Evaluation of Promega PowerSeq™ Auto/Y systems prototype on an admixed sample of Rio de Janeiro, Brazil: Population data, sensitivity, stutter and mixture studies
“…Our results were confirming those of [6,66] who reported flanking region SNPs at TPOX, whereas [69] only observed sequence variation at TPOX within the repeat region. In line with earlier studies, no additional sequence variation was found for D10S1248 [40,41,49,66,71], Penta E [40], and D22S1045 [40,42,66] (Table 3).…”
Section: Sequence Variationsupporting
confidence: 92%
“…Interestingly, we observed sequence variation at TPOX (Table S1, Table S6, Figure S6). This differs from numerous earlier studies [40-42, 49, 70-72] but is consistent with three reports [6,66,69] that recorded sequence variation at TPOX. Our results were confirming those of [6,66] who reported flanking region SNPs at TPOX, whereas [69] only observed sequence variation at TPOX within the repeat region.…”
Section: Sequence Variationsupporting
confidence: 91%
“…The majority of STRs included in the PowerSeq 46GY panel showed mean stutter ratios ranging from 10 to 15% for both categories (Table 2). Stutters appeared to be generally higher for MPS-based STR genotyping than for CE-based kits [46,47,63] (Table 2), which is in line with earlier reports [45,[64][65][66]. Rarely, we observed stutter values exceeding 20% (Table 2).…”
Here, we present the results from a population study that evaluated the performance of massively parallel sequencing (MPS) of short tandem repeats (STRs) with a particular focus on DNA intelligence databasing purposes. To meet this objective, 247 randomly selected reference samples, earlier being processed with conventional capillary electrophoretic (CE) STR sizing from the Austrian National DNA Database, were reanalyzed with the PowerSeq 46Y kit (Promega). This sample set provides MPS-based population data valid for the Austrian population to increase the body of sequence-based STR variation. The study addressed forensically relevant parameters, such as concordance and backward compatibility to extant amplicon-based genotypes, sequence-based stutter ratios, and relative marker performance. Of the 22 autosomal STR loci included in the PowerSeq 46GY panel, 99.98% of the allele calls were concordant between MPS and CE. Moreover, 25 new sequence variants from 15 markers were found in the Austrian dataset that are yet undescribed in the STRSeq online catalogue and were submitted for inclusion. Despite the high degree of concordance between MPS and CE derived genotypes, our results demonstrate the need for a harmonized allele nomenclature system that is equally applicable to both technologies, but at the same time can take advantage of the increased information content of MPS. This appears to be particularly important with regard to database applications in order to prevent false exclusions due to varying allele naming based on different analysis platforms and ensures backward compatibility.
“…Our results were confirming those of [6,66] who reported flanking region SNPs at TPOX, whereas [69] only observed sequence variation at TPOX within the repeat region. In line with earlier studies, no additional sequence variation was found for D10S1248 [40,41,49,66,71], Penta E [40], and D22S1045 [40,42,66] (Table 3).…”
Section: Sequence Variationsupporting
confidence: 92%
“…Interestingly, we observed sequence variation at TPOX (Table S1, Table S6, Figure S6). This differs from numerous earlier studies [40-42, 49, 70-72] but is consistent with three reports [6,66,69] that recorded sequence variation at TPOX. Our results were confirming those of [6,66] who reported flanking region SNPs at TPOX, whereas [69] only observed sequence variation at TPOX within the repeat region.…”
Section: Sequence Variationsupporting
confidence: 91%
“…The majority of STRs included in the PowerSeq 46GY panel showed mean stutter ratios ranging from 10 to 15% for both categories (Table 2). Stutters appeared to be generally higher for MPS-based STR genotyping than for CE-based kits [46,47,63] (Table 2), which is in line with earlier reports [45,[64][65][66]. Rarely, we observed stutter values exceeding 20% (Table 2).…”
Here, we present the results from a population study that evaluated the performance of massively parallel sequencing (MPS) of short tandem repeats (STRs) with a particular focus on DNA intelligence databasing purposes. To meet this objective, 247 randomly selected reference samples, earlier being processed with conventional capillary electrophoretic (CE) STR sizing from the Austrian National DNA Database, were reanalyzed with the PowerSeq 46Y kit (Promega). This sample set provides MPS-based population data valid for the Austrian population to increase the body of sequence-based STR variation. The study addressed forensically relevant parameters, such as concordance and backward compatibility to extant amplicon-based genotypes, sequence-based stutter ratios, and relative marker performance. Of the 22 autosomal STR loci included in the PowerSeq 46GY panel, 99.98% of the allele calls were concordant between MPS and CE. Moreover, 25 new sequence variants from 15 markers were found in the Austrian dataset that are yet undescribed in the STRSeq online catalogue and were submitted for inclusion. Despite the high degree of concordance between MPS and CE derived genotypes, our results demonstrate the need for a harmonized allele nomenclature system that is equally applicable to both technologies, but at the same time can take advantage of the increased information content of MPS. This appears to be particularly important with regard to database applications in order to prevent false exclusions due to varying allele naming based on different analysis platforms and ensures backward compatibility.
“…Besides these eight inconsistencies for the same locus, full concordance was obtained with 40 ng, 10 ng, and 2 ng of DNA both between replicates and between laboratories. In comparison, forensic genetic laboratories routinely generate DNA profiles from 100 to 200 pg DNA using commercial or in-house developed assays 31 – 34 . Figure 1 Sensitivity study.…”
Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.
“…STR flanking region sequence variation has been explored [ 346 ] and reports of population data and sequence variation were published for samples from India [ 347 ], France [ 348 ], China [ 349 , 350 ], Korea [ 351 ], Brazil [ 352 ], Tibet [ 353 ], and the United States [ 354 ].…”
Section: Emerging Technologies Research Studies and Other Topicsmentioning
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
