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

by Downing, James R , Rusch, Michael , Shurtleff, Sheila , Pounds, Stanley , Dalton, James D , Patel, Aman , Baker, Suzanne J , Dyer, Michael A , Gupta, Pankaj , Chen, Xiang , Nakitandwe, Joy , Easton, John , Parker, Matthew , Zhang, Jinghui , Ma, Jing , Patel, Samir , Ellison, David W , Holmfeldt, Linda , Wang, Jianmin , Payne, Debbie , Wu, Gang , Espy, Stephen , Roberts, Kathryn , Mullighan, Charles G

in 45/23 / 631/114/2785 / 631/67/69 / Adult / Algorithms / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical Engineering/Biotechnology / brief-communication / Cancer / Child / Computational Biology / Copy number variations / DNA - genetics / DNA Copy Number Variations - genetics / DNA sequencing / Gene Expression Regulation, Neoplastic / Genetic Markers / Genome / Genomics / Genomics - methods / Humans / Identification and classification / Innovations / Life Sciences / Neoplasms - genetics / Nucleotide sequencing / Proteomics / Software

2015

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

2015

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2015

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Journal Article

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

Downing, James R,

Rusch, Michael,

Shurtleff, Sheila,

Pounds, Stanley,

Dalton, James D,

Patel, Aman,

Baker, Suzanne J,

Dyer, Michael A,

Gupta, Pankaj,

Chen, Xiang,

Nakitandwe, Joy,

Easton, John,

Parker, Matthew,

Zhang, Jinghui,

Ma, Jing,

Patel, Samir,

Ellison, David W,

Holmfeldt, Linda,

Wang, Jianmin,

Payne, Debbie,

Wu, Gang,

Espy, Stephen,

Roberts, Kathryn,

Mullighan, Charles G

2015

Overview

CONSERTING detects somatic copy-number alterations from whole-genome sequence data with high accuracy and sensitivity and identifies breakpoints even in heterogeneous or impure tumors. 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.

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Publisher

Nature Publishing Group US,Nature Publishing Group

Subject

/ Adult

/ Biological Microscopy