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Massively parallel sequencing (MPS) technology has been recently introduced in forensic field. MiSeq FGx™ forensic genomics system (Illumina, Inc., San Diego) is the designed work flow for forensic DNA work. The system comprised of DNA library preparation kit, MPS instrument and data analysis software. In this study, 30 DNA samples of Thai population were sequenced using MiSeq FGx™ forensic genomics system. Twenty-seven loci autosomal STRs and 94 identity informative SNPs were used to analyzed. The data quality was observed following to these parameters; depth of coverage (DoC), allele coverage ratios (ACRs) and sequence coverage ratios (SCRs). For STR markers, the average DoC ranges were 523-11,534 reads per locus, average ACRs ranges were 0.81-0.95 (excluded D22S1045 with average ACRs of 0.28) and average SCRs ranges were 0.83-0.99. For SNP markers, the average DoC ranges were 46-4012 reads per locus, average ACRs ranges were 0.54-0.97 (excluded rs6955448 and rs338882 with average ACRs of 0.40 and 0.49 respectively). Some of SNP markers such as rs6955448, rs338882 and rs4530059 showed a high number of imbalanced individual's sample. Fourteenth of 30 samples showed low coverage threshold at rs1736442. Intra-STR allele sequence variants were identified in 10 loci from 12 of 30 samples. Finally, the STRs profiling from MiSeq FGx™ forensic genomics system revealed a concordant result with capillary electrophoresis (CE) data (using Investigator ® ID plex Plus Kit -QIAGEN and PowerPlex ® 16 System -Promega) in Thai population.

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