doi: 10.1111/j.1469-1809.2008.00477.x Identification and Characterization of CFTR Gene Mutations in Indian CF Patients N. Sharma 1 , M. Singh 2 , G. Kaur 3 , B. R. Thapa 4 and R. Prasad 1, * 1 Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India-160012 2 Department of Pediatrics, Advanced Pediatric Center, Post Graduate Institute of Medical Education and Research, Chandigarh, India-160012 3 Department of Physiology, Government Medical College and Hospital, Sector-32, Chandigarh, India-160032 4 Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Chandigarh, India-160012 Summary Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This study was performed on Indian CF patients (n = 50) to investigate the spectrum of mutations in the CFTR gene and their association with intragenic and extragenic marker haplotypes. We report identification of 14 previously known and eight novel mutations, namely 3986-3987delC, 876-6del4, 1792InsA, L69H, S158N, Q493L, I530L and E1329Q. The frequency of delta F508 was found to be 27%. Absolute linkage between delta F508 and the KM.19-GATT-TUB9-M470V-T854T haplotype (2-2-1-1-1) predicts a relatively recent appearance of delta F508 in Indian CF patients. Low frequency of delta F508 mutation and detection of eight novel and thirteen rare mutations reflect a heterogeneous spectrum of mutations in Indian CF patients. Failure to detect mutations in 34% of alleles indicates the possible presence of gross deletions involving one or more exons or may indicate the location of the molecular defects in either the noncoding parts of the gene or in the promoter region, which warrants analysis of those regions. Keywords: Cystic fibrosis, CFTR, Delta F508, ARMS PCR, SSCP, Haplotype Introduction Cystic Fibrosis (CF) is an autosomal recessive disease of ex- ocrine tissues characterized by the abnormal transport of ions and fluid across epithelial cell membranes. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are responsible for both classic and atypical presentations of the disease. The CFTR gene, identified about two decades ago (Riordan et al. 1989; Rommens et al., 1989), spans an approximately 240kb region on chro- mosome 7q31.3 (Kerem et al., 1989) and consists of 27 ex- ons (Zielenski et al., 1991). It encodes a membrane protein of 1,480-amino acids that functions as a cAMP-regulated chloride channel in exocrine epithelia (Bear et al., 1992). Over 1,400 sequence variations have been identified in the CFTR gene (http:www.genet.sickkids.on.ca/cftr/). Delta ∗ Corresponding author: Dr. Rajendra Prasad, Professor, Dept. of Biochemistry, Post Graduate Institute of Medical Educa- tion & Research, Chandigarh-160012. Phone:-0172-2755178; mobile# 9914208178; Fax:-91-172-2744401, 2745078. E-mail: fateh1977@yahoo.com F508 is the most common mutation with a frequency of 66% worldwide (Zielenski & Tsui, 1995). The frequencies and type of mutations found in populations vary accord- ing to the geographic and ethnic origin of the population studied. In Turkish CF patients, 36 mutations accounted for 75% of all CF chromosomes, and 41 CF chromosomes re- mained unidentified (Kilinc et al., 2002). Accurate knowl- edge of CF mutations in a specific population provides in- formation for CF prevention programs applicable through heterozygote screening and prenatal diagnosis. Studies performed on Indian patients or patients of In- dian origin report 19% to 44% frequency of the delta F508 mutation (Bowlers et al., 1993; Powers et al., 1996; Kabra et al., 2000); however, the data available on the spectrum of mutations in Indian CF patients is scanty. Haplotype as- sociations have been used to trace the origin and age of different CF mutations worldwide (Morral et al., 1993). There is no information available in this regard from the Indian subcontinent. Therefore, a study was planned both to characterize mutations in the CFTR gene in Indian CF patients and to determine associated intragenic and extra- genic marker haplotypes. 26 Annals of Human Genetics (2009) 73,26–33 C  2008 The Authors Journal compilation C  2008 Blackwell Publishing Ltd/University College London