ArticleJournal of computational biology : a journal of computational molecular cell biology2013
IPED: inheritance path-based pedigree reconstruction algorithm using genotype data.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- MalKinID: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent.Genetics · 2025Article
- Ancestral haplotype reconstruction in endogamous populations using identity-by-descent.PLoS computational biology · 2021Article
- Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo.Genetics · 2019Article
- Composite likelihood method for inferring local pedigrees.PLoS genetics · 2017Article
- A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data.Bioinformatics (Oxford, England) · 2017Article
- PRIMUS: rapid reconstruction of pedigrees from genome-wide estimates of identity by descent.American journal of human genetics · 2014Article
- Historical pedigree reconstruction from extant populations using PArtitioning of RElatives (PREPARE).PLoS computational biology · 2014Article
- IBD-Groupon: an efficient method for detecting group-wise identity-by-descent regions simultaneously in multiple individuals based on pairwise IBD relationships.Bioinformatics (Oxford, England) · 2013Article
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Authors and funding
5 authors.
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Abstract
The problem of inference of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. Various methods have been proposed to automate the process of pedigree reconstruction given the genotypes or haplotypes of a set of individuals. Current methods, unfortunately, are very time-consuming and inaccurate for complicated pedigrees, such as pedigrees with inbreeding. In this work, we propose an efficient algorithm that is able to reconstruct large pedigrees with reasonable accuracy. Our algorithm reconstructs the pedigrees generation by generation, backward in time from the extant generation. We predict the relationships between individuals in the same generation using an inheritance path-based approach implemented with an efficient dynamic programming algorithm. Experiments show that our algorithm runs in linear time with respect to the number of reconstructed generations, and therefore, it can reconstruct pedigrees that have a large number of generations. Indeed it is the first practical method for reconstruction of large pedigrees from genotype data.
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