Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

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Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Srfim) and filtering (SERVIC(4)E) algorithms. We sequenced 24 exons in two cohorts of 480 sam...

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Autores principales: Niranjan, Tejasvi S, Adamczyk, Abby, Bravo, Héctor Corrada, Taub, Margaret A, Wheelan, Sarah J, Irizarry, Rafael, Wang, Tao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308056/
https://www.ncbi.nlm.nih.gov/pubmed/21955804
http://dx.doi.org/10.1186/gb-2011-12-9-r93
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author Niranjan, Tejasvi S
Adamczyk, Abby
Bravo, Héctor Corrada
Taub, Margaret A
Wheelan, Sarah J
Irizarry, Rafael
Wang, Tao
author_facet Niranjan, Tejasvi S
Adamczyk, Abby
Bravo, Héctor Corrada
Taub, Margaret A
Wheelan, Sarah J
Irizarry, Rafael
Wang, Tao
author_sort Niranjan, Tejasvi S
collection PubMed
description Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Srfim) and filtering (SERVIC(4)E) algorithms. We sequenced 24 exons in two cohorts of 480 samples each, identifying 47 coding variants, including 30 present once per cohort. Validation by Sanger sequencing revealed an excellent combination of sensitivity and specificity for variant detection in pooled samples of both cohorts as compared to publicly available algorithms.
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spelling pubmed-33080562012-03-20 Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis Niranjan, Tejasvi S Adamczyk, Abby Bravo, Héctor Corrada Taub, Margaret A Wheelan, Sarah J Irizarry, Rafael Wang, Tao Genome Biol Method Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Srfim) and filtering (SERVIC(4)E) algorithms. We sequenced 24 exons in two cohorts of 480 samples each, identifying 47 coding variants, including 30 present once per cohort. Validation by Sanger sequencing revealed an excellent combination of sensitivity and specificity for variant detection in pooled samples of both cohorts as compared to publicly available algorithms. BioMed Central 2011 2011-09-28 /pmc/articles/PMC3308056/ /pubmed/21955804 http://dx.doi.org/10.1186/gb-2011-12-9-r93 Text en Copyright ©2011 Niranjan et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Niranjan, Tejasvi S
Adamczyk, Abby
Bravo, Héctor Corrada
Taub, Margaret A
Wheelan, Sarah J
Irizarry, Rafael
Wang, Tao
Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
title Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
title_full Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
title_fullStr Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
title_full_unstemmed Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
title_short Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
title_sort effective detection of rare variants in pooled dna samples using cross-pool tailcurve analysis
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308056/
https://www.ncbi.nlm.nih.gov/pubmed/21955804
http://dx.doi.org/10.1186/gb-2011-12-9-r93
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