Accuracy of polymerase chain reaction-restriction fragment length polymorphism for RET rs2435357 genotyping as Hirschsprung risk

被引:15
|
作者
Gunadi [1 ]
Dwihantoro, Andi [1 ]
Iskandar, Kristy [2 ]
Makhmudi, Akhmad [1 ]
Rochadi [1 ]
机构
[1] Univ Gadjah Mada, Dr Sardjito Hosp, Fac Med, Pediat Surg Div,Dept Surg, Jl Kesehatan 1, Yogyakarta 55281, Indonesia
[2] Univ Gadjah Mada, UGM Hosp, Fac Med, Dept Child Hlth, Yogyakarta, Indonesia
关键词
Hirschsprung; RET; rs2435357; Common variant; PCR-RFLP; TaqMan; Indonesia; PCR ASSAY; DISEASE; COMMON; RFLP; GENE;
D O I
10.1016/j.jss.2016.02.039
中图分类号
R61 [外科手术学];
学科分类号
摘要
Background: Recently, the common RET rs2435357 variant has been shown to be strongly related to Hirschsprung disease (HSCR) in the Indonesian population. This association study was conducted in developed areas using high-throughput TaqMan polymerase chain reaction (PCR) assay. Although the TaqMan method is less time-consuming, it requires a special more expensive PCR machine and a highly skilled analyst. In this study, we analyzed the usefulness of the PCR-restriction fragment length polymorphism (RFLP) method for genotyping RET rs2435357 polymorphism in Indonesian HSCR patients given the limitation of resource allocation for more expensive technologies. Materials and methods: We compared our previous genotyping results of RET rs2435357 in 53 HSCR patients and 86 controls using the TaqMan PCR assay with the PCR-RFLP technique. Furthermore, we included an additional 40 HSCR patients and 50 controls and subsequently genotyped all subjects using the PCR-RFLP method. Results: Compared with our previous genotyping data of RET rs2435357 using the TaqMan PCR assay, the PCR-RFLP method indicated 100% concordant results. The overall accuracy of the PCR-RFLP for RET rs2435357 genotyping was 100%. In addition, case-control analysis demonstrated that RET rs2435357 is significantly correlated with HSCR (P = 2.2 x 10(-13)) with an odds ratio of 5.1 (95% confidence interval = 3.2-8.1). The transmission disequilibrium test revealed that risk allele (T) at rs2435357 is significantly overtransmitted to probands at a transmission rate (tau) of 0.87 (P = 1.5 x 10(-6)). Conclusions: The PCR-RFLP method is reliable and affordable for genotyping of RET rs2435357 polymorphismin developing countries. Our results strengthen the proof that the RET rs2435357 variant is a genetic risk for HSCR in Indonesia. (C) 2016 Elsevier Inc. All rights reserved.
引用
收藏
页码:91 / 94
页数:4
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