A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them
Abstract Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a po...
Published in: | Molecular Ecology Resources |
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crwiley:10.1111/1755-0998.12502 2024-09-09T19:02:51+00:00 A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them Humble, E. Martinez‐Barrio, A. Forcada, J. Trathan, P. N. Thorne, M. A. S. Hoffmann, M. Wolf, J. B. W. Hoffman, J. I. Natural Environment Research Council Knut och Alice Wallenbergs Stiftelse Svenska Forskningsrådet Formas 2016 http://dx.doi.org/10.1111/1755-0998.12502 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12502 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12502 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 16, issue 4, page 909-921 ISSN 1755-098X 1755-0998 journal-article 2016 crwiley https://doi.org/10.1111/1755-0998.12502 2024-08-06T04:20:06Z Abstract Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a population, are often very low. A number of potential causes of assay failure have been identified, but none have been explored systematically. In particular, as SNPs are often developed from transcriptomes, parameters relating to the genomic context are rarely taken into account. Here, we assembled a draft Antarctic fur seal ( Arctocephalus gazella ) genome (assembly size: 2.41 Gb; scaffold/contig N 50 : 3.1 Mb/27.5 kb). We then used this resource to map the probe sequences of 144 putative SNPs genotyped in 480 individuals. The number of probe‐to‐genome mappings and alignment length together explained almost a third of the variation in validation success, indicating that sequence uniqueness and proximity to intron–exon boundaries play an important role. The same pattern was found after mapping the probe sequences to the Walrus and Weddell seal genomes, suggesting that the genomes of species divergent by as much as 23 million years can hold information relevant to SNP validation outcomes. Additionally, reanalysis of genotyping data from seven previous studies found the same two variables to be significantly associated with SNP validation success across a variety of taxa. Finally, our study reveals considerable scope for validation rates to be improved, either by simply filtering for SNPs whose flanking sequences align uniquely and completely to a reference genome, or through predictive modelling. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Weddell Seal walrus* Wiley Online Library Antarctic Weddell Molecular Ecology Resources 16 4 909 921 |
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Open Polar |
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Wiley Online Library |
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English |
description |
Abstract Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a population, are often very low. A number of potential causes of assay failure have been identified, but none have been explored systematically. In particular, as SNPs are often developed from transcriptomes, parameters relating to the genomic context are rarely taken into account. Here, we assembled a draft Antarctic fur seal ( Arctocephalus gazella ) genome (assembly size: 2.41 Gb; scaffold/contig N 50 : 3.1 Mb/27.5 kb). We then used this resource to map the probe sequences of 144 putative SNPs genotyped in 480 individuals. The number of probe‐to‐genome mappings and alignment length together explained almost a third of the variation in validation success, indicating that sequence uniqueness and proximity to intron–exon boundaries play an important role. The same pattern was found after mapping the probe sequences to the Walrus and Weddell seal genomes, suggesting that the genomes of species divergent by as much as 23 million years can hold information relevant to SNP validation outcomes. Additionally, reanalysis of genotyping data from seven previous studies found the same two variables to be significantly associated with SNP validation success across a variety of taxa. Finally, our study reveals considerable scope for validation rates to be improved, either by simply filtering for SNPs whose flanking sequences align uniquely and completely to a reference genome, or through predictive modelling. |
author2 |
Natural Environment Research Council Knut och Alice Wallenbergs Stiftelse Svenska Forskningsrådet Formas |
format |
Article in Journal/Newspaper |
author |
Humble, E. Martinez‐Barrio, A. Forcada, J. Trathan, P. N. Thorne, M. A. S. Hoffmann, M. Wolf, J. B. W. Hoffman, J. I. |
spellingShingle |
Humble, E. Martinez‐Barrio, A. Forcada, J. Trathan, P. N. Thorne, M. A. S. Hoffmann, M. Wolf, J. B. W. Hoffman, J. I. A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them |
author_facet |
Humble, E. Martinez‐Barrio, A. Forcada, J. Trathan, P. N. Thorne, M. A. S. Hoffmann, M. Wolf, J. B. W. Hoffman, J. I. |
author_sort |
Humble, E. |
title |
A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them |
title_short |
A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them |
title_full |
A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them |
title_fullStr |
A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them |
title_full_unstemmed |
A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them |
title_sort |
draft fur seal genome provides insights into factors affecting snp validation and how to mitigate them |
publisher |
Wiley |
publishDate |
2016 |
url |
http://dx.doi.org/10.1111/1755-0998.12502 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12502 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12502 |
geographic |
Antarctic Weddell |
geographic_facet |
Antarctic Weddell |
genre |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Weddell Seal walrus* |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Weddell Seal walrus* |
op_source |
Molecular Ecology Resources volume 16, issue 4, page 909-921 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/1755-0998.12502 |
container_title |
Molecular Ecology Resources |
container_volume |
16 |
container_issue |
4 |
container_start_page |
909 |
op_container_end_page |
921 |
_version_ |
1809816898059108352 |