Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
By Jarupon Fah Sathirapongsasuti, Hane Lee, B. Horst, G. Brunner, A. Cochran, S. Binder, John Quackenbush, Stanley F. Nelson. Bioinform., 2011
407 citations recorded by the source corpus.
Subfields: Cancer Research, Genetics
View Paper: https://www.semanticscholar.org/paper/63c0530c84e9241e877ab69d49677512fa9789f7
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Citations in the corpus
- Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (2013, methodology): “org/src/contrib/ Archive/ExomeCNV/ R BAM/pileup Using read depth and B-allele frequencies from exome sequencing data to detect CNVs and LOHs [49]”
- Best practices for variant calling in clinical sequencing (2020, methodology): “MOPS [45], CONTRA [46], CoNVEX [47], ExomeCNV [48], ExomeDepth [49], XHMM [50]”
- A survey of tools for variant analysis of next-generation genome sequencing data (2013, methodology): “Therefore, dedicated tools have been designed that consider the properties of exome capturing [84].”
- A robust model for read count data in exome sequencing experiments and implications for copy number variant calling (2012, background): “…follow a binomial distribution whose success rate is determined by genome-wide read count ratio between the test sample and the reference set, as well as the potential presence of CNVs. Additional covariates, such as GC content, can alter this success rate in situations where the effects of…”
- CONTRA: copy number analysis for targeted resequencing (2012, unknown): “Received on April 5, 2011; revised on February 27, 2012; accepted on March 23, 2012”
- Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. (2012, methodology): “Cancer studies have afforded themselves the use of per-sample case-control matching (tumor versus normal) to simplify depth normalization.(15) To augment the repertoire of tools for ‘‘variation hunting,’’ we developed XHMM (exome hidden Markov model, Figure 1), a statistical toolset for detecting ex”
- Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor (2012, methodology): “We performed the concurrence and mutual exclusion analysis on the significantly mutated genes that showed nonsilent mutations in at least five tumor cells by permutation test, as previously described (Sathirapongsasuti et al., 2011), with minor modifications.”