CONSERTING: integrating copy-number analysis with structural-variation detection.
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.
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.
Xiang
X
Chen
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.
Pankaj
P
Gupta
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.
Jianmin
J
Wang
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.
Joy
J
Nakitandwe
Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Kathryn
K
Roberts
Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
James D
JD
Dalton
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.
Matthew
M
Parker
Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Samir
S
Patel
Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Linda
0000000341403423
L
Holmfeldt
Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Debbie
D
Payne
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.
John
J
Easton
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.
Jing
J
Ma
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.
Michael
M
Rusch
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.
Gang
G
Wu
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.
Aman
A
Patel
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.
Suzanne J
SJ
Baker
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.
Michael A
MA
Dyer
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.
Sheila
S
Shurtleff
Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Stephen
S
Espy
Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
Stanley
S
Pounds
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.
James R
JR
Downing
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.
David W
DW
Ellison
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.
Charles G
0000000218711850
CG
Mullighan
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.
Jinghui
J
Zhang
D000328:Adult; D000465:Algorithms; D002648:Child; D019295:Computational Biology; D004247:DNA / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D005819:Genetic Markers; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D012984:Software
D005819:Genetic Markers; D004247:DNA