RESEARCH ARTICLE Contribution of susceptibility locus at HLA class I region and environmental factors to occurrence of nasopharyngeal cancer in Northeast India Meena Lakhanpal & Laishram Chandreshwor Singh & Tashnin Rahman & Jagnnath Sharma & M. Madhumangal Singh & Amal Chandra Kataki & Saurabh Verma & Pradeep Singh Chauhan & Y. Mohan Singh & Saima Wajid & Sujala Kapur & Sunita Saxena Received: 1 October 2014 /Accepted: 4 December 2014 # International Society of Oncology and BioMarkers (ISOBM) 2014 Abstract High incidence of nasopharyngeal carcinoma (NPC) has been reported from China, Southeast Asia and Northeast (NE) region of India. Populations at geographic regions having higher incidence of NPC display human leu- kocyte antigen (HLA) distribution patterns different from areas having low incidence. The current study has investigated the contribution of environmental risk factors and ethnic var- iation of microsatellite markers in HLA region for the high incidence of NPC in NE India. Genotyping of HLA region using 33 microsatellite markers by fragment length analysis was done in 220 study subjects (120 NPC patients and 100 healthy controls). Association analysis showed two adjacent microsatellite markers HL003 (allele 121) and D6S2704 (al- lele 218) in the HLA class I region having association with high risk of NPC while allele 127 of HL003 and allele 255 of D6S2678 conferred a protective effect. The environmental factors mainly use of firewood (odds ratio (OR)=3.797385, confidence interval (CI)=1.97–7.30, P <0), living in mud house (OR=3.46, CI=1.19–10.08, P =0.022) and consump- tion of alcohol (OR=2.11, CI=1.02–4.37, P =0.043) were found as major risk factors for NPC. Higher-order interaction showed combination of smoked food consumption and fire- wood use for cooking in multifactor dimensionality reduction (MDR) analysis and interaction of non-firewood users, non- ventilated houses and residence in mud houses in classifica- tion and regression tree (CART) analysis as the significant risk factors for NPC. Expression of Epstein–Barr virus (EBV) RNA was found in 92 % (23/25) of NPC cases suggesting its significant role in NPC aetiopathogenesis. This study iden- tified association of NPC with a susceptibility locus in the HLA class I region which has complex interaction with viral DNA and environmental factors. Keywords Nasopharyngeal cancer . HLA region . Microsatellite markers . Epstein-Barr virus . Northeast India Introduction Nasopharyngeal carcinoma (NPC) is a rare malignancy with distinct racial and geographic distribution affecting mainly South China, Southeast Asia, Middle east countries, North America and Eskimos in the Arctic [1, 2]. It is one of the most misdiagnosed and poorly understood disease due to vague clinical presentation. In addition, the fossa of Rosenmuller (lateral nasopharyngeal recess), which is the most common site for NPC, is difficult to examine clinically which leads to further delay in diagnosis. The highest incidence of NPC has been reported in Guangdong and Guangxi region of China Electronic supplementary material The online version of this article (doi:10.1007/s13277-014-2942-5) contains supplementary material, which is available to authorized users. M. Lakhanpal : L. C. Singh : S. Verma : P. S. Chauhan : S. Kapur : S. Saxena (*) Safdarjang Hospital Campus, Indian Council of Medical Research, National Institute of Pathology, New Delhi 110029, India e-mail: sunita_saxena@yahoo.com T. Rahman : J. Sharma : A. C. Kataki Dr. B. Barooah Cancer Institute, Guwahati 781 016, Assam, India M. M. Singh : Y. M. Singh Regional Institute of Medical Science, Imphal 795004, Manipur, India S. Wajid Department of Biotechnology, Jamia Hamdard, New Delhi 110062, India Tumor Biol. DOI 10.1007/s13277-014-2942-5