Identification and frequency estimation of inversion polymorphisms from haplotype data

Suzanne S. Sindi, Benjamin J. Raphael

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

Structural rearrangements, including copy-number alterations and inversions, are increasingly recognized as an important contributor to human genetic variation. Copy number variants are readily measured via array-based techniques like comparative genomic hybridization, but copy-neutral variants such as inversion polymorphisms remain difficult to identify without whole genome sequencing. We introduce a method to identify inversion polymorphisms and estimate their frequency in a population using readily available single nucleotide polymorphism (SNP) data. Our method uses a probabilistic model to describe a population as a mixture of forward and inverted chromosomes and identifies putative inversions by characteristic differences in haplotype frequencies around inversion breakpoints. On simulated data, our method accurately predicts inversions with frequencies as low as 25% in the population and reliably estimates inversion frequencies over a wide range. On the human HapMap Phase 2 data, we predict between 88 and 142 inversion polymorphisms with frequency ranging from 20 to 92 percent. Many of these correspond to known inversions or have other evidence supporting them, and the predicted inversion frequencies largely agree with the limited information presently available.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings
Pages418-433
Number of pages16
DOIs
StatePublished - Jul 17 2009
Externally publishedYes
Event13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009 - Tucson, AZ, United States
Duration: May 18 2009May 21 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5541 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009
CountryUnited States
CityTucson, AZ
Period5/18/095/21/09

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Fingerprint Dive into the research topics of 'Identification and frequency estimation of inversion polymorphisms from haplotype data'. Together they form a unique fingerprint.

  • Cite this

    Sindi, S. S., & Raphael, B. J. (2009). Identification and frequency estimation of inversion polymorphisms from haplotype data. In Research in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings (pp. 418-433). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5541 LNBI). https://doi.org/10.1007/978-3-642-02008-7_30