Estimating population size via line graph reconstruction

Bjarni V. Halldórsson, Dima Blokh, Roded Sharan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

We propose a novel graph theoretic method to estimate haplotype population size from genotype data. The method considers only the potential sharing of haplotypes between individuals and is based on transforming the graph of potential haplotype sharing into a line graph using a minimum number of edge and vertex deletions. We show that the problems are NP complete and provide exact integer programming solutions for them. We test our approach using extensive simulations of multiple population evolution and genotypes sampling scenarios. Our computational experiments show that when most of the sharings are true sharings the problem can be solved very fast and the estimated size is very close to the true size; when many of the potential sharings do not stem from true haplotype sharing, our method gives reasonable lower bounds on the underlying number of haplotypes. In comparison, a naive approach of phasing the input genotypes provides trivial upper bounds of twice the number of genotypes.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 12th International Workshop, WABI 2012, Proceedings
Pages69-80
Number of pages12
DOIs
StatePublished - 2012
Event12th International Workshop on Algorithms in Bioinformatics, WABI 2012 - Ljubljana, Slovenia
Duration: 10 Sep 201212 Sep 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7534 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference12th International Workshop on Algorithms in Bioinformatics, WABI 2012
Country/TerritorySlovenia
CityLjubljana
Period10/09/1212/09/12

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