Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
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 ne...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2020-07-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.120.401325 |
| _version_ | 1818906278586482688 |
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| author | Alexander F. Gileta Jianjun Gao Apurva S. Chitre Hannah V. Bimschleger Celine L. St. Pierre Shyam Gopalakrishnan Abraham A. Palmer |
| author_facet | Alexander F. Gileta Jianjun Gao Apurva S. Chitre Hannah V. Bimschleger Celine L. St. Pierre Shyam Gopalakrishnan Abraham A. Palmer |
| author_sort | Alexander F. Gileta |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T21:36:41Z |
| format | Article |
| id | doaj.art-3aa4bd3693ad45488193d7ee910dee76 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-19T21:36:41Z |
| publishDate | 2020-07-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-3aa4bd3693ad45488193d7ee910dee762022-12-21T20:04:46ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362020-07-011072195220510.1534/g3.120.4013257Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock RatsAlexander F. GiletaJianjun GaoApurva S. ChitreHannah V. BimschlegerCeline L. St. PierreShyam GopalakrishnanAbraham A. PalmerThe 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.http://g3journal.org/lookup/doi/10.1534/g3.120.401325genotyping-by-sequencingheterogeneous stockratimputation |
| spellingShingle | Alexander F. Gileta Jianjun Gao Apurva S. Chitre Hannah V. Bimschleger Celine L. St. Pierre Shyam Gopalakrishnan Abraham A. Palmer Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats G3: Genes, Genomes, Genetics genotyping-by-sequencing heterogeneous stock rat imputation |
| title | Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats |
| title_full | Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats |
| title_fullStr | Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats |
| title_full_unstemmed | Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats |
| title_short | Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats |
| title_sort | adapting genotyping by sequencing and variant calling for heterogeneous stock rats |
| topic | genotyping-by-sequencing heterogeneous stock rat imputation |
| url | http://g3journal.org/lookup/doi/10.1534/g3.120.401325 |
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