PSEUDOMARKER: A powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals

Tero Hiekkalinna, Alejandro A. Schäffer, Brian Lambert, Petri Norrgrann, Harald H.H. Göring, Joseph D. Terwilliger

    Research output: Contribution to journalArticle

    23 Scopus citations

    Abstract

    A decade ago, there was widespread enthusiasm for the prospects of genome-wide association studies to identify common variants related to common chronic diseases using samples of unrelated individuals from populations. Although technological advancements allow us to query more than a million SNPs across the genome at low cost, a disappointingly small fraction of the genetic portion of common disease etiology has been uncovered. This has led to the hypothesis that less frequent variants might be involved, stimulating a renaissance of the traditional approach of seeking genes using multiplex families from less diverse populations. However, by using the modern genotyping and sequencing technology, we can now look not just at linkage, but jointly at linkage and linkage disequilibrium (LD) in such samples. Software methods that can look simultaneously at linkage and LD in a powerful and robust manner have been lacking. Most algorithms cannot jointly analyze datasets involving families of varying structures in a statistically or computationally efficient manner. We have implemented previously proposed statistical algorithms in a user-friendly software package, PSEUDOMARKER. This paper is an announcement of this software package. We describe the motivation behind the approach, the statistical methods, and software, and we briefly demonstrate PSEUDOMARKER's advantages over other packages by example.

    Original languageEnglish (US)
    Pages (from-to)256-266
    Number of pages11
    JournalHuman Heredity
    Volume71
    Issue number4
    DOIs
    StatePublished - Sep 1 2011

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    Keywords

    • Computer software
    • Family-based association
    • Genome-wide association
    • Likelihood methods
    • Linkage analysis
    • Linkage disequilibrium
    • Study design

    ASJC Scopus subject areas

    • Genetics
    • Genetics(clinical)

    Cite this

    Hiekkalinna, T., Schäffer, A. A., Lambert, B., Norrgrann, P., Göring, H. H. H., & Terwilliger, J. D. (2011). PSEUDOMARKER: A powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals. Human Heredity, 71(4), 256-266. https://doi.org/10.1159/000329467