Remarkable variation in the informativeness of RFLP markers linked
to hemophilia B locus in Indian population groups: Implication in the strategy
for carrier detection
Affiliations: Human Genetics and Genomics and Division, Indian
Institute of Chemical Biology, Kolkata, India | Genome Research Group, Centre for Cellular and
Molecular Biology, Hyderabad, India | Indian Statistical Institute, Kolkata, India
Note: [] Corresponding author: Dr. Kunal Ray, Human Genetics &
Genomics Division, Indian Institute of Chemical Biology, 4 Raja S. C. Mullick
Road, Jadavpur, Kolkata – 700 032, India. Tel.: +91 33 2473 3491 (or 0492 or
6793); +91 33 2473 5197 (or 2472-3967); E-mail: [email protected],
[email protected]
Abstract: Hemophilia B, an X-linked recessive bleeding disorder, is caused by
heterogeneous mutations in the factor IX (F9) gene. Hence, carriers of the
disease are usually detected by F9 gene linked RFLP analysis. We aimed to test
a set of RFLP markers (DdeI, XmnI, MnlI, TaqI & HhaI), used worldwide
for carrier detection, to estimate its heterozygosity in different population
groups of India, and identify additional single nucleotide polymorphisms (SNPs)
if necessary. A total of 8 population groups encompassing different regions of
India, consisting of 107 unrelated normal females without any history of
hemophilia B in the family and 13 unrelated obligate carriers were recruited in
the study. Regions of F9 gene were amplified by PCR from genomic DNA of the
donors followed by restriction enzyme digestion and/or sequencing as
appropriate. Combined informativeness for the markers varied between 52–86%
among normal females belonging to different geographical locations of India.
Haplotype analysis revealed that the most prevalent haplotype lacked the
restriction sites for all five RFLP markers. Screening regions of F9 gene that
harbor 10 SNPs reported in dbSNP yielded only two SNPs, which increased the
overall informativeness in each population group and heterozygosity in the
obligate carriers for the disease from 38% to 69%. Our data show that
heterozygosity of commonly used RFLP markers is remarkably variable across
different regions of India. Thus prudent selection of the markers based on
specific population groups including usage of additional markers is recommended
for efficient carrier detection.
