Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: mouse forebrain weight
Authors
Lu, LuWei, Lai
Peirce, Jeremy L.
Wang, Xusheng
Zhou, Jianhua
Homayouni, Ramin
Williams, Robert W.
Airey, David C.
UMass Chan Affiliations
Department of MedicineDocument Type
Journal ArticlePublication Date
2008-09-25Keywords
AnimalsBlotting, Western
*Databases, Genetic
*Gene Expression Profiling
INDEL Mutation
Mice
Mice, Inbred C57BL
Mice, Inbred DBA
Organ Size
Polymorphism, Genetic
Promoter Regions, Genetic
Prosencephalon
Quantitative Trait Loci
RNA, Messenger
Reverse Transcriptase Polymerase Chain Reaction
Sequence Analysis, DNA
Suppressor of Cytokine Signaling Proteins
Troponin I
Genetics and Genomics
Life Sciences
Medicine and Health Sciences
Metadata
Show full item recordAbstract
BACKGROUND: Successful strategies for QTL gene identification benefit from combined experimental and bioinformatic approaches. Unique design aspects of the BXD recombinant inbred line mapping panel allow use of archived gene microarray expression data to filter likely from unlikely candidates. This prompted us to propose a simple five-filter protocol for candidate nomination. To filter more likely from less likely candidates, we required candidate genes near to the QTL to have mRNA abundance that correlated with the phenotype among the BXD lines as well as differed between the parental lines C57BL/6J and DBA/2J. We also required verification of mRNA abundance by an independent method, and finally we required either differences in protein levels or confirmed DNA sequence differences. RESULTS: QTL mapping of mouse forebrain weight in 34 BXD RI lines found significant association on chromosomes 1 and 11, with each C57BL/6J allele increasing weight by more than half a standard deviation. The intersection of gene lists that were within +/- 10 Mb of the strongest associated location, that had forebrain mRNA abundance correlated with forebrain weight among the BXD, and that had forebrain mRNA abundance differing between C57BL/6J and DBA/2J, produced two candidates, Tnni1 (troponin 1) and Asb3 (ankyrin repeat and SOCS box-containing protein 3). Quantitative RT-PCR confirmed the direction of an increased expression in C57BL/6J genotype over the DBA/2J genotype for both genes, a difference that translated to a 2-fold difference in Asb3 protein. Although Tnni1 protein differences could not be confirmed, a 273 bp indel polymorphism was discovered 1 Kb upstream of the transcription start site. CONCLUSION: Delivery of well supported candidate genes following a single quantitative trait locus mapping experiment is difficult. However, by combining available gene expression data with QTL mapping, we illustrated a five-filter protocol that nominated Asb3 and Tnni1 as candidates affecting increased mouse forebrain weight. We recommend our approach when (1) investigators are working with phenotypic differences between C57BL/6J and DBA/2J, and (2) gene expression data are available on http://www.genenetwork.org that relate to the phenotype of interest. Under these circumstances, measurement of the phenotype in the BXD lines will likely also deliver excellent candidate genes.Source
BMC Genomics. 2008 Sep 25;9:444. Link to article on publisher's siteDOI
10.1186/1471-2164-9-444Permanent Link to this Item
http://hdl.handle.net/20.500.14038/39480PubMed ID
18817551; 18817551Related Resources
Link to Article in PubMedRights
© 2008 Lu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.ae974a485f413a2113503eed53cd6c53
10.1186/1471-2164-9-444
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