ArticlePLoS computational biology2011
Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers.Planta · 2021Article
- DBS: a fast and informative segmentation algorithm for DNA copy number analysis.BMC bioinformatics · 2019Article
- ALLELE-SPECIFIC COPY NUMBER ESTIMATION BY WHOLE EXOME SEQUENCING.The annals of applied statistics · 2017Article
- Statistical Inference in Hidden Markov Models UsingJournal of the American Statistical Association · 2016Article
- Performance evaluation of DNA copy number segmentation methods.Briefings in bioinformatics · 2015Article
- Allele-specific copy number profiling by next-generation DNA sequencing.Nucleic acids research · 2015Article
- A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium.BMC bioinformatics · 2015Article
- Article
- Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer.Genome biology · 2014Article
- Identification of allelic imbalance with a statistical model for subtle genomic mosaicism.PLoS computational biology · 2014Article
- Article
- HaplotypeCN: copy number haplotype inference with Hidden Markov Model and localized haplotype clustering.PloS one · 2014Article
- Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method.BMC genomics · 2013Article
- SPARSE INTEGRATIVE CLUSTERING OF MULTIPLE OMICS DATA SETS.The annals of applied statistics · 2013Article
- Sex bias in copy number variation of olfactory receptor gene family depends on ethnicity.Frontiers in genetics · 2013Article
- Haplotype-based profiling of subtle allelic imbalance with SNP arrays.Genome research · 2013Article
- Getting DNA copy numbers without control samples.Algorithms for molecular biology : AMB · 2012Article
- Reconstructing DNA copy number by joint segmentation of multiple sequences.BMC bioinformatics · 2012Article
- Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data.BMC bioinformatics · 2012Article
- CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.Bioinformatics (Oxford, England) · 2012Article
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3 authors.
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Abstract
Chromosomal gains and losses comprise an important type of genetic change in tumors, and can now be assayed using microarray hybridization-based experiments. Most current statistical models for DNA copy number estimate total copy number, which do not distinguish between the underlying quantities of the two inherited chromosomes. This latter information, sometimes called parent specific copy number, is important for identifying allele-specific amplifications and deletions, for quantifying normal cell contamination, and for giving a more complete molecular portrait of the tumor. We propose a stochastic segmentation model for parent-specific DNA copy number in tumor samples, and give an estimation procedure that is computationally efficient and can be applied to data from the current high density genotyping platforms. The proposed method does not require matched normal samples, and can estimate the unknown genotypes simultaneously with the parent specific copy number. The new method is used to analyze 223 glioblastoma samples from the Cancer Genome Atlas (TCGA) project, giving a more comprehensive summary of the copy number events in these samples. Detailed case studies on these samples reveal the additional insights that can be gained from an allele-specific copy number analysis, such as the quantification of fractional gains and losses, the identification of copy neutral loss of heterozygosity, and the characterization of regions of simultaneous changes of both inherited chromosomes.
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