keywords

Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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

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Zenger, K. R., Khatkar, M. S., Tier, B., Hobbs, M., Cavanagh, J. A. L., Solkner, J., Hawken, R. J., Barris, W., & Raadsma, H. W. (2007). QC analyses of SNP array data: Experiences from a large population of dairy sires with 23.8 million data points. In AAABG. Association for the Advancement of Animal Breeding, & Genetics (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 17, pp. 123-126). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/4106

Zenger, K R ; Khatkar, M S ; Tier, Bruce et al. / QC analyses of SNP array data : Experiences from a large population of dairy sires with 23.8 million data points. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / AAABG: Association for the Advancement of Animal Breeding ; Genetics. Vol. 17 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2007. pp. 123-126

@inproceedings{6b8da64094ea4d4f97f8b2d43ad4cbe6,

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

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.",

keywords = "Quantitative Genetics (incl Disease and Trait Mapping Genetics)",

author = "Zenger, \{K R\} and Khatkar, \{M S\} and Bruce Tier and M Hobbs and Cavanagh, \{J A L\} and J Solkner and Hawken, \{R J\} and W Barris and Raadsma, \{H W\}",

year = "2007",

language = "English",

isbn = "1921208139",

volume = "17",

pages = "123--126",

editor = "\{Association for the Advancement of Animal Breeding\}, AAABG: and Genetics",

booktitle = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

note = "AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 23-09-2007 Through 26-09-2007",

}

Zenger, KR, Khatkar, MS, Tier, B, Hobbs, M, Cavanagh, JAL, Solkner, J, Hawken, RJ, Barris, W & Raadsma, HW 2007, QC analyses of SNP array data: Experiences from a large population of dairy sires with 23.8 million data points. in AAABG Association for the Advancement of Animal Breeding & Genetics (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 17, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 123-126, AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics, Armidale, Australia, 23/09/07. <https://hdl.handle.net/1959.11/4106>

QC analyses of SNP array data: Experiences from a large population of dairy sires with 23.8 million data points. / Zenger, K R; Khatkar, M S; Tier, Bruce et al.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / AAABG: Association for the Advancement of Animal Breeding; Genetics. Vol. 17 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2007. p. 123-126.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - QC analyses of SNP array data

T2 - AAABG 2007: 17th Conference of the Association for the Advancement of Animal Breeding and Genetics

AU - Zenger, K R

AU - Khatkar, M S

AU - Tier, Bruce

AU - Hobbs, M

AU - Cavanagh, J A L

AU - Solkner, J

AU - Hawken, R J

AU - Barris, W

AU - Raadsma, H W

PY - 2007

Y1 - 2007

N2 - 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.

AB - 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.

KW - Quantitative Genetics (incl Disease and Trait Mapping Genetics)

UR - http://trove.nla.gov.au/work/35062558?selectedversion=NBD42373479

UR - http://www.aaabg.org/livestocklibrary/2007/zenger123.pdf

M3 - Conference contribution

SN - 1921208139

VL - 17

SP - 123

EP - 126

BT - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

A2 - Association for the Advancement of Animal Breeding, AAABG:

A2 - Genetics, null

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

CY - Armidale, Australia

Y2 - 23 September 2007 through 26 September 2007

ER -

Zenger KR, Khatkar MS, Tier B, Hobbs M, Cavanagh JAL, Solkner J et al. QC analyses of SNP array data: Experiences from a large population of dairy sires with 23.8 million data points. In Association for the Advancement of Animal Breeding AAABG, Genetics, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 17. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2007. p. 123-126

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

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