Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs

Y.L. Lee; M.C. Bosse; W. Coppieters; R.F. Veerkamp; L. Karim; C. Oget-Ebrad; T. Druet; M.A.M. Groenen; M. Georges; A.C. Bouwman; C. Charlier

doi:10.3920/978-90-8686-940-4_542

Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs

Y.L. Lee
, M.C. Bosse
, W. Coppieters
, R.F. Veerkamp
, L. Karim
, C. Oget-Ebrad
, T. Druet
, M.A.M. Groenen
, M. Georges
, A.C. Bouwman
, C. Charlier

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

Abstract

Understanding how genomes, particularly genetic variants, instruct animals to develop and function is crucial for animal breeders. Copy number variants (CNVs), the gain or loss of DNA segments, can affect gene expression and alter phenotypes. However, most large-scale genetic analyses in animal breeding use single nucleotide polymorphism (SNP) genotypes from genotyping arrays, and efforts to incorporate CNVs are limited. In theory, variation from CNVs can be captured by SNPs, if they are in high linkage disequilibrium (LD). We evaluated the LD of CNV-SNP pairs in whole genome sequencing and genotyping array data. Our whole genome sequencing data showed that most CNVs have tagging SNPs. However, CNV-SNP pairs from genotyping array data were mostly in low LD, because most CNV-SNP pairs had unmatching allele frequencies. We conclude that most rare CNVs may not be fully captured by genotyping arrays.

Original language	English
Title of host publication	Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)
Subtitle of host publication	Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges
Editors	R.F. Veerkamp, Y. de Haas
Place of Publication	Wageningen
Publisher	Wageningen Academic Publishers
Pages	2249-2252
ISBN (Electronic)	9789086869404
DOIs	https://doi.org/10.3920/978-90-8686-940-4_542
Publication status	Published - 2022
Event	World Congress on Genetics Applied to Livestock Production: WCGALP 2022 - Rotterdam, Netherlands Duration: 3 Jul 2022 → 8 Jul 2022

Conference/symposium

Conference/symposium	World Congress on Genetics Applied to Livestock Production: WCGALP 2022
Country/Territory	Netherlands
City	Rotterdam
Period	3/07/22 → 8/07/22

Access to Document

10.3920/978-90-8686-940-4_542Licence: CC BY

https://edepot.wur.nl/586638Licence: CC BY

AF-16022 Breed4Food II (BO-63-001-009, BO-47-001-021, BO-22.04-025-001, BO-22.04-011-001, BO-22.02-011-001)
Veerkamp, R. (Project Leader)
1/01/14 → 31/12/21
Project: LVVN project

Cite this

Lee, Y. L., Bosse, M. C., Coppieters, W., Veerkamp, R. F., Karim, L., Oget-Ebrad, C., Druet, T., Groenen, M. A. M., Georges, M., Bouwman, A. C., & Charlier, C. (2022). Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs. In R. F. Veerkamp, & Y. de Haas (Eds.), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges (pp. 2249-2252). Article 542 Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-940-4_542

Lee, Y.L. ; Bosse, M.C. ; Coppieters, W. et al. / Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs. Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. editor / R.F. Veerkamp ; Y. de Haas. Wageningen : Wageningen Academic Publishers, 2022. pp. 2249-2252

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title = "Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs",

abstract = "Understanding how genomes, particularly genetic variants, instruct animals to develop and function is crucial for animal breeders. Copy number variants (CNVs), the gain or loss of DNA segments, can affect gene expression and alter phenotypes. However, most large-scale genetic analyses in animal breeding use single nucleotide polymorphism (SNP) genotypes from genotyping arrays, and efforts to incorporate CNVs are limited. In theory, variation from CNVs can be captured by SNPs, if they are in high linkage disequilibrium (LD). We evaluated the LD of CNV-SNP pairs in whole genome sequencing and genotyping array data. Our whole genome sequencing data showed that most CNVs have tagging SNPs. However, CNV-SNP pairs from genotyping array data were mostly in low LD, because most CNV-SNP pairs had unmatching allele frequencies. We conclude that most rare CNVs may not be fully captured by genotyping arrays.",

author = "Y.L. Lee and M.C. Bosse and W. Coppieters and R.F. Veerkamp and L. Karim and C. Oget-Ebrad and T. Druet and M.A.M. Groenen and M. Georges and A.C. Bouwman and C. Charlier",

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doi = "10.3920/978-90-8686-940-4\_542",

language = "English",

pages = "2249--2252",

editor = "R.F. Veerkamp and \{de Haas\}, Y.",

booktitle = "Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)",

publisher = "Wageningen Academic Publishers",

address = "Netherlands",

note = "World Congress on Genetics Applied to Livestock Production: WCGALP 2022 ; Conference date: 03-07-2022 Through 08-07-2022",

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Lee, YL, Bosse, MC, Coppieters, W, Veerkamp, RF, Karim, L, Oget-Ebrad, C, Druet, T, Groenen, MAM, Georges, M, Bouwman, AC & Charlier, C 2022, Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs. in RF Veerkamp & Y de Haas (eds), Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges., 542, Wageningen Academic Publishers, Wageningen, pp. 2249-2252, World Congress on Genetics Applied to Livestock Production: WCGALP 2022, Rotterdam, Netherlands, 3/07/22. https://doi.org/10.3920/978-90-8686-940-4_542

Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs. / Lee, Y.L.; Bosse, M.C.; Coppieters, W. et al.
Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. ed. / R.F. Veerkamp; Y. de Haas. Wageningen: Wageningen Academic Publishers, 2022. p. 2249-2252 542.

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

TY - GEN

T1 - Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs

AU - Lee, Y.L.

AU - Bosse, M.C.

AU - Coppieters, W.

AU - Veerkamp, R.F.

AU - Karim, L.

AU - Oget-Ebrad, C.

AU - Druet, T.

AU - Groenen, M.A.M.

AU - Georges, M.

AU - Bouwman, A.C.

AU - Charlier, C.

PY - 2022

Y1 - 2022

N2 - Understanding how genomes, particularly genetic variants, instruct animals to develop and function is crucial for animal breeders. Copy number variants (CNVs), the gain or loss of DNA segments, can affect gene expression and alter phenotypes. However, most large-scale genetic analyses in animal breeding use single nucleotide polymorphism (SNP) genotypes from genotyping arrays, and efforts to incorporate CNVs are limited. In theory, variation from CNVs can be captured by SNPs, if they are in high linkage disequilibrium (LD). We evaluated the LD of CNV-SNP pairs in whole genome sequencing and genotyping array data. Our whole genome sequencing data showed that most CNVs have tagging SNPs. However, CNV-SNP pairs from genotyping array data were mostly in low LD, because most CNV-SNP pairs had unmatching allele frequencies. We conclude that most rare CNVs may not be fully captured by genotyping arrays.

AB - Understanding how genomes, particularly genetic variants, instruct animals to develop and function is crucial for animal breeders. Copy number variants (CNVs), the gain or loss of DNA segments, can affect gene expression and alter phenotypes. However, most large-scale genetic analyses in animal breeding use single nucleotide polymorphism (SNP) genotypes from genotyping arrays, and efforts to incorporate CNVs are limited. In theory, variation from CNVs can be captured by SNPs, if they are in high linkage disequilibrium (LD). We evaluated the LD of CNV-SNP pairs in whole genome sequencing and genotyping array data. Our whole genome sequencing data showed that most CNVs have tagging SNPs. However, CNV-SNP pairs from genotyping array data were mostly in low LD, because most CNV-SNP pairs had unmatching allele frequencies. We conclude that most rare CNVs may not be fully captured by genotyping arrays.

U2 - 10.3920/978-90-8686-940-4_542

DO - 10.3920/978-90-8686-940-4_542

M3 - Conference paper

SP - 2249

EP - 2252

BT - Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)

A2 - Veerkamp, R.F.

A2 - de Haas, Y.

PB - Wageningen Academic Publishers

CY - Wageningen

T2 - World Congress on Genetics Applied to Livestock Production: WCGALP 2022

Y2 - 3 July 2022 through 8 July 2022

ER -

Lee YL, Bosse MC, Coppieters W, Veerkamp RF, Karim L, Oget-Ebrad C et al. Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs. In Veerkamp RF, de Haas Y, editors, Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. Wageningen: Wageningen Academic Publishers. 2022. p. 2249-2252. 542 doi: 10.3920/978-90-8686-940-4_542

Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs

Abstract

Conference/symposium

Access to Document

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Projects

AF-16022 Breed4Food II (BO-63-001-009, BO-47-001-021, BO-22.04-025-001, BO-22.04-011-001, BO-22.02-011-001)

Cite this