All polymorphisms studied in this paper [PMID: 23918589] , total : 13 polymorphisms

Title : A genome-wide association study reveals ARL15, a novel non-HLA susceptibility gene for rheumatoid arthritis in North Indians.

Abstract : OBJECTIVE: Genome-wide association studies (GWAS) and their subsequent meta-analyses have changed the landscape of genetics in rheumatoid arthritis (RA) by uncovering several novel genes. Such studies are heavily weighted by samples from Caucasian populations, but they explain only a small proportion of total heritability. Our previous studies in genetically distinct North Indian RA cohorts have demonstrated apparent allelic/genetic heterogeneity between North Indian and Western populations, warranting GWAS in non-European populations. We undertook this study to detect additional disease-associated loci that may be collectively important in the presence or absence of genes with a major effect. METHODS: High-quality genotypes for >600,000 single-nucleotide polymorphisms (SNPs) in 706 RA patients and 761 controls from North India were generated in the discovery stage. Twelve SNPs showing suggestive association (P < 5 x 10(-5)) were then tested in an independent cohort of 927 RA patients and 1,148 controls. Additional disease-associated loci were determined using support vector machine (SVM) analyses. Fine-mapping of novel loci was performed by using imputation. RESULTS: In addition to the expected association of the HLA locus with RA, we identified association with a novel intronic SNP of ARL15 (rs255758) on chromosome 5 (Pcombined = 6.57 x 10(-6); odds ratio 1.42). Genotype-phenotype correlation by assaying adiponectin levels demonstrated the functional significance of this novel gene in disease pathogenesis. SVM analysis confirmed this association along with that of a few more replication stage genes. CONCLUSION: In this first GWAS of RA among North Indians, ARL15 emerged as a novel genetic risk factor in addition to the classic HLA locus, which suggests that population-specific genetic loci as well as those shared between Asian and European populations contribute to RA etiology. Furthermore, our study reveals the potential of machine learning methods in unraveling gene-gene interactions using GWAS data.

Author : Negi S,Juyal G,Senapati S,Prasad P,Gupta A,Singh S,Kashyap S,Kumar A,Kumar U,Gupta R,Kaur S,Agrawal S,Aggarwal A,Ott J,Jain S,Juyal RC,Thelma BK,

Source : Arthritis Rheum. 2013 Dec;65(12):3026-35. doi: 10.1002/art.38110.

No.	Polymorphism name	Gene Symbol	Entrez Gene ID
1	rs4851269	LINC01104	150577
2	rs6542920	LINC01104	150577
3	rs1160542	LINC01104	150577
4	rs255758	ARL15	54622
5	rs1573649	HLA-DQB2	3120
6	rs561041	NA	NA
7	rs4910287	NA	NA
8	rs1037013	RIC8B	55188
9	rs7328282	DOCK9	23348
10	rs2094497	P2RX7	5027
11	rs12881250	NA	NA
12	rs2002212	IMPA2	3613
13	rs99041467	NA	NA