Title | CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing. |
Publication Type | Journal Article |
Year of Publication | 2018 |
Authors | Jiang, Yuchao, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson, and Nancy R. Zhang |
Journal | Genome Biol |
Volume | 19 |
Issue | 1 |
Pagination | 202 |
Date Published | 2018 Nov 26 |
ISSN | 1474-760X |
Keywords | DNA 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. |
DOI | 10.1186/s13059-018-1578-y |
Alternate Journal | Genome Biol |
Original Publication | CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. |
PubMed ID | 30477554 |
PubMed Central ID | PMC6260772 |
Grant List | P50 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 |
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