In the discovery cohort, genotyping was performed using the Illumina Bead-Array GWAS platform. Specifically, patients were genotyped using Illumina Human 610-Quad BeadChip and controls were genotyped on Illumina Hap550K-BeadChip [9 (link)]. The 13 single nucleotide polymorphisms (SNPs) identified/confirmed to be associated with IIP [7 (link)], rs2736100 (TERT), rs2076295 (DSP), rs4727443 (AZGP1), rs7934606 (MUC2), rs2034650 (IVD), rs1981997 (MAPT), rs12610495 (DPP9), rs6793295 (LRRC34), rs2609255 (FAM13A), rs11191865 (OBFC1), rs1278769 (ATP11A), rs1379326 (CSMD1) and an additional SNP rs17690703 (SPPL2C) [8 (link)], were investigated in the discovery cohort. We also investigated association of 13 SNPs with anti-topoisomerase 1 antibody (ATA) and anti-centromere antibody (ACA) positive subgroup patients. The SNPs reaching a nominal level of significance (p < 0.05) in the discovery cohort (rs6793295 and rs11191865) were genotyped in the replication cohort using TaqMan allele discrimination assays in a 7900HT fast real-time PCR system (Applied Biosystems, Foster City, CA, USA).
Wu M., Assassi S., Salazar G.A., Pedroza C., Gorlova O.Y., Chen W.V., Charles J., Taing M.L., Liao K., Wigley F.M., Hummers L.K., Shah A.A., Hinchcliff M., Khanna D., Schiopu E., Phillips K., Furst D.E., Steen V., Baron M., Hudson M., Zhou X., Pope J., Jones N., Docherty P., Khalidi N.A., Robinson D., Simms R.W., Silver R.M., Frech T.M., Fessler B.J., Fritzler M.J., Molitor J.A., Segal B.M., Movahedian M., Martín J., Varga J, & Mayes M.D. (2016). Genetic susceptibility loci of idiopathic interstitial pneumonia do not represent risk for systemic sclerosis: a case control study in Caucasian patients. Arthritis Research & Therapy, 18, 20.
Allele Anti centromere antibody Anti topoisomerase 1 antibody Assays Csmd1 Discrimination Dpp9 Gwas Human Mapt Muc2Patients Replication Single nucleotide polymorphisms Tert
Corresponding Organization :
Other organizations :
Dartmouth College, Johns Hopkins University, Northwestern University, University of Michigan–Ann Arbor, University of California, Los Angeles, Georgetown University Medical Center, Georgetown University, McGill University, St Joseph's Health Care, Western University, University of Alberta, Moncton Hospital, McMaster University, University of Manitoba, Boston University, Medical University of South Carolina, University of Utah, University of Alabama at Birmingham, University of Calgary, University of Minnesota, Instituto de Parasitología y Biomedicina "López - Neyra", Consejo Superior de Investigaciones Científicas
Association of 13 SNPs with anti-topoisomerase 1 antibody (ATA) and anti-centromere antibody (ACA) positive subgroup patients
control variables
Patients and controls were genotyped using different Illumina BeadChip platforms
controls
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