Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
Abstract Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as we...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-11-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-022-02789-6 |
| _version_ | 1828098542783168512 |
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| author | Julianne K. David Sean K. Maden Mary A. Wood Reid F. Thompson Abhinav Nellore |
| author_facet | Julianne K. David Sean K. Maden Mary A. Wood Reid F. Thompson Abhinav Nellore |
| author_sort | Julianne K. David |
| collection | DOAJ |
| description | Abstract Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs. Results We compared introns detected by 8 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens. We found significant disagreement among tools (Fleiss’ $$\kappa = 0.113$$ κ = 0.113 ) such that 47.7% of all detected intron retentions were not called by more than one tool. We also observed poor performance of all tools, with none achieving an F1-score greater than 0.26, and qualitatively different behaviors between general-purpose alternative splicing detection tools and tools confined to retained intron detection. Conclusions Short-read tools detect intron retention with poor recall and precision, calling into question the completeness and validity of a large percentage of putatively retained introns called by commonly used methods. |
| first_indexed | 2024-04-11T08:03:09Z |
| format | Article |
| id | doaj.art-ea62db3678a941dabe74f0c088a5f2e6 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-11T08:03:09Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-ea62db3678a941dabe74f0c088a5f2e62022-12-22T04:35:39ZengBMCGenome Biology1474-760X2022-11-0123112210.1186/s13059-022-02789-6Retained introns in long RNA-seq reads are not reliably detected in sample-matched short readsJulianne K. David0Sean K. Maden1Mary A. Wood2Reid F. Thompson3Abhinav Nellore4Computational Biology Program, Oregon Health & Science UniversityComputational Biology Program, Oregon Health & Science UniversityComputational Biology Program, Oregon Health & Science UniversityComputational Biology Program, Oregon Health & Science UniversityComputational Biology Program, Oregon Health & Science UniversityAbstract Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs. Results We compared introns detected by 8 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens. We found significant disagreement among tools (Fleiss’ $$\kappa = 0.113$$ κ = 0.113 ) such that 47.7% of all detected intron retentions were not called by more than one tool. We also observed poor performance of all tools, with none achieving an F1-score greater than 0.26, and qualitatively different behaviors between general-purpose alternative splicing detection tools and tools confined to retained intron detection. Conclusions Short-read tools detect intron retention with poor recall and precision, calling into question the completeness and validity of a large percentage of putatively retained introns called by commonly used methods.https://doi.org/10.1186/s13059-022-02789-6RNA-seqSplicingIntron retention |
| spellingShingle | Julianne K. David Sean K. Maden Mary A. Wood Reid F. Thompson Abhinav Nellore Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads Genome Biology RNA-seq Splicing Intron retention |
| title | Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads |
| title_full | Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads |
| title_fullStr | Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads |
| title_full_unstemmed | Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads |
| title_short | Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads |
| title_sort | retained introns in long rna seq reads are not reliably detected in sample matched short reads |
| topic | RNA-seq Splicing Intron retention |
| url | https://doi.org/10.1186/s13059-022-02789-6 |
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