A Microfluidic-Based SNP Genotyping Method for Hereditary Hearing-Loss Detection

• Published in: Analytical chemistry (Washington) 2019-05, Vol.91 (9), p.6111-6117
• Main Authors: Lu, Ying, Chen, Shan, Wei, Li, Sun, Lanhua, Liu, Houming, Xu, Youchun
• Format: Article
• Language: English
• Subjects: Analytical chemistry; Chemistry; Contamination; Disease detection; Gene deletion; Gene sequencing; Genetic analysis; Genotyping; Insertion; Microfluidics; Mutation; Single-nucleotide polymorphism
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.9b00652

The genotyping of SNPs (single nucleotide polymorphisms) is a prerequisite for the analysis of many genetic diseases, including hereditary hearing-loss. However, the existing methods for SNP detection suffer from a long detection period, tedious operation, and a high risk of carryover contamination. To address these challenges, a microfluidic chip is constructed for rapid and efficient SNP genotyping by dividing the sample into many independent chambers for Kompetitive Allele Specific PCR in this study. Using this strategy, multiple detection can be easily accomplished and the challenge for the establishment of multiplex PCR is fundamentally overcome. The entire detection can be finished within 2 h in a fully sealed manner with this method, which is quite simple compared to SNaPshot and MassArray. After assessment of the basic performance, this chip was applied to screen 15 mutations, including SNPs and InDels (insertion-deletion markers), that can cover more than 80% of cases of hereditary hearing-loss in China. Over 40 clinical samples were analyzed with this microfluidic chip for SNP genotyping, and the results are consistent with that obtained by Sanger sequencing, demonstrating its practicability and potential in the application of genetic disease detection.