cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries
Abstract 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 ex...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-12-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-04529-2 |
| _version_ | 1818969369138429952 |
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| author | Meifang Qi Utthara Nayar Leif S. Ludwig Nikhil Wagle Esther Rheinbay |
| author_facet | Meifang Qi Utthara Nayar Leif S. Ludwig Nikhil Wagle Esther Rheinbay |
| author_sort | Meifang Qi |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-20T14:19:29Z |
| format | Article |
| id | doaj.art-e63abeda4c1d400b9d4b0c88a680ac57 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-20T14:19:29Z |
| publishDate | 2021-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-e63abeda4c1d400b9d4b0c88a680ac572022-12-21T19:37:58ZengBMCBMC Bioinformatics1471-21052021-12-0122111410.1186/s12859-021-04529-2cDNA-detector: detection and removal of cDNA contamination in DNA sequencing librariesMeifang Qi0Utthara Nayar1Leif S. Ludwig2Nikhil Wagle3Esther Rheinbay4Center for Cancer Research, Massachusetts General HospitalHarvard Medical SchoolHarvard Medical SchoolHarvard Medical SchoolCenter for Cancer Research, Massachusetts General HospitalAbstract 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.https://doi.org/10.1186/s12859-021-04529-2ContaminationGenomicsSoftwareQuality controlcDNA |
| spellingShingle | Meifang Qi Utthara Nayar Leif S. Ludwig Nikhil Wagle Esther Rheinbay cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries BMC Bioinformatics Contamination Genomics Software Quality control cDNA |
| 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 | Contamination Genomics Software Quality control cDNA |
| url | https://doi.org/10.1186/s12859-021-04529-2 |
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