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cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries
BACKGROUND: Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709999/ https://www.ncbi.nlm.nih.gov/pubmed/34952565 http://dx.doi.org/10.1186/s12859-021-04529-2 |
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author | Qi, Meifang Nayar, Utthara Ludwig, Leif S. Wagle, Nikhil Rheinbay, Esther |
author_facet | Qi, Meifang Nayar, Utthara Ludwig, Leif S. Wagle, Nikhil Rheinbay, Esther |
author_sort | Qi, Meifang |
collection | PubMed |
description | BACKGROUND: Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous signal can lead to incorrect interpretation of research results. Yet, this problem is not routinely addressed in current sequence processing pipelines. RESULTS: We present cDNA-detector, a computational tool to identify and remove exogenous cDNA contamination in DNA sequencing experiments. We demonstrate that cDNA-detector can identify cDNAs quickly and accurately from alignment files. A source inference step attempts to separate endogenous cDNAs (retrocopied genes) from potential cloned, exogenous cDNAs. cDNA-detector provides a mechanism to decontaminate the alignment from detected cDNAs. Simulation studies show that cDNA-detector is highly sensitive and specific, outperforming existing tools. We apply cDNA-detector to several highly-cited public databases (TCGA, ENCODE, NCBI SRA) and show that contaminant genes appear in sequencing experiments where they lead to incorrect coverage peak calls. CONCLUSIONS: cDNA-detector is a user-friendly and accurate tool to detect and remove cDNA detection in NGS libraries. This two-step design reduces the risk of true variant removal since it allows for manual review of candidates. We find that contamination with intentionally and accidentally introduced cDNAs is an underappreciated problem even in widely-used consortium datasets, where it can lead to spurious results. Our findings highlight the importance of sensitive detection and removal of contaminant cDNA from NGS libraries before downstream analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04529-2. |
format | Online Article Text |
id | pubmed-8709999 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-87099992022-01-05 cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries Qi, Meifang Nayar, Utthara Ludwig, Leif S. Wagle, Nikhil Rheinbay, Esther BMC Bioinformatics Software BACKGROUND: Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous signal can lead to incorrect interpretation of research results. Yet, this problem is not routinely addressed in current sequence processing pipelines. RESULTS: We present cDNA-detector, a computational tool to identify and remove exogenous cDNA contamination in DNA sequencing experiments. We demonstrate that cDNA-detector can identify cDNAs quickly and accurately from alignment files. A source inference step attempts to separate endogenous cDNAs (retrocopied genes) from potential cloned, exogenous cDNAs. cDNA-detector provides a mechanism to decontaminate the alignment from detected cDNAs. Simulation studies show that cDNA-detector is highly sensitive and specific, outperforming existing tools. We apply cDNA-detector to several highly-cited public databases (TCGA, ENCODE, NCBI SRA) and show that contaminant genes appear in sequencing experiments where they lead to incorrect coverage peak calls. CONCLUSIONS: cDNA-detector is a user-friendly and accurate tool to detect and remove cDNA detection in NGS libraries. This two-step design reduces the risk of true variant removal since it allows for manual review of candidates. We find that contamination with intentionally and accidentally introduced cDNAs is an underappreciated problem even in widely-used consortium datasets, where it can lead to spurious results. Our findings highlight the importance of sensitive detection and removal of contaminant cDNA from NGS libraries before downstream analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04529-2. BioMed Central 2021-12-24 /pmc/articles/PMC8709999/ /pubmed/34952565 http://dx.doi.org/10.1186/s12859-021-04529-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Qi, Meifang Nayar, Utthara Ludwig, Leif S. Wagle, Nikhil Rheinbay, Esther cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries |
title | cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries |
title_full | cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries |
title_fullStr | cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries |
title_full_unstemmed | cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries |
title_short | cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries |
title_sort | cdna-detector: detection and removal of cdna contamination in dna sequencing libraries |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8709999/ https://www.ncbi.nlm.nih.gov/pubmed/34952565 http://dx.doi.org/10.1186/s12859-021-04529-2 |
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