551. SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
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Grace O. Silva, Joel S. Parker, Mengjie Chen, Charles M. Perou, Wei Sun, Lisle E. Mose, and Marni B. Siegel
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0301 basic medicine ,Cancer genome sequencing ,lcsh:QH426-470 ,DNA Copy Number Variations ,Gene Dosage ,Method ,The Cancer Genome Atlas ,Genomics ,Biology ,DNA sequencing ,Genetic Heterogeneity ,03 medical and health sciences ,Breast cancer ,Neoplasms ,Cluster Analysis ,Humans ,Sequencing ,Exome ,Whole genome ,lcsh:QH301-705.5 ,Exome sequencing ,Genetics ,Whole genome sequencing ,Copy number ,Gene Expression Profiling ,Whole exome ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Synthetic normal ,Exons ,Sequence Analysis, DNA ,lcsh:Genetics ,030104 developmental biology ,lcsh:Biology (General) ,DNA microarray ,Software ,Personal genomics - 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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1193-3) contains supplementary material, which is available to authorized users.
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