Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays
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Publication:2271345
Abstract: Chromosomal DNA is characterized by variation between individuals at the level of entire chromosomes (e.g., aneuploidy in which the chromosome copy number is altered), segmental changes (including insertions, deletions, inversions, and translocations), and changes to small genomic regions (including single nucleotide polymorphisms). A variety of alterations that occur in chromosomal DNA, many of which can be detected using high density single nucleotide polymorphism (SNP) microarrays, are linked to normal variation as well as disease and are therefore of particular interest. These include changes in copy number (deletions and duplications) and genotype (e.g., the occurrence of regions of homozygosity). Hidden Markov models (HMM) are particularly useful for detecting such alterations, modeling the spatial dependence between neighboring SNPs. Here, we improve previous approaches that utilize HMM frameworks for inference in high throughput SNP arrays by integrating copy number, genotype calls, and the corresponding measures of uncertainty when available. Using simulated and experimental data, we, in particular, demonstrate how confidence scores control smoothing in a probabilistic framework. Software for fitting HMMs to SNP array data is available in the R package VanillaICE.
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Cited in
(10)- Hidden Markov models approach to the analysis of array CGH data
- A hidden Markov-model for gene mapping based on whole-genome next generation sequencing data
- PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data
- A multilevel model to address batch effects in copy number estimation using SNP arrays
- A continuous-index hidden Markov jump process for modeling DNA copy number data
- A note on statistical method for genotype calling of high-throughput single-nucleotide polymorphism arrays
- Applications in genomics
- Reconstructing DNA copy number by penalized estimation and imputation
- Algorithmic Learning Theory
- Multi-profile hidden Markov model for mood, dietary intake, and physical activity in an intervention study of childhood obesity
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