Abstract: Objective To introduce a nucleic acid extraction-free processing method for non-invasive samples, combining with high throughput genotyping technology, for large-scale epidemiological monitoring and genetic analysis. Methods Instead of nucleic acid extraction, we lysed saliva/ buccal swabs and captured the target DNA directly to 96-well plate by sandwich hybridization using multiple oligo probes with universal tail sequences. We tested the feasibility of the new assay for saliva and buccal swabs, and evaluated the accuracy，repeatability and reliability by comparing with commercial multiplex SNP assay (iPLEX), for the detection of 23G6PD gene variants known to be at risk for primaquine-induced hemolysis in antimalarial therapy Results In this study, the treatment of non invasive samples was applied to high throughput genotyping, The accuracy of the results was 100% concordant with sequencing ，and better than that of the traditional iPLEX method with blood samples. The results also show that the repeatability and reliability is good. A typical 40 μl saliva or one buccal swab sample is sufficient for running 2 assays. A 384-samples can be processed from sample to result in a 36-hour workflow, with a hands-on time of 2 hours. Conclusions This study represents an efficient and cost-effective approach to multiplex SNP genotyping at population level. It’s among the first to demonstrate saliva and buccal swab’s role for accurate, sensitive and high-throughput DNA analysis, providing a more feasible solution for large scale, preemptive genotyping.

Key words: noninvasive samples, nucleic acid extraction , SNP genotyping