Phylogenetic Copy-Number Factorization of Multiple Tumor Samples
نویسندگان
چکیده
منابع مشابه
Copy Number Studies in Noisy Samples
System noise was analyzed in 77 Affymetrix 6.0 samples from a previous clinical study of copy number variation (CNV). Twenty-three samples were classified as eligible for CNV detection, 29 samples as ineligible and 25 were classified as being of intermediate quality. New software ("noise-free-cnv") was developed to visualize the data and reduce system noise. Fresh DNA preparations were more lik...
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Genomic instability is a classic hallmark of cancer and genetic disorders. Microarray-based comparative genomic hybridization (aCGH) has become the accepted technique for studying DNA sequence copy number alterations. While DNA extracted from freshly frozen tissues is optimal for aCGH analysis, in many cases only formalin-fixed, paraffin-embedded (FFPE) tissue material is available. Because DNA...
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MOTIVATION The accurate detection of copy number alterations (CNAs) in human genomes is important for understanding susceptibility to cancer and mechanisms of tumor progression. CNA detection in tumors from single nucleotide polymorphism (SNP) genotyping arrays is a challenging problem due to phenomena such as aneuploidy, stromal contamination, genomic waves and intra-tumor heterogeneity, issue...
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We present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use a finite-state transducer where the emitted read depth is conditioned on the mappability and GC-content of all reads that occur at a given base position. In this model, the read depth within a region is a mixture of binomials, which in simulations matches the...
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Application of the Next generation sequencing (NGS) technology has demonstrated that most tumor samples exhibit intra-tumor heterogeneity. Here we proposed SAPPH (Somatic Aberrations Prediction for Paired Heterogeneous tumor samples), as a new method for estimating tumor somatic copy number aberrations as well as inferring tumor subclone proportions from heterogeneous tumor sequencing data. Thi...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2018
ISSN: 1557-8666
DOI: 10.1089/cmb.2017.0253