Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly incre...

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Autores principales:	Caroline G Storer, Carita E Pascal, Steven B Roberts, William D Templin, Lisa W Seeb, James E Seeb
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6e465bd8c6694c85afda40abf7be20ee
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spelling	oai:doaj.org-article:6e465bd8c6694c85afda40abf7be20ee2021-11-18T08:08:11ZRank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.1932-620310.1371/journal.pone.0049018https://doaj.org/article/6e465bd8c6694c85afda40abf7be20ee2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23185290/?tool=EBIhttps://doaj.org/toc/1932-6203Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.Caroline G StorerCarita E PascalSteven B RobertsWilliam D TemplinLisa W SeebJames E SeebPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e49018 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Caroline G Storer Carita E Pascal Steven B Roberts William D Templin Lisa W Seeb James E Seeb Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.
description	Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.
format	article
author	Caroline G Storer Carita E Pascal Steven B Roberts William D Templin Lisa W Seeb James E Seeb
author_facet	Caroline G Storer Carita E Pascal Steven B Roberts William D Templin Lisa W Seeb James E Seeb
author_sort	Caroline G Storer
title	Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.
title_short	Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.
title_full	Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.
title_fullStr	Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.
title_full_unstemmed	Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.
title_sort	rank and order: evaluating the performance of snps for individual assignment in a non-model organism.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/6e465bd8c6694c85afda40abf7be20ee
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Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

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