SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.

TitleSynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
Publication TypeJournal Article
Year of Publication2017
AuthorsSilva, Grace O., Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou, and Mengjie Chen
JournalGenome Biol
Volume18
Issue1
Pagination66
Date Published2017 04 08
ISSN1474-760X
KeywordsCluster 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.

DOI10.1186/s13059-017-1193-3
Alternate JournalGenome Biol
Original PublicationSynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
PubMed ID28390427
PubMed Central IDPMC5385048
Grant ListR01 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