ArticlePloS one2013
SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data.Nature communications · 2020Article
- An accurate and powerful method for copy number variation detection.Bioinformatics (Oxford, England) · 2019Article
- Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.Genome research · 2018Article
- ALLELE-SPECIFIC COPY NUMBER ESTIMATION BY WHOLE EXOME SEQUENCING.The annals of applied statistics · 2017Article
- SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.Genome biology · 2017Article
- FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.Nucleic acids research · 2016Article
- Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples.Nucleic acids research · 2016Article
- Allele-specific copy-number discovery from whole-genome and whole-exome sequencing.Nucleic acids research · 2015Article
- Modified screening and ranking algorithm for copy number variation detection.Bioinformatics (Oxford, England) · 2015Article
- PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.Genome biology · 2015Article
- Somatic mosaicism in the human genome.Genes · 2014Review
- Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.Genome biology · 2014Article
- Inferring clonal composition from multiple sections of a breast cancer.PLoS computational biology · 2014Article
- High-definition reconstruction of clonal composition in cancer.Cell reports · 2014Article
- An improved understanding of cancer genomics through massively parallel sequencing.Translational cancer research · 2014Article
- Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine.Genome medicine · 2014Review
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Authors and funding
3 authors.
Funding
Abstract
Whole genome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. However, analysis of somatic copy-number changes from sequencing data is still challenging because of insufficient sequencing coverage, unknown tumor sample purity and subclonal heterogeneity. Here we describe a computational framework, named SomatiCA, which explicitly accounts for tumor purity and subclonality in the analysis of somatic copy-number profiles. Taking read depths (RD) and lesser allele frequencies (LAF) as input, SomatiCA will output 1) admixture rate for each tumor sample, 2) somatic allelic copy-number for each genomic segment, 3) fraction of tumor cells with subclonal change in each somatic copy number aberration (SCNA), and 4) a list of substantial genomic aberration events including gain, loss and LOH. SomatiCA is available as a Bioconductor R package at http://www.bioconductor.org/packages/2.13/bioc/html/SomatiCA.html.
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