ArticleBMC genomics2018
Indel detection from DNA and RNA sequencing data with transIndel.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 43 citations in OpenAlex.
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- ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations.Bioinformatics (Oxford, England) · 2023Article
- Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells.PLoS genetics · 2023Article
- Identification of a large intra-exonic deletion inTherapeutic advances in medical oncology · 2023Article
- LPS-Induced Liver Injury of Magang Geese through Toll-like Receptor and MAPK Signaling Pathway.Animals : an open access journal from MDPI · 2022Article
- Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment.GigaScience · 2021Article
- Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo.STAR protocols · 2021Article
- A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes.Molecular cell · 2021Article
- Neoantigen prediction in human breast cancer using RNA sequencing data.Cancer science · 2021Article
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundInsertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data.
resultsHere, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data. TransIndel exhibits competitive or superior performance over eight state-of-the-art indel detection tools on benchmarks using both synthetic and real DNA-seq data. Additionally, we applied transIndel to DNA-seq and RNA-seq datasets from 333 primary prostate cancer patients from The Cancer Genome Atlas (TCGA) and 59 metastatic prostate cancer patients from AACR-PCF Stand-Up- To-Cancer (SU2C) studies. TransIndel enhanced the taxonomy of DNA- and RNA-level alterations in prostate cancer by identifying recurrent FOXA1 indels as well as exitron splicing in genes implicated in disease progression.
conclusionsOur study demonstrates that transIndel is a robust tool for elucidation of medium- and large-sized indels from DNA-seq and RNA-seq data. Including RNA-seq in indel discovery efforts leads to significant improvements in sensitivity for identification of med-sized and large indels missed by DNA-seq, and reveals non-canonical RNA-splicing events in genes associated with disease pathology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.