Bone Gene Expression and Hip Geometry Association

Global gene expression profiling was performed in transiliac bone biopsies obtained from postmenopausal white women from Oslo, as described.^{(36 (link))} This permitted us to calculate the correlation values between hip geometry SNPs (and their proxies) and the transcript levels of genes in the vicinity of the identified loci. In brief, the women undergoing bone biopsies (50 to 86 years old) were free from diseases other than osteoporosis or receiving medication (past or present) possibly affecting bone remodeling or representing secondary causes of osteoporosis.^{(36 (link),37 (link))} RNA was purified and analyzed using Affymetrix HG U133 2.0 plus arrays as described.^{(36 (link))} Bone total RNA was subjected to global transcript profiling using HG-U133 plus 2.0 microarrays (Affymetrix). These data are available at the European Bioinformatics Institute (EMBL-EBI) ArrayExpress repository, ID: E-MEXP-1618 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-1618/).^{(17 (link),38 (link))} DXA scans from the bone donors were subjected to HSA. Filtered transcript levels from 80 bone biopsies were correlated with hip geometry data; results were adjusted for multiple testing using false-discovery rate (FDR).

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Hsu Y.H., Estrada K., Evangelou E., Ackert-Bicknell C., Akesson K., Beck T., Brown S.J., Capellini T., Carbone L., Cauley J., Cheung C.L., Cummings S.R., Czerwinski S., Demissie S., Econs M., Evans D., Farber C., Gautvik K., Harris T., Kammerer C., Kemp J., Koller D.L., Kung A., Lawlor D., Lee M., Lorentzon M., McGuigan F., Medina-Gomez C., Mitchell B., Newman A., Nielson C., Ohlsson C., Peacock M., Reppe S., Richards J.B., Robbins J., Sigurdsson G., Spector T.D., Stefansson K., Streeten E., Styrkarsdottir U., Tobias J., Trajanoska K., Uitterlinden A., Vandenput L., Wilson S.G., Yerges-Armstrong L., Young M., Zillikens C., Rivadeneira F., Kiel D.P, & Karasik D. (2019). Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research, 34(7), 1284-1296.

Publication 2019

HG-U133 plus 2.0 microarrays

Biopsies Bone Donors European Genes Medication Microarrays Osteoporosis Snps Women

Corresponding Organization : Bar-Ilan University

Other organizations : Harvard University, Broad Institute, Erasmus MC, Erasmus University Rotterdam, University of Ioannina, University of Rochester, Sir Charles Gairdner Hospital, Augusta University, University of Pittsburgh, University of Hong Kong, California Pacific Medical Center, Boston University, Indiana University – Purdue University Indianapolis, University of Virginia, Lovisenberg Diakonale Sykehus, University of Oslo, Office of Extramural Research, MRC Epidemiology Unit, University of Bristol, Translational Research Institute, University of Queensland, University of Gothenburg, University of Maryland, Baltimore, Oregon Health & Science University, Oslo University Hospital, McGill University, Jewish General Hospital, University of California, Davis, University of Iceland, King's College London, deCODE Genetics (Iceland), NIHR Oxford Musculoskeletal Biomedical Research Centre, University of Western Australia, GlaxoSmithKline (United Kingdom), GlaxoSmithKline (United States)

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Variable analysis

independent variables

Hip geometry SNPs (and their proxies)

dependent variables

Transcript levels of genes in the vicinity of the identified loci

control variables

Women undergoing bone biopsies were free from diseases other than osteoporosis or receiving medication (past or present) possibly affecting bone remodeling or representing secondary causes of osteoporosis

controls

No positive or negative controls were explicitly mentioned in the input protocol.

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