{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["7(6)"],"submitter":["Kalender Atak Z"],"pubmed_abstract":["With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted muta"],"journal":["PloS one"],"pagination":["e38463"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC3366948"],"repository":["biostudies-literature"],"pubmed_title":["High accuracy mutation detection in leukemia on a selected panel of cancer genes."],"pmcid":["PMC3366948"],"pubmed_authors":["Porcu M","Quentmeier H","Dirks WG","Kalender Atak Z","Cloos J","Aerts S","Cuppens H","Cools J","Vandenberghe P","Uyttebroeck A","Geerdens E","Lahortiga I","Vandepoel R","De Keersmaecker K","Gianfelici V","Pauwels D","Brys V"],"additional_accession":[]},"is_claimable":false,"name":"High accuracy mutation detection in leukemia on a selected panel of cancer genes.","description":"With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted muta","dates":{"release":"2012-01-01T00:00:00Z","publication":"2012","modification":"2026-04-30T17:58:46.83Z","creation":"2026-04-07T16:15:08.623Z"},"accession":"S-EPMC3366948","cross_references":{"pubmed":["22675565"],"doi":["10.1371/journal.pone.0038463"]}}