{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Roberts HE"],"funding":["Health Innovation Challenge Fund","Wellcome Trust"],"pagination":["6408"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7979876"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(1)"],"pubmed_abstract":["Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from s"],"journal":["Scientific reports"],"pubmed_title":["Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma."],"pmcid":["PMC7979876"],"funding_grant_id":["203141/Z/16/Z","R6-388 / WT 100127"],"pubmed_authors":["Buck D","Lockstone H","Taylor JC","Pagnamenta AT","Freeman C","Schuh A","Parkes D","Lopopolo M","Lonie L","Knight SJL","Roberts HE","Sharma E","Bowden R","Lunter G","Dreau H"],"additional_accession":[]},"is_claimable":false,"name":"Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma.","description":"Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from s","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Mar","modification":"2026-06-04T16:42:22.979Z","creation":"2024-11-08T21:47:42.674Z"},"accession":"S-EPMC7979876","cross_references":{"pubmed":["33742045"],"doi":["10.1038/s41598-021-85354-8"]}}