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IL12B SNPs and copy number variation in IL23R gene associated with susceptibility to leprosy
  1. Shafat Ali1,
  2. Amit Kumar Srivastava1,
  3. Rupali Chopra1,
  4. Shweta Aggarwal1,
  5. Vijay Kumar Garg3,
  6. Sambit Nath Bhattacharya4,
  7. Rameshwar Nath Koul Bamezai1,2
  1. 1National Centre of Applied Human Genetics, School of life Sciences, Jawaharlal Nehru University, New Delhi, India
  2. 2SMVDU, Katra, Jammu, J&K
  3. 3Department of Dermatology and Sexually Transmitted Diseases, Maulana Azad Medical College, Lok Nayak Jai Prakash Hospital, New Delhi, India
  4. 4Department of Dermatology and Venereology, University College of Medical Sciences and GTB Hospital, New Delhi, India
  1. Correspondence to Dr Rameshwar Nath Koul Bamezai, National Centre of Applied Human Genetics, School of life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; bame0200{at}mail.jnu.ac.in

Abstract

Background Genome-wide studies have identified both human leucocyte antigen (HLA) and non-HLA regions in association with leprosy. Involvement of novel functional loci within these regions has been proposed by us earlier.

Methods We investigated the role of 23 single nucleotide polymorphisms (SNPs) in IL12B and IL12RB2 in a total of 2345 individuals from India, using MassArray platform, along with the copy number variations in IL23R, IL12RB2 and IL10 genes in a representative set of 257 individuals, using real-time PCR.

Results SNP rs2853694 in IL12B gene (AA vs AC+CC, p=2.6E-04, OR=1.42 (1.17–1.70)) showed an association with leprosy. Pairwise interaction analysis followed by combined analysis of multiple SNPs identified that IL12B, TNF and BTNL2-DRA inter-genic SNPs provided a major risk towards leprosy (p=2.6E-08, OR=3.94 (2.43–6.38)), showing a further increase (p=3.6E-14) for combined risk genotype interactions. On the other hand, IL12B, BAT1, NFKBIL1 and LTA SNPs together showed a disposition towards protection (p=0.000011, OR=0.32 (0.19–0.53)) with a further increase (p=6.38E-10) for combined protective genotype-interactions. Copy number variation analysis showed an increased copy number of the IL23R gene (PB=36.4%, controls=20.2%; p=0.026) associated with the pauci-bacillary form of leprosy, which correlated with a trend towards enhanced expression in memory T cells in a preliminary observation.

Conclusions The observations made here highlight the importance of interaction between specific genetic backgrounds of immune response related genes in the outcome of Mycobacterium leprae infection.

  • Complex traits
  • Genetic epidemiology
  • Infectious Diseases
  • Copy-number
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