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Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction
The ability to accurately characterize DNA variant proportions using PCR amplification is key to many genetic studies, including studying tumor heterogeneity, 16S microbiome, viral and immune receptor sequencing. We develop a novel generalizable ultrasensitive amplicon barcoding approach that signif...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7324614/ https://www.ncbi.nlm.nih.gov/pubmed/32601361 http://dx.doi.org/10.1038/s41598-020-67290-1 |
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author | Ahmed, Ibrahim Tucci, Felicia A. Aflalo, Aure Smith, Kenneth G. C. Bashford-Rogers, Rachael J. M. |
author_facet | Ahmed, Ibrahim Tucci, Felicia A. Aflalo, Aure Smith, Kenneth G. C. Bashford-Rogers, Rachael J. M. |
author_sort | Ahmed, Ibrahim |
collection | PubMed |
description | The ability to accurately characterize DNA variant proportions using PCR amplification is key to many genetic studies, including studying tumor heterogeneity, 16S microbiome, viral and immune receptor sequencing. We develop a novel generalizable ultrasensitive amplicon barcoding approach that significantly reduces the inflation/deflation of DNA variant proportions due to PCR amplification biases and sequencing errors. This method was applied to immune receptor sequencing, where it significantly improves the quality and estimation of diversity of the resulting library. |
format | Online Article Text |
id | pubmed-7324614 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-73246142020-07-01 Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction Ahmed, Ibrahim Tucci, Felicia A. Aflalo, Aure Smith, Kenneth G. C. Bashford-Rogers, Rachael J. M. Sci Rep Article The ability to accurately characterize DNA variant proportions using PCR amplification is key to many genetic studies, including studying tumor heterogeneity, 16S microbiome, viral and immune receptor sequencing. We develop a novel generalizable ultrasensitive amplicon barcoding approach that significantly reduces the inflation/deflation of DNA variant proportions due to PCR amplification biases and sequencing errors. This method was applied to immune receptor sequencing, where it significantly improves the quality and estimation of diversity of the resulting library. Nature Publishing Group UK 2020-06-29 /pmc/articles/PMC7324614/ /pubmed/32601361 http://dx.doi.org/10.1038/s41598-020-67290-1 Text en © The Author(s) 2020 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/. |
spellingShingle | Article Ahmed, Ibrahim Tucci, Felicia A. Aflalo, Aure Smith, Kenneth G. C. Bashford-Rogers, Rachael J. M. Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction |
title | Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction |
title_full | Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction |
title_fullStr | Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction |
title_full_unstemmed | Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction |
title_short | Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction |
title_sort | ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7324614/ https://www.ncbi.nlm.nih.gov/pubmed/32601361 http://dx.doi.org/10.1038/s41598-020-67290-1 |
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