Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions.
The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultr...
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doaj-123857163e614b0db6a7774585bf40ee2020-11-25T01:45:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01127e018130410.1371/journal.pone.0181304Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions.Heewon SeoYoomi ParkByung Joo MinMyung Eui SeoJu Han KimThe Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58.2%, 18.7%, and 23.1% of the variants, respectively. We identified four distinct error patterns of variant calling that may be bioinformatically corrected when using different strategies: simplicity region, SNV cluster, peripheral sequence read, and base inversion. Local de novo assembly successfully corrected 201 (38.7%) of the 519 highly likely or likely false positives. We also demonstrate that the two sequencing kits from Thermo Fisher (the Ion PI Sequencing 200 kit V3 and the Ion PI Hi-Q kit) exhibit different error profiles across different error types. A refined calling algorithm with better polymerase may improve the performance of the Ion Proton sequencing platform.http://europepmc.org/articles/PMC5524428?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Heewon Seo Yoomi Park Byung Joo Min Myung Eui Seo Ju Han Kim |
spellingShingle |
Heewon Seo Yoomi Park Byung Joo Min Myung Eui Seo Ju Han Kim Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions. PLoS ONE |
author_facet |
Heewon Seo Yoomi Park Byung Joo Min Myung Eui Seo Ju Han Kim |
author_sort |
Heewon Seo |
title |
Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions. |
title_short |
Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions. |
title_full |
Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions. |
title_fullStr |
Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions. |
title_full_unstemmed |
Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions. |
title_sort |
evaluation of exome variants using the ion proton platform to sequence error-prone regions. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2017-01-01 |
description |
The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58.2%, 18.7%, and 23.1% of the variants, respectively. We identified four distinct error patterns of variant calling that may be bioinformatically corrected when using different strategies: simplicity region, SNV cluster, peripheral sequence read, and base inversion. Local de novo assembly successfully corrected 201 (38.7%) of the 519 highly likely or likely false positives. We also demonstrate that the two sequencing kits from Thermo Fisher (the Ion PI Sequencing 200 kit V3 and the Ion PI Hi-Q kit) exhibit different error profiles across different error types. A refined calling algorithm with better polymerase may improve the performance of the Ion Proton sequencing platform. |
url |
http://europepmc.org/articles/PMC5524428?pdf=render |
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