{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Liu S"],"funding":["United States Department of Defense | United States Army | Army Medical Command | Congressionally Directed Medical Research Programs","NIDDK NIH HHS","U.S. Department of Health & Human Services | NIH | National Cancer Institute","NCI NIH HHS"],"pagination":["506"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8079361"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["4(1)"],"pubmed_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) o"],"journal":["Communications biology"],"pubmed_title":["Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer."],"pmcid":["PMC8079361"],"funding_grant_id":["P30 DK120531","1R56CA229262-01","W81XWH-16-1-0541","R56 CA229262"],"pubmed_authors":["Yu YP","Balamotis M","Liu S","Luo JH","Wu I","Ren B","Ben Yehezkel T"],"additional_accession":[]},"is_claimable":false,"name":"Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer.","description":"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) o","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Apr","modification":"2026-06-12T08:53:12.86Z","creation":"2025-04-07T09:26:57.466Z"},"accession":"S-EPMC8079361","cross_references":{"pubmed":["33907296"],"doi":["10.1038/s42003-021-02024-1"]}}