biostudies-literatureUnknown7(6)Kalender Atak ZWith 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 mutaPloS onee38463https://www.ebi.ac.uk/biostudies/studies/S-EPMC3366948biostudies-literatureHigh accuracy mutation detection in leukemia on a selected panel of cancer genes.PMC3366948Porcu MQuentmeier HDirks WGKalender Atak ZCloos JAerts SCuppens HCools JVandenberghe PUyttebroeck AGeerdens ELahortiga IVandepoel RDe Keersmaecker KGianfelici VPauwels DBrys VfalseHigh accuracy mutation detection in leukemia on a selected panel of cancer genes.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 muta2012-01-01T00:00:00Z20122026-04-30T17:58:46.83Z2026-04-07T16:15:08.623ZS-EPMC33669482267556510.1371/journal.pone.0038463