ArticleBioinformatics (Oxford, England)2010
Inferring combined CNV/SNP haplotypes from genotype data.
Article in Bioinformatics (Oxford, England), 2010. 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.
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species.Frontiers in plant science · 2022Review
- Article
- Detecting Somatic Mutations in Normal Cells.Trends in genetics : TIG · 2018Review
- Population genetics of immune-related multilocus copy number variation in Native Americans.Journal of the Royal Society, Interface · 2017Article
- InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.Nucleic acids research · 2016Article
- Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle.PloS one · 2016Article
- Copy number variations and genetic admixtures in three Xinjiang ethnic minority groups.European journal of human genetics : EJHG · 2015Article
- Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations.Scientific reports · 2015Article
- Large multiallelic copy number variations in humans.Nature genetics · 2015Article
- Article
- Estimating copy numbers of alleles from population-scale high-throughput sequencing data.BMC bioinformatics · 2015Article
- Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.BMC genetics · 2014Article
- A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns.Frontiers in genetics · 2014Article
- A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data.EURASIP journal on bioinformatics & systems biology · 2014Article
- Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.Molecular ecology resources · 2013Article
- A method for calling copy number polymorphism using haplotypes.Frontiers in genetics · 2013Article
- Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene.Genome biology and evolution · 2013Article
- Fast detection of de novo copy number variants from SNP arrays for case-parent trios.BMC bioinformatics · 2012Article
- Haplotype phasing: existing methods and new developments.Nature reviews. Genetics · 2011Review
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Authors and funding
7 authors.
Funding
Abstract
motivationCopy number variations (CNVs) are increasingly recognized as an substantial source of individual genetic variation, and hence there is a growing interest in investigating the evolutionary history of CNVs as well as their impact on complex disease susceptibility. CNV/SNP haplotypes are critical for this research, but although many methods have been proposed for inferring integer copy number, few have been designed for inferring CNV haplotypic phase and none of these are applicable at genome-wide scale. Here, we present a method for inferring missing CNV genotypes, predicting CNV allelic configuration and for inferring CNV haplotypic phase from SNP/CNV genotype data. Our method, implemented in the software polyHap v2.0, is based on a hidden Markov model, which models the joint haplotype structure between CNVs and SNPs. Thus, haplotypic phase of CNVs and SNPs are inferred simultaneously. A sampling algorithm is employed to obtain a measure of confidence/credibility of each estimate.
resultsWe generated diploid phase-known CNV-SNP genotype datasets by pairing male X chromosome CNV-SNP haplotypes. We show that polyHap provides accurate estimates of missing CNV genotypes, allelic configuration and CNV haplotypic phase on these datasets. We applied our method to a non-simulated dataset-a region on Chromosome 2 encompassing a short deletion. The results confirm that polyHap's accuracy extends to real-life datasets. AVAILABILITY: Our method is implemented in version 2.0 of the polyHap software package and can be downloaded from http://www.imperial.ac.uk/medicine/people/l.coin.
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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.