EGAGenomicsIllumina OncoArrayhttps://ega-archive.org/datasets/EGAD0001000119256479EGA dataset EGAD00010001192EGA<h4>Background</h4>Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits.<h4>Methods</h4>The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background.<h4>Results</h4>The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis.<h4>Conclusions</h4>Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures.<h4>Impact</h4>Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers.Amos Christopher I CI, Dennis Joe J, Wang Zhaoming Z, Byun Jinyoung J, Schumacher Fredrick R FR, Gayther Simon A SA, Casey Graham G, Hunter David J DJ, Sellers Thomas A TA, Gruber Stephen B SB, Dunning Alison M AM, Michailidou Kyriaki K, Fachal Laura L, Doheny Kimberly K, Spurdle Amanda B AB, Li Yafang Y, Xiao Xiangjun X, Romm Jane J, Pugh Elizabeth E, Coetzee Gerhard A GA, Hazelett Dennis J DJ, Bojesen Stig E SE, Caga-Anan Charlisse C, Haiman Christopher A CA, Kamal Ahsan A, Luccarini Craig C, Tessier Daniel D, Vincent Daniel D, Bacot François F, Van Den Berg David J DJ, Nelson Stefanie S, Demetriades Stephen S, Goldgar David E DE, Couch Fergus J FJ, Forman Judith L JL, Giles Graham G GG, Conti David V DV, Bickeböller Heike H, Risch Angela A, Waldenberger Melanie M, Brüske-Hohlfeld Irene I, Hicks Belynda D BD, Ling Hua H, McGuffog Lesley L, Lee Andrew A, Kuchenbaecker Karoline K, Soucy Penny P, Manz Judith J, Cunningham Julie M JM, Butterbach Katja K, Kote-Jarai Zsofia Z, Kraft Peter P, FitzGerald Liesel L, Lindström Sara S, Adams Marcia M, McKay James D JD, Phelan Catherine M CM, Benlloch Sara S, Kelemen Linda E LE, Brennan Paul P, Riggan Marjorie M, O'Mara Tracy A TA, Shen Hongbing H, Shi Yongyong Y, Thompson Deborah J DJ, Goodman Marc T MT, Nielsen Sune F SF, Berchuck Andrew A, Laboissiere Sylvie S, Schmit Stephanie L SL, Shelford Tameka T, Edlund Christopher K CK, Taylor Jack A JA, Field John K JK, Park Sue K SK, Offit Kenneth K, Thomassen Mads M, Schmutzler Rita R, Ottini Laura L, Hung Rayjean J RJ, Marchini Jonathan J, Amin Al Olama Ali A, Peters Ulrike U, Eeles Rosalind A RA, Seldin Michael F MF, Gillanders Elizabeth E, Seminara Daniela D, Antoniou Antonis C AC, Pharoah Paul D P PD, Chenevix-Trench Georgia G, Chanock Stephen J SJ, Simard Jacques J, Easton Douglas F DFOvary Cancer, Cancer of the Ovary, data, Cancer of Ovary, ovarian neoplasm, Neoplasms, Ovarian Cancer, Ovary, ovarian epithelial cancer, Ovary Neoplasm., OC, Ovary Neoplasms, Cancers, Ovary Cancers, primary ovarian cancer, ovary neoplasm, malignant tumour of ovary, ovarian cancer, Ovarian Neoplasm, epithelial, Ovarian, tumor of the Ovary, malignant Ovarian tumor, Neoplasm, Ovarian Cancers, Cancergenetic, familial, Readability, inherited genetic, common., Understanding, constitutitional genetic, hereditarydata.degree (angle), Surrogate Endpoints, Laboratory, Success, Data Mapping, columna vertebralis, Pass, growth and development, Visible Light, Tumor, Multifactorial Causality, Enabling, 5730420M11Rik, Relative, vertebral region, sequencing assay, Benefit Risk Assessment, Method, Biological, Causations, Lifestyle Factor, hnu, Related, Ethnic Group, Analysis, Consortium, imprinted and ancient gene protein, Centers, SET, Project ENABLE, ethnicity, Selection, Genomes, Illumina Sequencing, procedures, Selected, Based, DmelCG4299, set, Pick, Inherited Susceptibility, Familiar, sample, Homo sapiens disease, Relationship, 705, Pharmacogenetic Study, Tumors, close to, Participation, Spine, anatomical protrusion, sequencing_assay, Radiation, Viral, UNQ391/PRO726, CONTINUOUS, familial, assessment, AACR, Light, Procedure, Life Styles, Benign, LIGHT, Evaluated, Marker, Algorithm, Relative Risks, PCA, Educate, finances, Industrial, Industrial Arts, HLA-DR-associated protein II, HVEML, End Points, DI-2, Definite Attribution, I-2Dm, salaries, Benign Neoplasms, Benefit-Risk Assessment, whole genome, Methodological, Immunologic, Controls, Laboratory Marker, Malignant Neoplasms, I-2PP1, Multiple, light quantum, TAF-IBETA, Festa, TAF-Ibeta, Nepal Bhasa, financial management, E430016J11Rik, {STEP}, Effects, Clinical Marker, Neoplasms, Inherited Predisposition, STEPS Intervention, Principal Components Analysis, Ly113, mapping, New Lesion, Biopolymer Sequencing, Predisposing Factors, Sites, disease or disorder, Technique, U19, Lifestyle Factors, NCI Consortium or Network, BM040, Clinical, Risk-Benefit, Lichtquant, 2pp2a, Participating, Benefit-Risk Assessments, Sequencing, CG10574, Neoplasias, Study, PERFORMED, Quality Controls, 2PP2A, dSET, dSet, photon, TR2, constitutitional genetic, Including, Biologic, Cancer, New, NEW, Multifactorial Causalities, fees, Choice, Perform, SINGLE, Life Style Induced Illness, Malignant Neoplasm, Mapping, Traits, Serum Markers, disorders, Factor, CD258, genetic susceptibility, Principal Component Analysis, Immune Marker, near to, MT, I-2PP2A, Have, Surrogate End Point, Successful, chemical analysis, Dm I-2, Neoplasm, condition, IMPACT, imprinted and ancient gene protein homolog, Multiple Causation, background, Lifestyles, Predisposing Factor, SDTM-ETHNIC, Relative Risk, Biologic Markers, Definitely Related to Intervention, New Lesion Identification, susceptibility, Single Person, primary cancer, Evaluate, ensemble, Benefit-Risk, HVEM-L, Surrogate, CDISC SDTM Ethnic Group Terminology, Endpoints, postnatal growth, American Association of Cancer Research., Cancers, malignant tumor, {Step}, Causation, Photoradiations, Specific, vicinity of, Genetic Susceptibility, Solitary, Collaboration, hereditary, Fine, Neoplasia, Alone, Immune Markers, Backbone, Networks, IPP2A2, Biological Markers, Viral Marker, spinal column, determination, Risk Analyses, ETHNICITY, Risk-Benefit Assessments, postnatal development, Biochemical, Endpoint, Nurture, Serum, Techniques, Laboratory Markers, Reinforcing Factor, diseases, pathogenesis, AW048865, diseases and disorders, Health Risk Assessments, Newari, Effect, vertebral column skeleton, foton, Definite, human disease, Continuous, SVN, Identification, Spinal column, TAF-I, Association, SI, Elected, Lifestyle, backbone, genetic, Novel, Ethnic Origins, IGAAD, TNFSF14, STEPS to Enhance Physical Activity (STEPS), Risk Benefit Assessment, Immune, Markers, Methodological Studies, DmelCG10574, malignant neoplasm, Had, Viral Markers, Malignancies, Choose, Select, Has, gamma, Passed, Multifactorial, phapii, PHARMACOGENETIC, wide/broad, and Consortia, Surrogate Endpoint, Arts, Risks and Benefits, StF-IT-1, Multiple Causations, Biochemical Markers, Health Risk Assessment, Slovenia, Biologic Marker, results, Evaluation, Risk Assessment, STEPS to Enhance Physical Activity, dorsal spine, Continuing, Diseases, Predisposing, NOS, overlap, Adverse Event Definitely Related to Intervention, Adverse Event Related to Intervention, Assessed, Visible Radiations, Benefits and Risks, Visible Radiation, Factors, Risk, Nucleic Acid Sequencing, Continue, Control, common, Quality, CG4299, Picked, Methodological Study, Identified, disease, wide, Health, spine, Biochemical Marker, Election, Ethnic Origin, Base, Risk Assessments, Assess, microarray, inherited genetic, i2pp2a, Sequence Analysis, postcranial axial skeleton, other disease, Procedures, Step Unit of Distance, FESTA-L, Clinical Markers, FESTA-S, axial skeleton, Consortium or Network, Benign Neoplasm, Network, genetic predisposition, broad, Malignant, Ximpact, Continued, Illumina, PHAPII, protrusion, Surrogate End Points, ONGO, Surrogate Markers, SEQUENCING, Evaluation Procedure, Relations, Studies, Site, study, Biomarker, Malignancy, ETHNIC, Biological Marker, ipp2a2, causes, financing, Visible, non-neoplastic, funding, Immunologic Markers, Newar Language, ONGOING, taf-ibeta, Continual, causality, disorder, Known, Immunologic Marker, Possess, Molecular Biology, SLOVENIA, Risk-Benefit Assessment, Enabling Factors, igaad, End Point, Certain, Risk Analysis, medical condition, Reinforcing, Ancestry, Related Attribution, Enabling Factor, impact-a, group, development, Environmental, ENABLE, I2PP2A, rare (European definition), techniques, Illumina Sequencing Technology, Environment, Causality, Chose, STEPS, Performed, Reinforcing Factors, Radiations, Basic, Serum Marker, Assessment, Causalities, Chosen, Risks, Basis, Photoradiation, arc degree, TRAITS, sample population, Surrogate Marker, introduction, NUCLEIC ACID SEQUENCING, LTg, Specified, cost, dSET/TAF-Ibeta, 2610030F17Rik, Only, approaches, Ethnicity, Inclusive, assay, Single, Total, AA407739, growth, Ongoing, RWDD5, vertebral column, Advise Before Life Ends, methodology, Health RiskfalseOCAC OncoArray dataGermline genotype data on 56,479 ovarian cancer cases and controls2018-07-18 09:51:00EGAD00010001192960627697780EGAC00001000616EGAS00001002305