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PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data

Chen Wang, Jared M. Evans, Aditya V. Bhagwate, Naresh Prodduturi, Vivekananda Sarangi, Mridu Middha, Hugues Sicotte, Peter T. Vedell, Steven N. Hart, Gavin R. Oliver, Jean-Pierre A. Kocher, Matthew J. Maurer (+4 others)
2014 Computer applications in the biosciences : CABIOS  
Motivation: Exome sequencing (exome-seq) data, which are typically used for calling exonic mutations, have also been utilized in detecting DNA copy number variations (CNVs).  ...  Compared with other CNV-calling algorithms using data from a lymphoma exome-seq study, PatternCNV has higher sensitivity and specificity.  ...  DISCUSIONS AND CONCLUSIONS We introduce PatternCNV, a software package designed to focus on exon-level CNV detection from exome-seq data.  ... 
doi:10.1093/bioinformatics/btu363 pmid:24876377 pmcid:PMC4155258 fatcat:xwx7wpn7ajblhnobrrtz32vcu4

Genomic and phenotypic characterization of a broad panel of patient derived xenografts reflects the diversity of glioblastoma

Rachael A Vaubel, Shulan Tian, Dioval Remonde, Mark A. Schroeder, Ann C. Mladek, Gaspar J. Kitange, Alissa Caron, Thomas M Kollmeyer, Rebecca Grove, Sen Peng, Brett L. Carlson, Daniel J Ma (+22 others)
2019 Clinical Cancer Research  
Integrated molecular profiling was performed by whole-exome sequencing (WES, n = 83), RNA-sequencing (n = 68), and genome-wide methylation profiling (n = 76).  ...  WES data from 24 patient tumors was compared with derivative models. PDXs recapitulate many key phenotypic and molecular features of patient tumors.  ...  We are also grateful for the Mayo Clinic Medical Genome Facility Genome Analysis Core for contribution to this manuscript.  ... 
doi:10.1158/1078-0432.ccr-19-0909 pmid:31852831 pmcid:PMC7056576 fatcat:uymndhfwavhxfnlayotbeati5i

Sequencing Structural Variants in Cancer for Precision Therapeutics

Geoff Macintyre, Bauke Ylstra, James Brenton, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
In this review we survey the landscape of 'actionable' structural variants in cancer and identify promising detection strategies based on massively-parallel sequencing.  ...  The majority of assays used for solid tumour profiling use DNA sequencing to interrogate somatic point mutations because they are relatively easy to identify and interpret.  ...  Cibulskis, K. et al. (2013) Sensitive detection of somatic point mutations in Wang, C. et al. (2014) PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.  ... 
doi:10.17863/cam.1611 fatcat:6t3ybe3ah5ayxotiwkjb4haucm