Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
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Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats. / Gileta, Alexander F.; Gao, Jianjun; Chitre, Apurva S.; Bimschleger, Hannah; St Pierre, Celine L.; Gopalakrishnan, Shyam; Palmer, Abraham A.
In: G3: Genes, Genomes, Genetics (Bethesda), Vol. 10, No. 7, 2020, p. 2195-2205.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
AU - Gileta, Alexander F.
AU - Gao, Jianjun
AU - Chitre, Apurva S.
AU - Bimschleger, Hannah
AU - St Pierre, Celine L.
AU - Gopalakrishnan, Shyam
AU - Palmer, Abraham A.
PY - 2020
Y1 - 2020
N2 - The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.
AB - The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.
KW - genotyping-by-sequencing
KW - heterogeneous stock
KW - rat
KW - imputation
KW - GENOME-WIDE ASSOCIATION
KW - HIGH-THROUGHPUT
KW - SNP DISCOVERY
KW - IMPUTATION
KW - FRAMEWORK
KW - TOOL
KW - TRAITS
KW - MOUSE
KW - GBS
KW - MAP
U2 - 10.1534/g3.120.401325
DO - 10.1534/g3.120.401325
M3 - Journal article
C2 - 32398234
VL - 10
SP - 2195
EP - 2205
JO - G3: Genes, Genomes, Genetics (Bethesda)
JF - G3: Genes, Genomes, Genetics (Bethesda)
SN - 2160-1836
IS - 7
ER -
ID: 248503251