A closer look at Verogen's Forenseq™ DNA Signature Prep kit autosomal and Y-STR data for streamlined analysis of routine reference samples.

Massively parallel sequencing (MPS) provides forensic DNA laboratories an option to overcome the limitations associated with CE and current STR assays. Verogen's MPS ForenseqTM DNA Signature kit concomitantly amplifies 27 autosomal, 7 X-, and 24 Y-STRs. In addition, 94 identity, 56 ancestry, and 22 phenotypic-informative SNPs are included for a total of over 200 markers in one multiplex. An internal validation of this platform was conducted using reference samples to investigate whether the Forenseq™ DNA Signature Prep kit, specifically primer panel B, has the capability to provide consistent and accurate typing/sequencing data. The data presented in this report is limited to that corresponding to autosomal and Y-STRs. Results suggest that the system can consistently generate accurate genotyping data when up to 40 high-quality, high-quantity (i.e. 1 ng) single source samples are pooled into a sequencing reaction. The results generated were used to determine appropriate analysis parameters and thresholds for streamlined data interpretation of reference samples.

Development and validation of a Luminex assay for detection of a predictive biomarker for PROSTVAC-VF therapy.

Cancer therapies can provide substantially improved survival in some patients while other seemingly similar patients receive little or no benefit. Strategies to identify patients likely to respond well to a given therapy could significantly improve health care outcomes by maximizing clinical benefits while reducing toxicities and adverse effects. Using a glycan microarray assay, we recently reported that pretreatment serum levels of IgM specific to blood group A trisaccharide (BG-Atri) correlate positively with overall survival of cancer patients on PROSTVAC-VF therapy. The results suggested anti-BG-Atri IgM measured prior to treatment could serve as a biomarker for identifying patients likely to benefit from PROSTVAC-VF. For continued development and clinical application of serum IgM specific to BG-Atri as a predictive biomarker, a clinical assay was needed. In this study, we developed and validated a Luminex-based clinical assay for measuring serum IgM specific to BG-Atri. IgM levels were measured with the Luminex assay and compared to levels measured using the microarray for 126 healthy individuals and 77 prostate cancer patients. This assay provided reproducible and consistent results with low %CVs, and tolerance ranges were established for the assay. IgM levels measured using the Luminex assay were found to be highly correlated to the microarray results with R values of 0.93-0.95. This assay is a Laboratory Developed Test (LDT) and is suitable for evaluating thousands of serum samples in CLIA certified laboratories that have validated the assay. In addition, the study demonstrates that discoveries made using neoglycoprotein-based microarrays can be readily migrated to a clinical assay.