Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle

Md Mesbah-Uddin; Bernt Guldbrandtsen; Mogens Sandø Lund; Goutam Sahana

Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle

Md Mesbah-Uddin, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana

Center for Quantitative Genetics and Genomics

Research output: Contribution to book/anthology/report/proceeding › Article in proceedings › Research › peer-review

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Abstract

We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all the bi-allelic variants within a given deletion locus, and fitted a Gaussian mixture model to the observed RD. We validated our method on brachyspina associated deletion of chromosome 21 (Chr21:21,184,869-21,188,202), which was segregating in our deletion-discovery population of Holstein cattle. We analysed the RD data of 55 progeny tested Holstein bulls with published recessive code for brachyspina (8 carriers and 47 non-carriers) along with 5 carriers from the discovery population (confirmed by assembling the breakpoint sequences). Using our approach we were able to genotype the carriers and non-carriers with 95% accuracy, and a false discovery rate of 18.8%. Keywords: read-depth genotyping, Gaussian mixture model, deletion, copy number variation, dairy cattle

Original language	English
Title of host publication	Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018 : Volume Electronic Poster Session - Molecular Genetics 3
Number of pages	4
Volume	11
Publication date	2018
Article number	662
Publication status	Published - 2018
Event	The 11th World Congress on Genetics Applied to Livestock Production - Aotea Centre, Auckland 1010, Auckland, New Zealand Duration: 11 Feb 2018 → 16 Feb 2018 Conference number: 11

Conference

Conference	The 11th World Congress on Genetics Applied to Livestock Production
Number	11
Location	Aotea Centre, Auckland 1010
Country/Territory	New Zealand
City	Auckland
Period	11/02/2018 → 16/02/2018

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http://www.wcgalp.org/proceedings/2018/genotype-call-chromosomal-deletions-using-read-depth-whole-genome-sequence-variants

Cite this

Mesbah-Uddin, M., Guldbrandtsen, B., Lund, M. S., & Sahana, G. (2018). Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle. In Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018: Volume Electronic Poster Session - Molecular Genetics 3 (Vol. 11). Article 662 http://www.wcgalp.org/proceedings/2018/genotype-call-chromosomal-deletions-using-read-depth-whole-genome-sequence-variants

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title = "Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle",

abstract = "We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all the bi-allelic variants within a given deletion locus, and fitted a Gaussian mixture model to the observed RD. We validated our method on brachyspina associated deletion of chromosome 21 (Chr21:21,184,869-21,188,202), which was segregating in our deletion-discovery population of Holstein cattle. We analysed the RD data of 55 progeny tested Holstein bulls with published recessive code for brachyspina (8 carriers and 47 non-carriers) along with 5 carriers from the discovery population (confirmed by assembling the breakpoint sequences). Using our approach we were able to genotype the carriers and non-carriers with 95% accuracy, and a false discovery rate of 18.8%. Keywords: read-depth genotyping, Gaussian mixture model, deletion, copy number variation, dairy cattle",

author = "Md Mesbah-Uddin and Bernt Guldbrandtsen and Lund, {Mogens Sand{\o}} and Goutam Sahana",

year = "2018",

language = "English",

volume = "11",

booktitle = "Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018",

note = "The 11th World Congress on Genetics Applied to Livestock Production ; Conference date: 11-02-2018 Through 16-02-2018",

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Mesbah-Uddin, M, Guldbrandtsen, B, Lund, MS & Sahana, G 2018, Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle. in Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018: Volume Electronic Poster Session - Molecular Genetics 3. vol. 11, 662, The 11th World Congress on Genetics Applied to Livestock Production , Auckland, New Zealand, 11/02/2018. <http://www.wcgalp.org/proceedings/2018/genotype-call-chromosomal-deletions-using-read-depth-whole-genome-sequence-variants>

Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle. / Mesbah-Uddin, Md; Guldbrandtsen, Bernt; Lund, Mogens Sandø et al.
Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018: Volume Electronic Poster Session - Molecular Genetics 3. Vol. 11 2018. 662.

Research output: Contribution to book/anthology/report/proceeding › Article in proceedings › Research › peer-review

TY - GEN

T1 - Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle

AU - Mesbah-Uddin, Md

AU - Guldbrandtsen, Bernt

AU - Lund, Mogens Sandø

AU - Sahana, Goutam

N1 - Conference code: 11

PY - 2018

Y1 - 2018

N2 - We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all the bi-allelic variants within a given deletion locus, and fitted a Gaussian mixture model to the observed RD. We validated our method on brachyspina associated deletion of chromosome 21 (Chr21:21,184,869-21,188,202), which was segregating in our deletion-discovery population of Holstein cattle. We analysed the RD data of 55 progeny tested Holstein bulls with published recessive code for brachyspina (8 carriers and 47 non-carriers) along with 5 carriers from the discovery population (confirmed by assembling the breakpoint sequences). Using our approach we were able to genotype the carriers and non-carriers with 95% accuracy, and a false discovery rate of 18.8%. Keywords: read-depth genotyping, Gaussian mixture model, deletion, copy number variation, dairy cattle

AB - We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all the bi-allelic variants within a given deletion locus, and fitted a Gaussian mixture model to the observed RD. We validated our method on brachyspina associated deletion of chromosome 21 (Chr21:21,184,869-21,188,202), which was segregating in our deletion-discovery population of Holstein cattle. We analysed the RD data of 55 progeny tested Holstein bulls with published recessive code for brachyspina (8 carriers and 47 non-carriers) along with 5 carriers from the discovery population (confirmed by assembling the breakpoint sequences). Using our approach we were able to genotype the carriers and non-carriers with 95% accuracy, and a false discovery rate of 18.8%. Keywords: read-depth genotyping, Gaussian mixture model, deletion, copy number variation, dairy cattle

M3 - Article in proceedings

VL - 11

BT - Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018

T2 - The 11th World Congress on Genetics Applied to Livestock Production

Y2 - 11 February 2018 through 16 February 2018

ER -