Enhanced kinship analysis and STR-based DNA typing for human identification in mass fatality incidents: the Swissair flight 111 disaster

A bioinformatic tool was developed to assist with the victim identification initiative that followed the Swissair Flight 111 disaster. Making use of short tandem repeat (STR) DNA typing data generated with AmpFlSTR Profiler Plus (PP) and AmpFlSTR COfiler(CO) kits, the software systematically compared each available STR genotype with every other genotype. The matching algorithm was based on the search for: (i) direct matches to genotypes derived from personal effects; and (ii) potential kinship associations between victims and next-of-kin, as measured by allele sharing at individual loci. The software greatly assisted parentage analysis by enabling kinship evaluation in situations where complete parentage trios were unavailable and, in some situations, with distantly related relatives. Exclusion of fortuitous kinship associations (FKA) was made possible through the recovery at the disaster site of at least one remains for every sought-after victim, and was incorporated into the kinship software. The data from the 13 combined STR loci produced 6 and 23 times fewer FKAs when compared with PP alone and AmpFlSTR Profiler (PR) alone, respectively. Identification leads or confirmations of identification were obtained for 218 victims for which DNA reference samples (personal effects and kin) had been submitted. Confirmation of an inferred kinship association was sought through frequency and likelihood calculations, as well as corroborative data from other identification modalities. The use of a simple, yet powerful, automated genotype comparison approach and the use of megaplexes with high power of discrimination (PD) values extended considerably the identification capabilities in the case of the Swissair disaster. The DNA typing identification modality proved to be a valuable component of the large arsenal of identification tools deployed in the aftermath of this disaster.     

Systematic analysis of stutter percentages and allele peak height and peak area ratios at heterozygous STR loci for forensic casework and database samples

To assist the interpretation of STR DNA typing results from forensic casework samples containing mixtures, the range of heterozygous allele peak height and peak area ratios (HR) and stutter percentages (stutter %) for the loci comprised in the AmpFlSTR Profiler Plus (PP) kit were assessed on 468 database and 275 casework single source samples. Stutter % medians were similar for database and casework samples, ranging from 2% to 7%. The upper limit of the stutter value range was 16%, calculated as median +3 SD, although lower locus-specific values could be used. HR medians were 93 +/- 6.5% for database samples, 88 +/- 12% for casework samples. For casework samples, the maximum signal imbalance noted was 52%, calculated as median -3 SD. No significant difference was observed between peak height and peak area calculated values. This study shows the importance of selecting the proper reference database for the establishment of HR threshold values.     

The evaluation of the extent of transporting or "tracking" an identifiable ignitable liquid (gasoline) throughout fire scenes during the investigative process

Tests have determined that boots or shoes of individuals at a fire scene do not transport sufficient contaminants ("tracking") through the fire scene to produce a positive laboratory result for the presence of gasoline in a fire scene that was not present at the time of the fire. Questions about the validity of forensic laboratory results have been raised on the basis that low-level gasoline residues detected in the laboratory samples could have been the result of transporting the residue by footwear contaminated from the fire scene ("tracking"). The data collected in this study establish that "tracking" does not lead to false-positive laboratory results. Canines trained and experienced in the detection of trace ignitable liquid residues were also utilized in this study. The canine results confirmed that properly trained canines show a higher sensitivity than do standard ASTM laboratory techniques for fire debris analysis. In a few cases, canines responded to contamination, but laboratory testing (which is the definitive indicator) did not produce positive results.     

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).     

Determination of group affiliation of isolated spermatozoa after separation from squamous epithelium cells

Outlined in the paper are outlooks for determining a group affiliation of sperm in traces, left in material evidence, within forensic biological expertise. A technique is suggested to separate the spermatozoids from the vaginal epithelium cells--it has been used up to now in genetics alone. The method involves the available reagents and does not need any extra training. Its elaboration and introduction would resolve one of the most often-encountered issues set by the investigating office.     

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.     

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.