A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types

• Published in: Biosensors & bioelectronics Vol. 115; pp. 70 - 76
• Main Authors: Liu, Xiaonan, Zhang, Chao, Zhao, Mengye, Liu, Kewu, Li, Hang, Li, Ningning, Gao, Linlin, Yang, Xuemin, Ma, Ting, Zhu, Juanli, Hui, Wenli, Hua, Kai, Cui, Yali
• Format: Journal Article
• Language: English
• Published: England Elsevier B.V 15.09.2018
• Subjects: Aldehyde Dehydrogenase, Mitochondrial - genetics; Aldehyde Dehydrogenase, Mitochondrial - isolation & purification; ALDH2; Biosensing Techniques; Genotype; Genotyping Techniques; Humans; Isothermal amplification; Methylenetetrahydrofolate Reductase (NADPH2) - genetics; Methylenetetrahydrofolate Reductase (NADPH2) - isolation & purification; MTHFR; Multifarious sample types; Point-of-Care Systems; Polymorphism, Single Nucleotide - genetics; Single nucleotide polymorphism; MTHFR; Multifarious sample types; Single nucleotide polymorphism; ALDH2; Isothermal amplification
• ISSN: 0956-5663; 1873-4235
• DOI: 10.1016/j.bios.2018.05.021

Genotyping of single nucleotide polymorphisms (SNPs) in point-of-care (POC) settings could be further improved through simplifying the treatment of samples. In this study, we devised an accurate, rapid and easy-to-use SNP detection system based on direct loop-mediated isothermal amplification (LAMP) without DNA extraction, known as Direct-LAMP. Samples from various sources (including whole blood, dried blood spot, buccal swab and saliva), treated with NaOH, can be used directly in amplification. The turnaround time was about 30 min from sample collection to provision of results. The accuracy was evaluated by assessing the polymorphisms of methylenetetrahydrofolate reductase (MTHFR) C677T and aldehyde dehydrogenase-2 (ALDH2) Glu504Lys, which are better known for their critical role in folate and ethanol metabolism, respectively. Completely consistent genotyping results reveal that Direct-LAMP is generally concordant with sequencing. This system can serve as a very promising platform in the fields of disease predisposition, drug metabolism and personalized medicine. [Display omitted] •Devised a SNP detection system combining DNA amplification directly with LAMP without DNA purification.•Biological samples for the Direct-LAMP system are various.•The genotyping result can be provided within 30 min.•The Direct-LAMP system can serve as a promising POCT for genotyping.