The QIAGEN 140-locus single-nucleotide polymorphism (SNP) panel for forensic identification using massively parallel sequencing (MPS): an evaluation and a direct-to-PCR trial

© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Massively parallel sequencing (MPS) of identity informative single-nucleotide polymorphisms (IISNPs) enables hundreds of forensically relevant markers to be analysed simultaneously. Generating DNA sequence data enables more detailed analysis including identification of sequence variations between individuals. The GeneRead DNAseq 140 IISNP MPS panel (QIAGEN) has been evaluated on both the MiSeq (Illumina) and Ion PGM™ (Applied Biosystems) MPS platforms using the GeneRead DNAseq Targeted Panels V2 library preparation workflow (QIAGEN). The aims of this study were to (1) determine if the GeneRead DNAseq panel is effective for identity testing by assessing deviation from Hardy-Weinberg (HWE) and pairwise linkage equilibrium (LE); (2) sequence samples with the GeneRead DNAseq panel on the Ion PGM™ using the QIAGEN workflow and assess specificity, sensitivity and accuracy; (3) assess the efficacy of adding biological samples directly to the GeneRead DNAseq PCR, without prior DNA extraction; and (4) assess the effect of varying coverage and allele frequency thresholds on genotype concordance. Analyses of the 140 SNPs for HWE and LE using Fisher’s exact tests and the sequential Bonferroni correction revealed that one SNP was out of HWE in the Japanese population and five SNP combinations were commonly out of LE in 13 of 14 populations. The panel was sensitive down to 0.3125 ng of DNA input. A direct-to-PCR approach (without DNA extraction) produced highly concordant genotypes. The setting of appropriate allele frequency thresholds is more effective for reducing erroneous genotypes than coverage thresholds

The structure and properties of silver-doped phosphate-based glasses

An undoped and two silver-doped (0, 3 and 5 mol% Ag) phosphate glass compositions were investigated for their structure and properties. These compositions had in a previous study been investigated for their antimicrobial properties, and were found to be extremely potent at inhibiting the micro-organisms tested. Thermal, X-ray diffraction (XRD), nuclear magnetic resonance (NMR) and X-ray absorption Near Edge Structure (XANES) studies were used to elucidate the structure of the compositions investigated, whilst degradation and ion release studies were conducted to investigate their properties. No significant differences were found between the T (g) values of the silver containing glasses, while XRD analysis revealed the presence of a NaCa(PO3)(3) phase. NMR showed the dominance of Q(2) species, and XANES studies revealed the oxidation state of silver to be in the +1 form. No correlation was seen between the degradation and cation release profiles observed, and the P3O93 anion was the highest released anionic species, which correlated well with the XRD and NMR studies. Overall, it was ascertained that using Ag2SO4 as a precursor, and producing compositions containing 3 and 5 mol% Ag, the levels of silver ions released were within the acceptable cyto/biocompatible range

Monoclonal antibodies inhibit prion replication and delay the development of prion disease

Prion diseases such as Creutzfeldt-Jakob disease (CJD) are fatal, neuro-degenerative disorders with no known therapy. A proportion of the UK population has been exposed to a bovine spongiform encephalopathy-like prion strain and are at risk of developing variant CJD. A hallmark of prion disease is the transformation of normal cellular prion protein (PrP(C)) into an infectious disease-associated isoform, PrP(Sc). Recent in vitro studies indicate that anti-PrP monoclonal antibodies with little or no affinity for PrP(Sc) can prevent the incorporation of PrP(C) into propagating prions. We therefore investigated in a murine scrapie model whether anti-PrP monoclonal antibodies show similar inhibitory effects on prion replication in vivo. We found that peripheral PrP(Sc) levels and prion infectivity were markedly reduced, even when the antibodies were first administered at the point of near maximal accumulation of PrP(Sc) in the spleen. Furthermore, animals in which the treatment was continued remained healthy for over 300 days after equivalent untreated animals had succumbed to the disease. These findings indicate that immunotherapeutic strategies for human prion diseases are worth pursuing