Visualization of haplotype sharing patterns in pedigree samples

Sulgi Kim, Mohamad Saad, Debby W. Tsuang, Ellen M. Wijsman

Research output: Contribution to journalArticle

Abstract

Objectives: A particular approach to the visualization of descent of founder DNA copies in a pedigree has been suggested, which helps to understand haplotype sharing patterns among subjects of interest. However, the approach does not provide the information in an ideal format to show haplotype sharing patterns. Therefore, we aimed to find an efficient way to visualize such sharing patterns and to demonstrate that our tool provides useful information for finding an informative subset of subjects for a sequence study. Methods: The visualization package, SharedHap, computes and visualizes a novel metric, the SharedHap proportion, which quantifies haplotype sharing among a set of subjects of interest. We applied SharedHap to simulated and real pedigree datasets to illustrate the approach. Results: SharedHap successfully represents haplotype sharing patterns that contribute to linkage signals in both simulated and real datasets. Using the visualizations we were also able to find ideal sets of subjects for sequencing studies. Conclusions: Our novel metric that can be computed using the SharedHap package provides useful information about haplotype sharing patterns among subjects of interest. The visualization of the SharedHap proportion provides useful information in pedigree studies, allowing for a better selection of candidate subjects for use in further sequencing studies.

Original languageEnglish
Pages (from-to)1-8
Number of pages8
JournalHuman Heredity
Volume78
Issue number1
DOIs
Publication statusPublished - 1 Jan 2014
Externally publishedYes

Fingerprint

Pedigree
Haplotypes
Patient Selection
DNA
Datasets

Keywords

  • Gene mapping
  • IBD
  • Linkage analysis
  • Sampling subjects
  • Sequence
  • Sequencing

ASJC Scopus subject areas

  • Medicine(all)
  • Genetics
  • Genetics(clinical)

Cite this

Visualization of haplotype sharing patterns in pedigree samples. / Kim, Sulgi; Saad, Mohamad; Tsuang, Debby W.; Wijsman, Ellen M.

In: Human Heredity, Vol. 78, No. 1, 01.01.2014, p. 1-8.

Research output: Contribution to journalArticle

Kim, Sulgi ; Saad, Mohamad ; Tsuang, Debby W. ; Wijsman, Ellen M. / Visualization of haplotype sharing patterns in pedigree samples. In: Human Heredity. 2014 ; Vol. 78, No. 1. pp. 1-8.
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