Original Article

Summary of contributions to GAW15 Group 16: Processing/normalization of expression traits

  1. Aurélie Labbe1,2,†,*,
  2. Jeanette McClintick3,‡,
  3. Maria Martinez4,§

Article first published online: 28 NOV 2007

DOI: 10.1002/gepi.20290

Issue

Genetic Epidemiology

Genetic Epidemiology

Supplement: Genetic Analysis Workshop 15: Summaries of the Design and Analysis of Genomic Data

Volume 31, Issue S1, pages S132–S138, 2007

Additional Information

How to Cite

Labbe, A., McClintick, J. and Martinez, M. (2007), Summary of contributions to GAW15 Group 16: Processing/normalization of expression traits. Genet. Epidemiol., 31: S132–S138. doi: 10.1002/gepi.20290

Author Information

  1. 1

    Département de mathématiques et de statistique, Université Laval, Québec, Canada

  2. 2

    Centre de Recherche Université Laval Robert Giffard, Québec, Canada

  3. 3

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana

  4. 4

    INSERM, U563, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; Université de Toulouse III Paul-Sabatier, Toulouse, France

  1. †

    Aurélie Labbe, Jeanette McClintick, and Maria Martinez contributed equally to this work.

  2. ‡

    Aurélie Labbe, Jeanette McClintick, and Maria Martinez contributed equally to this work.

  3. §

    Aurélie Labbe, Jeanette McClintick, and Maria Martinez contributed equally to this work.

*Département de mathématiques et de statistique, Université Laval, Québec, Canada

Publication History

  1. Issue published online: 28 NOV 2007
  2. Article first published online: 28 NOV 2007

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Keywords:

  • gene expression;
  • eQTL analysis;
  • LOD score;
  • microarray data;
  • data processing

Abstract

Here, we summarize the contributions to group 16 of Genetic Analysis Workshop 15, held in Florida, U.S.A. The theme of this group was preprocessing of expression quantitative trait loci (eQTL) studies using the Affymetrix platform. The objective of the Genetic Analysis Workshop 15 problem 1 dataset was to use transcript levels that are measured using DNA microarrays as quantitative traits and localize the genes or other features of the DNA that control gene expression by quantitative trait loci linkage analyses. All contributors of this group used the microarray expression profiles (problem 1) data. Various approaches and questions were examined to investigate the effects of preprocessing methods and/or gene filtering on the interpretation of data, specifically on heritability estimates of gene expression and on linkage results. In addition, some contributors focused on the statistical issues involved in large-scale genetic analyses of quantitative traits that account for or build composite phenotypes from a large number of correlated traits. Since the true eQTLs are not known in the problem 1 data, results from the 11 studies cannot be fully evaluated for the methods employed. However, several common trends were found. All reports concluded that preprocessing statistical analyses may have an important impact on eQTL analyses and on the identification of cis-/trans-regulators and/or major biological pathways. Genet. Epidemiol. 31(Suppl. 1):S132–S138, 2007. © 2007 Wiley-Liss, Inc.

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