CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing.

TitleCODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing.
Publication TypeJournal Article
Year of Publication2018
AuthorsJiang, Yuchao, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson, and Nancy R. Zhang
JournalGenome Biol
Volume19
Issue1
Pagination202
Date Published2018 11 26
ISSN1474-760X
KeywordsDNA Copy Number Variations, Genomics, High-Throughput Nucleotide Sequencing, Humans, Melanoma
Abstract

High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that lead to false discoveries and low sensitivity. We describe CODEX2, as a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples. We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent. CODEX2 outperforms existing methods and, in particular, significantly improves sensitivity for common CNVs.

DOI10.1186/s13059-018-1578-y
Alternate JournalGenome Biol
Original PublicationCODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing.
PubMed ID30477554
PubMed Central IDPMC6260772
Grant ListP50 CA174523 / NH / NIH HHS / United States
R35 GM118102 / NH / NIH HHS / United States
R01 HG006137 / NH / NIH HHS / United States
T32 ES007018 / NH / NIH HHS / United States
P01 CA114046 / NH / NIH HHS / United States
P01 CA142538 / CA / NCI NIH HHS / United States
P01 CA142538 / NH / NIH HHS / United States
Project: