Adipose Tissue Gene Expression and Copy-Number in Obesity
The discovery sample included 149 Swedish families (342 subjects) ascertained through an obesity-discordant sib-pair (BMI difference>10kg/m2)6 (link). Gene expression for 29,546 transcripts (16,563 Ensembl genes) was measured in subcutaneous adipose tissue using the Affymetrix Human Genome U133 Plus 2.0 microarray. GWAS signal intensity data from Illumina 610K-Quad arrays were available for 348,150 probes lying within each transcript plus 30kb upstream and downstream to encompass the coding regions and their internal and nearby regulatory regions. Quantitative real-time PCR (qPCR) was carried out to infer relative copy-number measurements reflecting the underlying copy-number distribution at AMY1 and AMY2, respectively, using the TaqMan assays Hs07226362_cn and Hs04204136_cn on an Applied Biosystems 7900HT Real-Time PCR System. Association analyses were carried out for 481 subjects with complete data on BMI and dual-energy X-ray absorptiometry (DEXA)-derived fat mass.
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Falchi M., Moustafa J.S., Takousis P., Pesce F., Bonnefond A., Andersson-Assarsson J.C., Sudmant P.H., Dorajoo R., Al-Shafai M.N., Bottolo L., Ozdemir E., So H.C., Davies R.W., Patrice A., Dent R., Mangino M., Hysi P.G., Dechaume A., Huyvaert M., Skinner J., Pigeyre M., Caiazzo R., Raverdy V., Vaillant E., Field S., Balkau B., Marre M., Visvikis-Siest S., Weill J., Poulain-Godefroy O., Jacobson P., Sjostrom L., Hammond C.J., Deloukas P., Sham P.C., McPherson R., Lee J., Tai E.S., Sladek R., Carlsson L.M., Walley A., Eichler E.E., Pattou F., Spector T.D, & Froguel P. (2014). Low copy number of the salivary amylase gene predisposes to obesity. Nature genetics, 46(5), 492-497.
Assays Dual energy x ray absorptiometryGene expressionGenes Gwas Human genome MicroarrayObesity Quantitative real time pcr Regulatory regions Subcutaneous adipose tissue
Corresponding Organization :
Other organizations :
Imperial College London, Institut Pasteur de Lille, Centre National de la Recherche Scientifique, University of Washington, University of Hong Kong, University of Ottawa, European Genomic Institute for Diabetes, Ottawa Hospital, St Thomas' Hospital, King's College London, Université de Lille, University of East Anglia, Wellcome Sanger Institute, Centre de recherche en Epidémiologie et Santé des Populations, Inserm, Université Claude Bernard Lyon 1, Assistance Publique – Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Université de Lorraine, Lille’s Cardiology Hospital, University of Gothenburg, National University of Singapore, National University Health System, National University Hospital, McGill University
Gene expression for 29,546 transcripts (16,563 Ensembl genes) measured in subcutaneous adipose tissue
Copy-number measurements reflecting the underlying copy-number distribution at AMY1 and AMY2 genes
Body Mass Index (BMI)
Dual-energy X-ray absorptiometry (DEXA)-derived fat mass
control variables
None explicitly mentioned
controls
Positive control: None mentioned
Negative control: None mentioned
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