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

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...

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Vydané v:The Journal of surgical research Ročník 203; číslo 1; s. 91 - 94
Hlavní autori: Gunadi, Dwihantoro, Andi, Iskandar, Kristy, Makhmudi, Akhmad, Rochadi
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Elsevier Inc 01.06.2016
Predmet:
Amplified Fragment Length Polymorphism Analysis
Case-Control Studies
Common variant
Female
Genetic Markers
Genotype
Genotyping Techniques
Hirschsprung
Hirschsprung Disease - diagnosis
Hirschsprung Disease - genetics
Humans
Indonesia
Male
PCR-RFLP
Polymorphism, Restriction Fragment Length
Proto-Oncogene Proteins c-ret - genetics
RET
Risk Assessment
rs2435357
TaqMan
RET
Common variant
TaqMan
rs2435357
PCR-RFLP
Hirschsprung
Indonesia
ISSN:0022-4804, 1095-8673
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Shrnutí: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. 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. 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 × 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 (τ) of 0.87 (P = 1.5 × 10−6). The PCR-RFLP method is reliable and affordable for genotyping of RET rs2435357 polymorphism in developing countries. Our results strengthen the proof that the RET rs2435357 variant is a genetic risk for HSCR in Indonesia.
Bibliografia:ObjectType-Article-1
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ISSN:0022-4804
1095-8673
DOI:10.1016/j.jss.2016.02.039