Searching thousands of genomes to classify somatic and novel structural variants using STIX

Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current struct...

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Autores principales: Chowdhury, Murad, Pedersen, Brent S., Sedlazeck, Fritz J., Quinlan, Aaron R., Layer, Ryan M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2022
Materias:
Brief Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007735/
https://www.ncbi.nlm.nih.gov/pubmed/35396485
http://dx.doi.org/10.1038/s41592-022-01423-4
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author Chowdhury, Murad
Pedersen, Brent S.
Sedlazeck, Fritz J.
Quinlan, Aaron R.
Layer, Ryan M.
author_facet Chowdhury, Murad
Pedersen, Brent S.
Sedlazeck, Fritz J.
Quinlan, Aaron R.
Layer, Ryan M.
author_sort Chowdhury, Murad
collection PubMed
description Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current structural variant catalogs. We present STIX, a method that, instead of relying on variant calls, indexes and searches the raw alignments from thousands of samples to enable more comprehensive allele frequency estimation.
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spelling pubmed-90077352022-04-29 Searching thousands of genomes to classify somatic and novel structural variants using STIX Chowdhury, Murad Pedersen, Brent S. Sedlazeck, Fritz J. Quinlan, Aaron R. Layer, Ryan M. Nat Methods Brief Communication Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current structural variant catalogs. We present STIX, a method that, instead of relying on variant calls, indexes and searches the raw alignments from thousands of samples to enable more comprehensive allele frequency estimation. Nature Publishing Group US 2022-04-08 2022 /pmc/articles/PMC9007735/ /pubmed/35396485 http://dx.doi.org/10.1038/s41592-022-01423-4 Text en © The Author(s) 2022, corrected publication 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Brief Communication
Chowdhury, Murad
Pedersen, Brent S.
Sedlazeck, Fritz J.
Quinlan, Aaron R.
Layer, Ryan M.
Searching thousands of genomes to classify somatic and novel structural variants using STIX
title Searching thousands of genomes to classify somatic and novel structural variants using STIX
title_full Searching thousands of genomes to classify somatic and novel structural variants using STIX
title_fullStr Searching thousands of genomes to classify somatic and novel structural variants using STIX
title_full_unstemmed Searching thousands of genomes to classify somatic and novel structural variants using STIX
title_short Searching thousands of genomes to classify somatic and novel structural variants using STIX
title_sort searching thousands of genomes to classify somatic and novel structural variants using stix
topic Brief Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9007735/
https://www.ncbi.nlm.nih.gov/pubmed/35396485
http://dx.doi.org/10.1038/s41592-022-01423-4
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