Title | SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. |
Publication Type | Journal Article |
Year of Publication | 2017 |
Authors | Silva, Grace O., Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou, and Mengjie Chen |
Journal | Genome Biol |
Volume | 18 |
Issue | 1 |
Pagination | 66 |
Date Published | 2017 Apr 08 |
ISSN | 1474-760X |
Keywords | Cluster Analysis, Computational Biology, DNA Copy Number Variations, Exome, Exons, Gene Dosage, Gene Expression Profiling, Genetic Heterogeneity, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, Reproducibility of Results, Sequence Analysis, DNA, Software |
Abstract | Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues limit current CNA calling based upon DNA sequencing. We present SynthEx, a novel tool for detecting CNAs from whole exome and genome sequencing. SynthEx utilizes a "synthetic-normal" strategy to overcome technical and financial issues. In terms of accuracy and precision, SynthEx is highly comparable to array-based methods and outperforms sequencing-based CNA detection tools. SynthEx robustly identifies CNAs using sequencing data without the additional costs associated with matched normal specimens. |
DOI | 10.1186/s13059-017-1193-3 |
Alternate Journal | Genome Biol |
Original Publication | SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. |
PubMed ID | 28390427 |
PubMed Central ID | PMC5385048 |
Grant List | R01 CA082659 / CA / NCI NIH HHS / United States P30 CA015704 / CA / NCI NIH HHS / United States P30 CA016086 / CA / NCI NIH HHS / United States R01 CA148761 / CA / NCI NIH HHS / United States P50 CA058223 / CA / NCI NIH HHS / United States P01 CA142538 / CA / NCI NIH HHS / United States F30 CA200345 / CA / NCI NIH HHS / United States |
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