title: Systematic assessment of the performance of illumina's MiSeq FGx™ forensic genomics system.
abstract: This study assesses the performance of Illumina's MiSeq FGx System for forensic genomics by systematically analyzing single source samples, evaluating concordance, sensitivity and repeatability, as well as describing the quality of the reported outcomes. DNA from 16 individuals (9 males/7 females) in nine separate runs showed consistent STR profiles at DNA input ≥400 pg, and two full profiles were obtained with 50 pg DNA input. However, this study revealed that the outcome of a single sample does not merely depend on its DNA input but is also influenced by the total amount of DNA loaded onto the flow cell from all samples. Stutter and sequence or amplification errors can make the identification of true alleles difficult, particularly for heterozygous loci that show allele imbalance. Sequencing of 16 individuals' STRs revealed genetic variations at 14 loci at frequencies suggesting improvement of mixture deconvolution. The STR loci D1S1656 and DXS10103 were most susceptible to drop outs, and D22S1045 and DYS385a-b showed heterozygote imbalance.  Most stutters were typed at TH01 and DYS385a-b, while amplification or sequencing errors were observed mostly at D7S820 and D19S433. Overall, Illumina's MiSeq FGx System produced reliable and repeatable results.  aSTRs showed fewer drop outs than the Y- and X-STRs.
authors.affiliation: Office of Chief Medical Examiner, Department of Forensic Biology, New York, NY, USA.
authors.forename: Nouran
authors.initials: N
authors.lastname: Almalki
authors.affiliation: Office of Chief Medical Examiner, Department of Forensic Biology, New York, NY, USA.
authors.forename: Hoi Yan
authors.initials: HY
authors.lastname: Chow
authors.affiliation: Office of Chief Medical Examiner, Department of Forensic Biology, New York, NY, USA.
authors.forename: Vishakha
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Office of Chief Medical Examiner, Department of Forensic Biology, New York, NY, USA.
authors.forename: Katie
authors.initials: K
authors.lastname: Hart
authors.affiliation: Office of Chief Medical Examiner, Department of Forensic Biology, New York, NY, USA.
authors.forename: Donald
authors.initials: D
authors.lastname: Siegel
authors.affiliation: Office of Chief Medical Examiner, Department of Forensic Biology, New York, NY, USA.
authors.forename: Elisa
authors.initials: E
authors.lastname: Wurmbach
mesh_terms: D000483:Alleles; D004247:DNA / Q000032:analysis*; D016172:DNA Fingerprinting / Q000379:methods*; D019075:Electrophoresis, Capillary / Q000379:methods; D005260:Female; D053803:Forensic Genetics; D014644:Genetic Variation; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D017421:Sequence Analysis
chemical_list: D004247:DNA
keywords: Massively parallel sequencing; Sensitivity; Short tandem repeats