Objective: To set up a new method, which is sensitive, low cost, rapid and suitable for clinical application for FTO gene rs9930506 variant genotyping basing on high resolution melting (HRM) platform, and to preliminarily put into practice in susceptibility analysis for metabolic syndrome (MS) in Beijing.
Methods: Unlabelled probe with C3-spacer block specific for rs9930506 variant has been designed according to the Refseq from GenBank. With LC-Green plus dye pre-mixed, we scanned the signal for the genotype analysis after PCR amplification and HRM reaction. Restriction fragment length polymorphism (RFLP) and PCR-sequencing methods were designed as 2 control genotyping methods for the evaluation of accuracy and convenience. Afterwards, the HRM-based method was put into practice in metabolic syndrome patients (n = 500) and control groups (n = 500) for rs9930506 genotyping, and primarily study the association between rs9930506 and MS.
Results: All the 3 methods could genotype rs9930506 appropriately, although the 2 control methods seemed to be a little time-inefficient. The call rate of HRM-method was 100% and sampling accuracy reached 99.3% according to sequencing results. In the MS group, AA, AG and GG genotypes were found in 290, 185 and 25 cases, respectively. And in the control group, those were found in 344, 138 and 18 cases. No genotype distribution difference was detected between control group and HapMap-CHB data (P = 0.520). The genotype distributions were all in Hardy-Weinberg equilibrium in each group. AA genotype of rs9930506 seemed to reduce the risk for MS (OR = 0.626, 95%CI = 0.483 - 0.812).
Conclusions: The AA genotype of rs9930506 variant in FTO might be a protective factor for MS in Beijing population. The susceptibility related genotyping in clinical samples could be more rapid, precise and inexpensive with the development of HRM in genotyping.