ArticleCommunications biology2021
Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- Next-Generation Sequencing: A Review of Its Transformative Impact on Cancer Diagnosis, Treatment, and Resistance Management.Diagnostics (Basel, Switzerland) · 2025Review
- Anchorage accurately assembles anchor-flanked synthetic long reads.Algorithms for molecular biology : AMB · 2025Article
- Toward clinical long-read genome sequencing for rare diseases.Nature genetics · 2025Review
- Deep Spatial Sequencing Revealing Differential Immune Responses in Human Hepatocellular Carcinoma.bioRxiv : the preprint server for biology · 2025Article
- Deep spatial sequencing revealing differential immune responses in human hepatocellular carcinoma.Frontiers in cell and developmental biology · 2025Article
- Utility analyses of AVITI sequencing chemistry.BMC genomics · 2024Article
- Utility Analyses of AVITI Sequencing Chemistry.bioRxiv : the preprint server for biology · 2024Article
- Advances in single-cell long-read sequencing technologies.NAR genomics and bioinformatics · 2024Article
- Article
- Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2024Article
- Recent advances in cancer fusion transcript detection.Briefings in bioinformatics · 2023Review
- Large-Scale Complete Sequencing and Haplotyping of 1-10 kb DNA Molecules Using Short Massively Parallel Reads.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.Foods (Basel, Switzerland) · 2022Review
- Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease.Human molecular genetics · 2022Review
- 16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis.PeerJ · 2022Article
- Dynamic Transcriptome Sequencing of Bovine Alphaherpesvirus Type 1 and Host Cells Carried Out by a Multi-Technique Approach.Frontiers in genetics · 2021Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
The characterization of human gene expression is limited by short read lengths, high error rates and large input requirements. Here, we used a synthetic long read (SLR) sequencing approach, LoopSeq, to generate accurate sequencing reads that span full length transcripts using standard short read data. LoopSeq identified isoforms from control samples with 99.4% accuracy and a 0.01% per-base error rate, exceeding the accuracy reported for other long-read technologies. Applied to targeted transcriptome sequencing from colon cancers and their metastatic counterparts, LoopSeq revealed large scale isoform redistributions from benign colon mucosa to primary colon cancer and metastatic cancer and identified several previously unknown fusion isoforms. Strikingly, single nucleotide variants (SNVs) occurred dominantly in specific isoforms and some SNVs underwent isoform switching in cancer progression. The ability to use short reads to generate accurate long-read data as the raw unit of information holds promise as a widely accessible approach in transcriptome sequencing.
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