Knee_OA_Functional_Genomics - EGA European Genome-Phenome Archive

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001003355	From 17 patients undergoing knee joint replacement surgery for osteoarthritis, we collected 4 samples each: intact cartilage, degraded cartilage, synovium, and meniscus. We also collected blood for DNA analysis. Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09.	Illumina HiSeq 2500	72
EGAD00010001285	Genotyping of knee osteoarthritis patients who have undergone total joint replacement	Illumina InfiniumCoreExome-24v1-1_A	17
EGAD00010001287	Array methylation profiling of knee osteoarthritis patients who have undergone total joint replacement	Illumina HumanMethylation450K	68

Publications	Citations
Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis. Zengini E, Hatzikotoulas K, Tachmazidou I, Steinberg J, Hartwig FP, Southam L, Hackinger S, Boer CG, Styrkarsdottir U, Gilly A, Suveges D, Killian B, Ingvarsson T, Jonsson H, Babis GC, McCaskie A, Uitterlinden AG, van Meurs JBJ, Thorsteinsdottir U, Stefansson K, Davey Smith G, Wilkinson JM, Zeggini E. Nat Genet 50: 2018 549-558	150
Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data. Tachmazidou I, Hatzikotoulas K, Southam L, Esparza-Gordillo J, Haberland V, Zheng J, Johnson T, Koprulu M, Zengini E, Steinberg J, Wilkinson JM, Bhatnagar S, Hoffman JD, Buchan N, Süveges D, arcOGEN Consortium, Yerges-Armstrong L, Smith GD, Gaunt TR, Scott RA, McCarthy LC, Zeggini E. Nat Genet 51: 2019 230-236	237
Accelerating functional gene discovery in osteoarthritis. Butterfield NC, Curry KF, Steinberg J, Dewhurst H, Komla-Ebri D, Mannan NS, Adoum AT, Leitch VD, Logan JG, Waung JA, Ghirardello E, Southam L, Youlten SE, Wilkinson JM, McAninch EA, Vancollie VE, Kussy F, White JK, Lelliott CJ, Adams DJ, Jacques R, Bianco AC, Boyde A, Zeggini E, Croucher PI, Williams GR, Bassett JHD. Nat Commun 12: 2021 467	26
A molecular quantitative trait locus map for osteoarthritis. Steinberg J, Southam L, Roumeliotis TI, Clark MJ, Jayasuriya RL, Swift D, Shah KM, Butterfield NC, Brooks RA, McCaskie AW, Bassett JHD, Williams GR, Choudhary JS, Wilkinson JM, Zeggini E. Nat Commun 12: 2021 1309	36
Linking chondrocyte and synovial transcriptional profile to clinical phenotype in osteoarthritis. Steinberg J, Southam L, Fontalis A, Clark MJ, Jayasuriya RL, Swift D, Shah KM, Brooks RA, McCaskie AW, Wilkinson JM, Zeggini E. Ann Rheum Dis 80: 2021 1070-1074	22
A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis. Katsoula G, Steinberg J, Tuerlings M, Coutinho de Almeida R, Southam L, Swift D, Meulenbelt I, Wilkinson JM, Zeggini E. Hum Mol Genet 31: 2022 2090-2105	10
eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs. Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. PLoS Genet 19: 2023 e1010932	6