PLASQ: A generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Human cancer is largely driven by the acquisition of mutations. One class of such mutations is copy number polymorphisms, comprised of deviations from the normal diploid two copies of each autosomal chromosome per cell. We describe a probe-level allele-specific quantitation (PLASQ) procedure to determine copy number contributions from each of the parental chromosomes in cancer cells from single-nucleotide polymorphism (SNP) microarray data. Our approach is based upon a generalized linear model that takes advantage of a novel classification of probes on the array. As a result of this classification, we are able to fit the model to the data using an expectation-maximization algorithm designed for the purpose. We demonstrate a strong model fit to data from a variety of cell types. In normal diploid samples, PLASQ is able to genotype with very high accuracy. Moreover, we are able to provide a generalized genotype in cancer samples (e.g., CCCCT at an amplified SNP). Our approach is illustrated on a variety of lung cancer cell lines and tumors, and a number of events are validated by independent computational and experimental means. An R software package containing the methods is freely available.
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References in zbMATH (referenced in 6 articles , 1 standard article )
Showing results 1 to 6 of 6.
- Scharpf, Robert B.; Ruczinski, Ingo; Carvalho, Benilton; Doan, Betty; Chakravarti, Aravinda: A multilevel model to address batch effects in copy number estimation using SNP arrays (2011)
- Wang, Quan; Qu, Jianghan; Cheng, Xiaoxing; Kang, Yongjian; Wan, Lin; Qian, Minping; Deng, Minghua: A study of biases of DNA copy number estimation based on PICR model (2011)
- Bengtsson, Henrik; Neuvial, Pierre; Speed, Terence P.: Tumorboost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays (2010) ioport
- Greenman, Chris D.; Bignell, Graham; Butler, Adam; Edkins, Sarah; Hinton, Jon: PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data (2010)
- Scharpf, Robert B.; Parmigiani, Giovanni; Pevsner, Jonathan; Ruczinski, Ingo: Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays (2008)
- Laframboise, Thomas; Harrington, David; Weir, Barbara A.: PLASQ: A generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data (2007)