Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Ahmed, Ibrahim, Tucci, Felicia A., Aflalo, Aure, Smith, Kenneth G. C., Bashford-Rogers, Rachael J. M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
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
_version_ 1783551974152601600
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
work_keys_str_mv AT ahmedibrahim ultrasensitiveampliconbarcodingfornextgenerationsequencingfacilitatingsequenceerrorandamplificationbiascorrection
AT tuccifeliciaa ultrasensitiveampliconbarcodingfornextgenerationsequencingfacilitatingsequenceerrorandamplificationbiascorrection
AT aflaloaure ultrasensitiveampliconbarcodingfornextgenerationsequencingfacilitatingsequenceerrorandamplificationbiascorrection
AT smithkennethgc ultrasensitiveampliconbarcodingfornextgenerationsequencingfacilitatingsequenceerrorandamplificationbiascorrection
AT bashfordrogersrachaeljm ultrasensitiveampliconbarcodingfornextgenerationsequencingfacilitatingsequenceerrorandamplificationbiascorrection