SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
| Autor: | Grace O. Silva, Joel S. Parker, Mengjie Chen, Charles M. Perou, Wei Sun, Lisle E. Mose, Marni B. Siegel |
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| Jazyk: | angličtina |
| Předmět: |
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 |
| Zdroj: | Genome Biology Genome Biology, Vol 18, Iss 1, Pp 1-14 (2017) |
| ISSN: | 1474-760X |
| DOI: | 10.1186/s13059-017-1193-3 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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