• Estimation haplotype frequency of XV-2c, KM.19, T854T, and TUB18 markers at the CFTR gene in Khorasan Razavi province of Iran
  • Tayebeh Hamzehloei,1,* Aida Gholoobi,2 Keyvan Karimi,3
    1. Dr Tayebeh Hamzehloei, Mashhad University of medical sciences, Genetics department, Mashhad-Iran.
    2. Mashhad University of medical sciences, Genetics department, Mashhad-Iran.
    3. Mashhad University of medical science, Pediatrics department. Mashhad-Iran.


  • Introduction: Haplotype phasing is an approach for the carrier detection and prenatal diagnosis of genetic diseases like cystic fibrosis (CF), an autosomal recessive disorder, in a more convenient manner. The CFTR gene region contains several linked polymorphic markers to detect CF. Therefore, in this research, we investigated the efficiency of XV2c-KM19-T854T-TUB18 haplotype phasing in 14 nuclear families as CF cases and 75 unrelated healthy individuals as the controls referred to Mashhad University of Medical Sciences teaching hospitals in Northeastern IRAN.
  • Methods: We collected blood samples from 14 nuclear families as cases and 75 unrelated individuals as the controls. Then we extracted genomic DNA using the salting-out procedure. We genotyped four markers of XV-2c, KM19, T854T, and TUB18 by the PCR-RFLP method. We calculated haplotype frequency using FBAT and PHASE (Haplotype frequency estimation computer software).
  • Results: We designated the results of genotyping markers as follows: the digested and undigested alleles were termed number 1 and number 2, respectively. For each haplotype, each four-digit number represents the XV-2c, KM19, T854T, and TUB18 markers, respectively. Among the 15 estimated haplotypes identified for four biallelic markers in each case and control group, five haplotypes [2122, 1222, 2222, 2212, 1111] showed a frequency of more than 5% based on the FBAT program. Besides, nine haplotypes [2122, 1222, 2222, 2212, 1122, 1221, 1211, 1212, 2221] showed higher frequency (≥5%) based on PHASE program. Furthermore, except for the XV-2c marker, from all included polymorphisms of this study, only allele two was seen as a dominant allele in Khorasan Razavi population.
  • Conclusion: This case-control study showed that KM19 has the highest degrees of heterozygosity among cases; therefore, it may be more reliable when compared to other markers. We calculated its p-value as 0.03466125 based on the χ2 test for this marker which indicates a significant difference between cases and controls. Therefore in this study, we found KM19 a better indicator for genetic evaluations when compared to others. However, a combination of XV2c-KM19-T854T-TUB18 could be helpful.­­ This investigation showed five informative haplotypes [2122,1222,2222,2212,1111], which could be valuable in performing carrier and prenatal diagnoses of the CFTR gene mutations in the Khorasan Razavi population. However, investigation for other potentially linked markers to the CFTR gene; is recommended to establish the best possible diagnostic approach.
  • Keywords: Cystic fibrosis (CF), Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), Linkage Analysis.