Locus-specific brackets for reliable typing of Y-chromosome short tandem repeat markers

Short tandem repeat (STR) loci, widely used as genetic markers in disease diagnostic studies and human identity applications, are traditionally genotyped through comparison of allele sizes to a sequenced allelic ladder. Allelic ladders permit a floating bin allele calling method to be utilized, which enables reliable allele calling across laboratories, instrument platforms, and electrophoretic conditions. Precise sizing methods for STR allele calling involving fixed bins can also be used when a high degree of precision has been demonstrated within an instrument platform and a set of electrophoretic conditions. An alternative method for reliable genotyping of STR markers, locus-specific brackets (LSBs), is introduced here. LSBs are artificial alleles created through molecular biology manipulations to be shorter or longer than alleles commonly seen in populations under investigation. The size and repeat number of measured alleles are interpolated between the two LSB products that are mixed with the polymerase chain reaction-amplified STR alleles. The advantages and limitations of the LSB approach are described along with a concordance study between the LSB typing approach and other STR typing methods. Complete agreement was observed with 162 samples studied at 5 Y-chromosome loci.     

Slippage mutation rates in 15 autosomal short tandem repeat loci for forensic purposes in a Southeastern Brazilian population

Well‐defined estimates of mutation rates in highly polymorphic tetranucleotide STR loci are a prerequisite for human identification in genetics laboratory routines useful for civil and criminal investigations. Studying 15 autosomal STR loci of forensic interest (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPOX, and vWA), we detected 193 slippage mutations (189 one‐step and four two‐step mutations) in 148 875 parent‐child allelic transfers from 5171 paternity cases with true biological relationship (15 096 individuals; 4754 trios and 417 duos; 9925 meiosis) from the state of São Paulo, a very representative population of Brazil. The overall mutation rate was 1.3 × 10^?3 and the highest rates were observed at loci vWA (2.8 × 10^?3), FGA and D18S51 (2.7 × 10^?3 for both), while loci TH01 and TPOX did not present any mutations. The mean slippage mutation rate of paternal origin (1.8 × 10^?3) was six times higher than that observed for maternal origin (0.3 × 10^?3).     

Genetic polymorphisms of 20 short tandem repeat loci from the Han population in Henan,China

The aim of this study was to investigate the genetic polymorphism of 20 short tandem repeat (STR) loci including D1S1656, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA in Han population of Henan, China and to assess its value in forensic science. Genomic DNA was extracted from 274 blood samples of unrelated healthy individuals in the Henan Han population. Alleles were amplified with PowerPlex® 21 system kit and PCR products were detected with ABI3130 genetic analyzer (Applied Biosystems) and the data were analyzed with modified PowerStats v1.2. A total of 229 alleles were observed in this Han population and the allelic frequencies ranged from 0.0020 to 0.5090 in the present study. Observed genotype distributions for each locus do not show deviations from Hardy–Weinberg equilibrium expectations (p < 0.05). The combined power of discrimination, combined power of exclusion, and combined matching probability of this 20 STR loci were 0.999999999, 0.999999994603, and 4.0433 × 10^?24, respectively. The 20 STR loci are highly polymorphic in the Han population of Henan, China and they may be of great value in forensic science and human population genetics.     

Precision and accuracy in fluorescent short tandem repeat DNA typing: assessment of benefits imparted by the use of allelic ladders with the AmpF/STR Profiler Plus kit

Base-calling precision of short tandem repeat (STR) allelic bands on dynamic slab-gel electrophoresis systems was evaluated. Data was collected from over 6000 population database allele peaks generated from 468 population database samples amplified with the AmpF/STR Profiler Plus (PP) kit and electrophoresed on ABD 377 DNA sequencers. Precision was measured by way of standard deviations and was shown to be essentially the same, whether using fixed or floating bin genotyping. However, the allelic ladders have proven more sensitive to electrophoretic variations than database samples, which have caused some floating bins of D18S51 to shift on occasion. This observation prompted the investigation of polyacrylamide gel formulations in order to stabilize allelic ladder migration. The results demonstrate that, although alleles comprised in allelic ladders and questioned samples run on the same gel should migrate in an identical manner, this premise needs to be verified for any given electrophoresis platform and gel formulation. We show that the compilation of base-calling data is a very informative and useful tool for assessing the performance stability of dynamic gel electrophoresis systems, stability on which depends genotyping result quality.     

A sensitive and selective liquid chromatographic/electrospray ionization tandem mass spectrometric assay for the simultaneous quantification of alpha-,beta-arteether and its metabolite dihydroartemisinin in plasma,useful for pharmacokinetic studies

A sensitive, selective, specific and rapid liquid chromatographic/electrospray ionization tandem mass spectrometric assay method was developed and validated for the simultaneous quantitation of alpha-,beta-arteether (alpha-,beta-AE) and its metabolite alpha-dihydroartemisinin (DHA) in monkey plasma using the propyl ether analogue of beta-arteether (PE) as an internal standard. The method involves a simple two-step liquid-liquid extraction with hexane. The analytes were chromatographed on a C(18) reversed-phase chromatographic column by isocratic elution with methanol-ammonium acetate buffer (pH 4) (92 : 8, v/v) and analysed by mass spectrometry in the multiple reaction monitoring mode. The chromatographic run time was 7 min and the weighted (1/x(2)) calibration curves were linear over the range 0.78-200 ng ml(-1). The method was validated in terms of accuracy, precision, absolute recovery, freeze-thaw stability, bench-top stability and re-injection reproducibility. The limit of detection and lower limit of quantification in monkey plasma were 0.39 and 0.78 ng ml(-1) respectively for all the analytes. The intra- and inter-batch precision and accuracy were found to be well within acceptable limits (<15%). All three analytes were stable even after three freeze-thaw cycles (deviation < 15%). The average absolute recoveries of alpha-,beta-AE, DHA and PE, used as an internal standard, from spiked plasma samples were 85.85 +/- 6.56, 70.10 +/- 7.06, 54.37 +/- 3.39 and 93.90 +/- 6.9%, respectively. The assay method described here could be applied to study the pharmacokinetics of alpha-,beta-AE and DHA in rhesus monkeys.     

Desirability functions as response in a d‐optimal design for evaluating the extraction and purification steps of six tranquillizers and an anti‐adrenergic by liquid chromatography‐tandem mass spectrometry

Internal standards can be added at different stages of an analytical procedure. When they are added at the beginning of a multiresidue method and their behavior is not exactly the same as that of the analytes, the intended correction for small variations within the analytical process could not be achieved. Because of this, in the present work, the use of d ‐optimal designs together with desirability functions is proposed to state the experimental response under study. The overall desirability function used relates two analytical criteria: to assess a similar chemical behavior of each analyte in relation to its internal standard and to avoid a significant reduction of the absolute peak area of the internal standards. This strategy has been applied to the analysis of the effect of four factors related to the extraction and purification steps of six tranquillizers and a β‐blocker from pig muscle analyzed by liquid chromatography–tandem mass spectrometry. The effect of those factors has been evaluated by means of an ad hoc d ‐optimal design consisting of only 11 experiments. The resulting levels of the four factors that enable to achieve the greatest overall desirability have also been compared with those obtained when either the standardized or absolute peak area has been considered as response. Differences in both the significant factors and their optimum levels have been observed. It is noticeable that the experimental effort necessary to study the effect of the factors has been reduced by more than 50% thanks to the d ‐optimal design. Copyright © 2015 John Wiley & Sons, Ltd.