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Nat Methods. 2015 Jun;12(6):527-30. doi: 10.1038/nmeth.3394. Epub 2015 May 4.

CONSERTING: integrating copy-number analysis with structural-variation detection.

Author information

1
1] Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Pediatric Cancer Genome Project, St. Jude Children's Research Hospital and Washington University School of Medicine, Memphis, Tennessee, USA.
2
1] Pediatric Cancer Genome Project, St. Jude Children's Research Hospital and Washington University School of Medicine, Memphis, Tennessee, USA. [2] Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [3] Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA.
3
1] Pediatric Cancer Genome Project, St. Jude Children's Research Hospital and Washington University School of Medicine, Memphis, Tennessee, USA. [2] Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
4
Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
5
1] Pediatric Cancer Genome Project, St. Jude Children's Research Hospital and Washington University School of Medicine, Memphis, Tennessee, USA. [2] Pediatric Cancer Genome Project Laboratory, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
6
1] Pediatric Cancer Genome Project, St. Jude Children's Research Hospital and Washington University School of Medicine, Memphis, Tennessee, USA. [2] Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
7
Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
8
Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

Abstract

We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), an algorithm for detecting somatic copy-number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation on the basis of changes in read depth and the detection of localized structural variations, with high accuracy and sensitivity. Analysis of 43 cancer genomes from both pediatric and adult patients revealed novel oncogenic CNAs, complex rearrangements and subclonal CNAs missed by alternative approaches.

PMID:
25938371
PMCID:
PMC4591043
DOI:
10.1038/nmeth.3394
[Indexed for MEDLINE]
Free PMC Article

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