ArticleBioinformatics (Oxford, England)2010
Efficient identification of identical-by-descent status in pedigrees with many untyped individuals.
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 10 papers.
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Who cites it
10 citing papers in PubMed.
- scHaplotyper: haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data.BMC bioinformatics · 2020Article
- Isomorphism and similarity for 2-generation pedigrees.BMC bioinformatics · 2015Article
- Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.American journal of human genetics · 2014Article
- Privacy preserving protocol for detecting genetic relatives using rare variants.Bioinformatics (Oxford, England) · 2014Article
- Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.Nature methods · 2014Article
- Article
- HapFABIA: identification of very short segments of identity by descent characterized by rare variants in large sequencing data.Nucleic acids research · 2013Article
- Identifying bipolar disorder susceptibility loci in a densely affected pedigree.Molecular psychiatry · 2013Article
- IPED: inheritance path-based pedigree reconstruction algorithm using genotype data.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference.Journal of computational biology : a journal of computational molecular cell biology · 2011Article
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Authors and funding
3 authors.
Funding
Abstract
motivationInference of identical-by-descent (IBD) probabilities is the key in family-based linkage analysis. Using high-density single nucleotide polymorphism (SNP) markers, one can almost always infer haplotype configurations of each member in a family given all individuals being typed. Consequently, the IBD status can be obtained directly from haplotype configurations. However, in reality, many family members are not typed due to practical reasons. The problem of IBD/haplotype inference is much harder when treating untyped individuals as missing.
resultsWe present a novel hidden Markov model (HMM) approach to infer the IBD status in a pedigree with many untyped members using high-density SNP markers. We introduce the concept of inheritance-generating function, defined for any pair of alleles in a descent graph based on a pedigree structure. We derive a recursive formula for efficient calculation of the inheritance-generating function. By aggregating all possible inheritance patterns via an explicit representation of the number and lengths of all possible paths between two alleles, the inheritance-generating function provides a convenient way to theoretically derive the transition probabilities of the HMM. We further extend the basic HMM to incorporate population linkage disequilibrium (LD). Pedigree-wise IBD sharing can be constructed based on pair-wise IBD relationships. Compared with traditional approaches for linkage analysis, our new model can efficiently infer IBD status without enumerating all possible genotypes and transmission patterns of untyped members in a family. Our approach can be reliably applied on large pedigrees with many untyped members, and the inferred IBD status can be used for non-parametric genome-wide linkage analysis. AVAILABILITY: The algorithm is implemented in Matlab and is freely available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available on Bioinformatics online.
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