Considering a performance test of forensic genomics system on massively parallel sequencing technology

Abstract

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.

The concordance of length- and sequence-based STRs used in forensic markers with guidance for practice

“…In Fig 2, dropout, stutter interference and low read count sign categories were the main cause for disagreed results between these two analysis tools. D22S1045 and DYS392 were well-known markers of poor performance in Forenseq® Signature prep kit (Verogen) (3, 7, 20, 21) and a high percentage of dropout was expected. Moreover, in this study a high percentage of dropouts was first reported in Penta E and DYS19.…”

A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution

“…Some of the loci have been highlighted as performing poorly. Many studies have observed high levels of heterozygote imbalance in D22S1045 (Churchill et al, ; Just et al, ; Sukawutthiya, Sathirapatya, & Vongpaisarnsin, ). DYS392 exhibited high amounts of LDO and ADO (Churchill et al, ;Just et al, ; Wendt et al, ), even in libraries with high total read counts.…”

“…Sukawutthiya et al () sequenced 30 Thai population blood samples with DPMB from 1 FTA punch. Each sample had a call rate for all loci of between 90 and 100%.…”

“…Two studies have compared the performance of the Fore-nSeq™ SNP results to the HID-Ion AmpliSeq™ Identity Panel sequenced on the Ion PGM (Apaga et al, 2017;Churchill et al, 2016) and found the accuracy rate to be 100%, the only differences due to heterozygote imbalance and ADO. Sukawutthiya et al (2017) sequenced 30 Thai population blood samples with DPMB from 1 FTA punch. Each sample had a call rate for all loci of between 90 and 100%.…”