Validation study of the TrueAllele automated data review system

The New York State Convicted Offender DNA Databank is the first U.S. lab to complete an internal validation of the TrueAllele expert data review system. TrueAllele is designed to assess short tandem repeat (STR) DNA data based on several key features such as peak height, shape, area, and position relative to a standard ladder and use this information to make accurate allele calls. The software then prioritizes the allele calls based on several user-defined rules. As a result, the user need only review low-quality data. The validation of this system consisted of an extensive optimization phase and a large concordance phase. During optimization, the rule settings were tailored to minimize the amount of high-quality data viewed by the user. In the concordance phase, a large dataset was typed in parallel with the ABI software Gene Scan and Genotyper (manual review) and TrueAllele (automated review) for comparison of allele calls and sample state assignment. Only one significant difference was discovered out of 2048 samples in the concordance study. In this case, TrueAllele revealed a spike in the profile that was interpreted as a DNA peak by the analyst in Genotyper. TrueAllele was designed to focus the review on poor data and to eliminate the need for complete reanalysis technical review. This validation project proved TrueAllele to be dependable for use at the NYS Convicted Offender DNA Databank.     

Analysis of nitrite in adulterated urine samples by capillary electrophoresis

A simple method for analyzing nitrite in urine has been developed to confirm and quantify the amount of nitrite in potentially adulterated urine samples. The method involved separation of nitrite by capillary electrophoresis and direct UV detection at 214 nm. Separation was performed using a bare fused silica capillary and a 25 mM phosphate run buffer at a pH of 7.5. Sample preparation consisted of diluting the urine samples 1:20 with run buffer and internal standard, and centrifuging for 5 min at 2500 rpm. The sample was hydrodynamically injected, then separated using -25 kV with the column maintained at 35 degrees C. The method had upper and lower limits of linearity of 1500 and 80 microg/mL nitrite, respectively, and a limit of detection of 20 microg/mL. The method was evaluated using the National Committee for Clinical Laboratory Standards (NCCLS) protocol (Document EP10-A2), and validated using controls, standards, and authentic urine samples. Ten anions, ClO-, CrO4(-2), NO3-, HCO3-, I-, CH3COO-, F-, SO4-, S2O8(-2), and Cl-, were tested for potential interference with the assay. Interferences with quantitation were noted for only CrO4(-2) and S2O8(-2). High concentrations of Cl- interfered with the chromatography. The method had acceptable accuracy, precision, and specificity.     

Polymorphism of the central region of D-loop of mitochondrial DNA and personality identification by forensic medicine methods

Polymorphism of mDNA D-loop central region (CR), positions 16366-0072) was studied versus hypervariable sections (HVS1), positions 16024-16365, and HVS2, positions 00073-00340, for a sample of 71 residents of the Russian Federation. Ten polymorphic positions with 56 nucleotide substitutions, 55 of which are transitions, were detect in the CR section; no insertions or deletions were found there. It was proven as possible to use the mDNA CR locus as an additional identification marker in the forensic-expert of the mDNA control region. The probability of random coincidence (RC) of haplotypes in joint typing of HVS1, HVS2 and CR made 0.0208, which is 1.4-fold less versus the same parameter for haplotypes HVS1/HVS2 (RC = 0.0284).     

A definition of the nomenclature of allele variants and a description of allele polymorphism within a molecular-genetic individualization system based on the pentanucleotide tandem replication of HUMCD4

While analyzing the available published data, we found significant differences in definition of alleles of the HUMCD4 polymorphic chromosome locus. It is an obstacle for comparing the expertise results obtained while using the locus as molecular individualization system in different laboratories and, as a consequence, it hinders the use of the said marker in building up a reference database. The structure of the HUMCD4 locus was analytically investigated and the distribution of the locus alleles was systemized in a sample of 407 persons (citizens of Russia who are not blood relatives) within the present case study for the purpose of a detailed definition of its allele's characteristics. We worked out recommendations related with the nomenclature standardization of alleles of the HIMCD4 locus and specified the main population features of the locus polymorphism on the bases of the studied sample of Russia's citizens. The results can be used as reference parameters in interpreting the findings of the molecular-genetic identification expertise and examinations and in building up databases.     

Toxicity of non-steroid anti-inflammatory drugs

Data are reported on toxicity of a majority of non-steroid anti-inflammatory drugs (NSAD), which are the most frequently used in clinical practice and whose chemical structures are different. The action mechanism and side effects of some NSAD, in particular, of diclofenac, ibuprofen and indometacin, are also in the focus of attention.     

Studies of the allelic diversity in micro-satellite locus D16S539, F13B, FESFPS, TH01, and TROX in European population of Russia Ural region using capillary electrophoresis

Allelic frequencies of chromosome micro-satellite locuses D16S539, F13B, FESFPS, TH01 and TPOX were determined, within the case study, in a sampling of Europeoidal individuals residing in Russia's Ural Region. The allelic variants were analyzed by capillary electrophoresis after the enzyme amplification in polymerase chain reaction with fluorescent primers. The genotypic frequencies of the studied locuses were shown not to divert with statistical reliability from Hardy-Weinberg equilibrium. The estimated aggregate discriminative potential for a panel of 5 studied locuses made 0.99995. No nonequilibrium was found by linkage between alleles of all lucuses examined within the present case study or between their alleles and the alleles of previously investigated locuses D7S820 and D13S317. The implemented testing of the population homogeneity of allelic frequencies of investigated locuses for 3 samplings of Europeoids showed a deviation for locus FESFPS versus the Ural and Polish samplings and for locus F13B in the Ural and North America samplings. The distribution of allelic frequencies of other locuses was homogenous in the compared samplings.