Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Standard

Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. / Mesbah-Uddin, Md; Guldbrandtsen, Bernt; Lund, Mogens Sandø; Boichard, Didier; Sahana, Goutam.

I: Journal of Dairy Science, Bind 102, Nr. 12, 2019, s. 11193-11206.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Harvard

Mesbah-Uddin, M, Guldbrandtsen, B, Lund, MS, Boichard, D & Sahana, G 2019, 'Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle', Journal of Dairy Science, bind 102, nr. 12, s. 11193-11206. https://doi.org/10.3168/jds.2019-16946

APA

Mesbah-Uddin, M., Guldbrandtsen, B., Lund, M. S., Boichard, D., & Sahana, G. (2019). Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. Journal of Dairy Science, 102(12), 11193-11206. https://doi.org/10.3168/jds.2019-16946

CBE

Mesbah-Uddin M, Guldbrandtsen B, Lund MS, Boichard D, Sahana G. 2019. Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. Journal of Dairy Science. 102(12):11193-11206. https://doi.org/10.3168/jds.2019-16946

MLA

Vancouver

Author

Mesbah-Uddin, Md ; Guldbrandtsen, Bernt ; Lund, Mogens Sandø ; Boichard, Didier ; Sahana, Goutam. / Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. I: Journal of Dairy Science. 2019 ; Bind 102, Nr. 12. s. 11193-11206.

Bibtex

@article{cddd8b037bc84b56bd3fed9da910116c,
title = "Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle",
abstract = "Genotype imputation, often focused on SNP and small insertions and deletions (indels; size ≤50 bp), is a crucial step for association mapping and estimation of genomic breeding values. Here, we present strategies to impute genotypes for large chromosomal deletions (size >50 bp), along with SNP and indels in cattle. The pipelines include a strategy for extending the whole-genome sequence reference panel for large deletions, a 2-step genotype refinement approach using Beagle4 and SHAPEIT2 software, and finally, joint imputation of SNP, indels, and large deletions to the existing SNP array-typed population using Minimac3 software. Using these pipelines we achieved an imputation accuracy of the squared Pearson correlation (r2) > 0.6 at minor allele frequencies as low as 0.7% for SNP and indels, and 0.2% for large deletions. This highlights the potential of our approach to build a haplotype reference panel and impute different classes of sequence variants across a wide allele frequency spectrum with high accuracy.",
keywords = "Gaussian mixture model, chromosomal deletion, copy-number variation, imputation, structural variant",
author = "Md Mesbah-Uddin and Bernt Guldbrandtsen and Lund, {Mogens Sand{\o}} and Didier Boichard and Goutam Sahana",
year = "2019",
doi = "10.3168/jds.2019-16946",
language = "English",
volume = "102",
pages = "11193--11206",
journal = "Journal of Dairy Science",
issn = "0022-0302",
publisher = "Elsevier Inc.",
number = "12",

}

RIS

TY - JOUR

T1 - Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle

AU - Mesbah-Uddin, Md

AU - Guldbrandtsen, Bernt

AU - Lund, Mogens Sandø

AU - Boichard, Didier

AU - Sahana, Goutam

PY - 2019

Y1 - 2019

N2 - Genotype imputation, often focused on SNP and small insertions and deletions (indels; size ≤50 bp), is a crucial step for association mapping and estimation of genomic breeding values. Here, we present strategies to impute genotypes for large chromosomal deletions (size >50 bp), along with SNP and indels in cattle. The pipelines include a strategy for extending the whole-genome sequence reference panel for large deletions, a 2-step genotype refinement approach using Beagle4 and SHAPEIT2 software, and finally, joint imputation of SNP, indels, and large deletions to the existing SNP array-typed population using Minimac3 software. Using these pipelines we achieved an imputation accuracy of the squared Pearson correlation (r2) > 0.6 at minor allele frequencies as low as 0.7% for SNP and indels, and 0.2% for large deletions. This highlights the potential of our approach to build a haplotype reference panel and impute different classes of sequence variants across a wide allele frequency spectrum with high accuracy.

AB - Genotype imputation, often focused on SNP and small insertions and deletions (indels; size ≤50 bp), is a crucial step for association mapping and estimation of genomic breeding values. Here, we present strategies to impute genotypes for large chromosomal deletions (size >50 bp), along with SNP and indels in cattle. The pipelines include a strategy for extending the whole-genome sequence reference panel for large deletions, a 2-step genotype refinement approach using Beagle4 and SHAPEIT2 software, and finally, joint imputation of SNP, indels, and large deletions to the existing SNP array-typed population using Minimac3 software. Using these pipelines we achieved an imputation accuracy of the squared Pearson correlation (r2) > 0.6 at minor allele frequencies as low as 0.7% for SNP and indels, and 0.2% for large deletions. This highlights the potential of our approach to build a haplotype reference panel and impute different classes of sequence variants across a wide allele frequency spectrum with high accuracy.

KW - Gaussian mixture model

KW - chromosomal deletion

KW - copy-number variation

KW - imputation

KW - structural variant

UR - http://www.scopus.com/inward/record.url?scp=85073058596&partnerID=8YFLogxK

U2 - 10.3168/jds.2019-16946

DO - 10.3168/jds.2019-16946

M3 - Journal article

C2 - 31606212

VL - 102

SP - 11193

EP - 11206

JO - Journal of Dairy Science

JF - Journal of Dairy Science

SN - 0022-0302

IS - 12

ER -