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HLA class II SNP interactions and the association with type 1 diabetes mellitus in Bengali speaking patients of Eastern India

Oindrila Raha1, Biswanath Sarkar1, Bhaskar VKS Lakkakula2, Veerraju Pasumarthy3, Sudhakar Godi3, Subhankar Chowdhury4, Pradip Raychaudhuri5 and Raghavendra Rao Vadlamudi6*

Author Affiliations

1 Anthropological Survey of India, Kolkata, West Bengal 700016, India

2 Department of Biomedical Sciences, Sri Ramachandra University, Chennai 600 116, India

3 Department of Human Genetics, Andhra University, Visakhapatnam 530003, India

4 Endocrinology Department, SSKM Hospital, Kolkata, India

5 Calcutta Medical College & Hospital, Kolkata, India

6 Department of Anthropology, University of Delhi, North Campus, Delhi 110 007, India

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Journal of Biomedical Science 2013, 20:12  doi:10.1186/1423-0127-20-12

Published: 27 February 2013



Several studies have demonstrated a fundamental role for the HLA in the susceptibility of, or protection to, type 1 diabetes mellitus (T1DM). However, this has not been adequately studied in Asian Indian populations. To assess the frequency of HLA class II (DPA1, DPB1, DQA1, DQB1 and DRB1) associated to susceptibility or protection toT1DM in a Bengali population of India with diabetes.


Single nucleotide polymorphism study. The HLA genotyping was performed by a polymerase chain reaction followed by their HLA-DP, DQ, and DRB1 genotypes and haplotypes by sequencing method. The results are studied by Plink software. The χ2 tests were used for the inferential statistics. To our knowledge, this study is the first of a kind which has attempted to check the HLA association with T1DM by SNPs analysis. The study recruited 151 patients with T1DM and same number of ethno-linguistic, sex matched non-diabetic controls. The present study found a significant SNP rs7990 of HLA-DQA1 (p = 0.009) negative correlation, again indicating that risk from HLA is considerably more with T1DM.


This study demonstrates that the HLA class-II alleles play a major role in genetic basis of T1DM.

HLA; T1DM; SNP; India; Haplotyping; Alleles