ArticleGenome biology2021
MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A comprehensive evaluation of long-read de novo transcriptome assembly.Genome biology · 2026Article
- Benchmarking RNA-seq Tools for Real-World Diagnostic Applications.Research square · 2026Article
- Benchmarking RNA-seq Tools for Real-World Diagnostic Applications.medRxiv : the preprint server for health sciences · 2026Article
- Reference-free inferring of transcriptomic events in cancer cells on single-cell data.BMC cancer · 2024Article
- Outlier Expression of Isoforms by Targeted or Total RNA Sequencing Identifies Clinically Significant Genomic Variants in Hematolymphoid Tumors.The Journal of molecular diagnostics : JMD · 2023Article
- Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing.Genes · 2023Article
- Novel gene-intergenic fusion involving ubiquitin E3 ligase UBE3C causes distal hereditary motor neuropathy.Brain : a journal of neurology · 2023Article
- Toblerone: detecting exon deletion events in cancer using RNA-seq.F1000Research · 2023Article
- Novornabreak: Local Assembly for Novel Splice Junction and Fusion Transcript Detection from RNA-Seq Data.Journal of bioinformatics and systems biology : Open access · 2023Article
- Using Genomic Variation to Distinguish Ovarian High-Grade Serous Carcinoma from Benign Fallopian Tubes.International journal of molecular sciences · 2022Article
- The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma.NAR cancer · 2022Article
- A guide for the diagnosis of rare and undiagnosed disease: beyond the exome.Genome medicine · 2022Review
- Toward transcriptomics as a primary tool for rare disease investigation.Cold Spring Harbor molecular case studies · 2022Article
- JAFFAL: detecting fusion genes with long-read transcriptome sequencing.Genome biology · 2022Article
- Discovery of clinically relevant fusions in pediatric cancer.BMC genomics · 2021Article
- Slinker: Visualising novel splicing events in RNA-Seq data.F1000Research · 2021Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting > 85% of variants while no other method is able to achieve this. We posit that MINTIE will be able to identify new disease variants across a range of disease types.
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