Combining global genome and transcriptome approaches to identify the candidate genes of small-effect quantitative trait loci in collagen-induced arthritis Xinhua Yu1, Kristin Bauer1, Dirk Koczan2, Hans-Jürgen Thiesen2 and Saleh M Ibrahim1 1Immunogenetics 2Institute Group, University of Rostock, Schillingallee, 18055 Rostock, Germany for Immunology, University of Rostock, Schillingallee, 18055 Rostock, Germany Corresponding author: Saleh M Ibrahim, Received: 19 Sep 2006 Revisions requested: 16 Oct 2006 Revisions received: 5 Dec 2006 Accepted: 23 Jan 2007 Published: 23 Jan 2007 Arthritis Research & Therapy 2007, 9:R3 (doi:) This article is online at: © 2007 Yu et al.; licensee BioMed Central Ltd. This is an open. | Available online http content 9 1 R3 Research article Combining global genome and transcriptome approaches to identify the candidate genes of small-effect quantitative trait loci in collagen-induced arthritis Xinhua Yu1 Kristin Bauer1 Dirk Koczan2 Hans-Jurgen Thiesen2 and Saleh M Ibrahim1 1Immunogenetics Group University of Rostock Schillingallee 18055 Rostock Germany institute for Immunology University of Rostock Schillingallee 1 8055 Rostock Germany Corresponding author Saleh M Ibrahim Received 19 Sep 2006 Revisions requested 16 Oct 2006 Revisions received 5 Dec 2006 Accepted 23 Jan 2007 Published 23 Jan 2007 Arthritis Research Therapy 2007 9 R3 doi ar21 08 This article is online at http content 9 1 R3 2007 Yu et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Open Access Abstract Quantitative traits such as complex diseases are controlled by many small-effect genes that are difficult to identify. Here we present a novel strategy to identify the candidate genes for small-effect quantitative trait loci QTL in collagen induced arthritis CIA using global genome and transcriptome approaches. First we performed genome linkage analysis in F2 progeny of the CIA susceptible and resistant strains to search for small-effect QTL. Second we detected gene expression patterns of both strains during CIA. The candidate genes were identified using three criteria they are located in a genomic region linked to CIA they are disease-specific differentially expressed during CIA and they are strain-specific differentially expressed regarding the two parental strains. Eight small-effect QTL controlling CIA severity were identified. Of 22 000 screened genes
