ArticleThe annals of applied statistics2008
Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.
Article in The annals of applied statistics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Obesity due to MC4R deficiency is associated with reduced cholesterol, triglycerides and cardiovascular disease risk.Nature medicine · 2025Article
- Genome-wide analysis of copy number variants and normal facial variation in a large cohort of Bantu Africans.HGG advances · 2022Article
- Genome-wide copy number variations in a large cohort of bantu African children.BMC medical genomics · 2021Article
- Article
- Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program.Stem cell research · 2020Article
- Integrity of Induced Pluripotent Stem Cell (iPSC) Derived Megakaryocytes as Assessed by Genetic and Transcriptomic Analysis.PloS one · 2017Article
- Article
- Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26.American journal of human genetics · 2015Article
- The Role of Constitutional Copy Number Variants in Breast Cancer.Microarrays (Basel, Switzerland) · 2015Review
- Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.BMC genetics · 2014Article
- A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk.BMC genetics · 2014Article
- A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer.Cancer informatics · 2014Article
- biomvRhsmm: genomic segmentation with hidden semi-Markov model.BioMed research international · 2014Article
- Multi-profile hidden Markov model for mood, dietary intake, and physical activity in an intervention study of childhood obesity.Statistics in medicine · 2013Article
- PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays.Bioinformatics (Oxford, England) · 2013Article
- Evaluation of calling algorithms for array-CGH.Frontiers in genetics · 2013Article
- Fast detection of de novo copy number variants from SNP arrays for case-parent trios.BMC bioinformatics · 2012Article
- Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.BMC genomics · 2012Article
- Reconstructing DNA copy number by joint segmentation of multiple sequences.BMC bioinformatics · 2012Article
- Article
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Authors and funding
4 authors.
Funding
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 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.