Detection of single nucleotide polymorphisms (SNP) in equine coat color genes using SNaPshot TM multiplex kit or pluronic F‐108 tri‐block copolymer and capillary electrophoresis

Sanger sequencing and deconvolution of polyclonal infections: a quantitative approach to monitor drug-resistant Plasmodium falciparum

BACKGROUND

Anti-malarial drug resistance in Plasmodium falciparum is a major public health problem in malaria-endemic regions. Although various technical improvements in sequencing methods have been introduced to identify SNPs, the conventional approach with current tools does not discriminate mixed infections, and thus can be improved for more sensitive surveillance of anti-malarial resistance to better inform control strategies.

METHODS

We developed a computational approach for deconvolution of chromatograms generated by standard Sanger sequencing of PCR amplicons in order to quantify molecular marker variants of anti-malarial drug resistance genes [Plasmodium falciparum dihydropteorate synthase (Pfdhps) and P. falciparum dihydrofolate reductase (Pfdhfr)]. We validated this computational approach using mixtures of V1/S and FCR3 at varying proportions between 0 and 100%, then applied it to field samples collected in Doneguebougou, Mali in 2018. We determined the mean fraction of resistance alleles in individual samples, as well as the prevalence of infections carrying resistant parasites.

FINDINGS

We observed a highly significant correlation between the predicted and measured proportions of V1/S and FCR3 alleles in mixed laboratory samples (all p < 0.001). Among field samples, the mean fraction of resistant Pfdhps alleles was 4.7% 431V, 95.9% 436F/A, 49.9% 437G, 0.0% 540E, 1.2% 581G and 1.5% 613S/T; corresponding prevalences were 50.0%, 100%, 72.5%, 0.0%, 25.0%, and 12.5%, respectively. The mean fraction of resistant Pfdhfr alleles was 0.6% 16V, 11.1% 50R, 89.0% 51I, 98.3% 59R, 74.7% 108T/N, 8.6% 140L and 8.7% 164L; corresponding prevalences were 12.5%, 75.0%, 100%, 100%, 100%, 50.0%, and 28.6%, respectively. We identified two new point mutations on the Pfdhps gene at codons D484T and D545N.

INTERPRETATION

Computational deconvolution of sequencing chromatograms can discriminate varying proportions of antimalarial drug-sensitive versus -resistant alleles. This cost-effective and quantitative variant-sequencing approach will be useful for population-based surveys that characterize mixed infections at the individual level to survey known and unknown mutations in P. falciparum drug-resistance genes.

FUNDING

This work was supported by the Division of Intramural Research of the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH). HM was supported by the African Postdoctoral Training Initiative (APTI) Fellowship program jointly managed by the US NIH, The African Academy of Sciences (AAS) and Bill & Melinda Gates Foundation (BMGF); Grant Reference Number: APTI-18-01.

A review of electrophoretic separations in temperature-responsive Pluronic thermal gels

Gel electrophoresis is a ubiquitous bioanalytical technique used in research laboratories to validate protein and nucleic acid samples. Polyacrylamide and agarose have been the gold standard gel materials for decades, but an alternative class of polymer has emerged with potentially superior performance. Pluronic thermal gels are water-soluble polymers that possess the unique ability to undergo a change in viscosity in response to changing temperature. Thermal gels can reversibly convert between low-viscosity liquids and high-viscosity solid gels using temperature as an adjustable parameter. The properties of thermal gels provide unmatched flexibility as a dynamic separations matrix to measure analytes ranging from small molecules to cells. This review article describes the physical and chemical properties of Pluronic thermal gels to provide a fundamental overview of polymer behavior. The performance of thermal gels is then reviewed to highlight their applications as a gel matrix for electrokinetic separations in capillary, microfluidic, and slab gel formats. The use of dynamic temperature-responsive gels in bioanalytical separations is an underexplored area of research but one that holds exciting potential to achieve performance unattainable with conventional static polymers.

Resolving human DNA mixtures with F-108 polymer and capillary electrophoresis single-strand conformational polymorphism analysis

Current technologies have increased the sensitivity for analyzing forensic DNA samples, especially those considered "touch samples." Because of this, there has been an increase in the number of forensic mixtures-two or more contributors within a single sample-submitted to the crime laboratories. Therefore, the need to resolve these mixtures has increased as well. Several technologies are currently utilized, but many of them are time consuming and do not resolve the entire profile. Therefore, CE-Single-Strand Conformational Polymorphisms coupled with the Pluronic F-108 polymer was assessed for its ability to resolve human forensic mixtures. This technique has been able to detect sequence variation, such as single nucleotide polymorphism in short tandem repeat loci, such as D7S820 and vWA. Samples were first analyzed with the Performance Optimized Polymer-7, and mixtures created from samples that shared alleles. These samples were sequenced to detect single base-pair mutations and evaluated with the F-108 and CE-Single Strand Conformational Polymorphism analysis. Results from this study indicated the method would serve as a valuable screening tool to detect base sequence variation between individuals when they share alleles in a mixture and before using Massive Parallel Sequencing technology to distinguish which bases differ.