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PubMed1995

DNA forensic science 1995.

After digression by a National Research Council committee, forensic use of DNA identification is returning to methods that do not violate population genetics and statistics. Polemic has been replaced by normal science as advances are made in molecular techniques and presentation of evidence. Rigorous quality control over the chain of custody and likelihood calculations still need to be implemented, and evidence extended on the structure of forensic populations and the operating characteristics of alternative tests.

Confidence Intervals↗
PubMed2005

African Jordanian population genetic database on fifteen short tandem repeat genetic loci.

AIM: To establish a genetic database of the African-Jordanian population for forensic and paternity testing purposes. METHOD: Allelic distribution at fifteen short tandem repeat (STR) loci was determined for 95 healthy unrelated African-Jordanians. The 15 autosomal STR loci, included within the GenePrint PowerPlex 16 system, were amplified from the subset of the 95 DNA extracts isolated from the population sample. Electrophoresis for each polymerase chain reaction (PCR) product was carried out using the ABI Prism 310 Genetic Analyzer and the length of the amplified DNA fragments was determined using the Genotype 2.0 and PowerTyper 16 Macro softwares. Calculations of allelic frequencies, forensic efficiency parameters, Hardy-Weinberg departure, and quantitative analysis of the allele frequencies in various populations were determined. RESULTS: DNA extracts were successfully amplified and the genetic database was compiled. All tested loci showed no significant statistical deviation from Hardy-Weinberg expectations. Furthermore, no significant difference was observed between the sample population under investigation and other population genetic databases. CONCLUSION: The loci investigated here proved to be sufficiently polymorphic for forensic purposes, since the forensic efficiency values suggest that they are very discriminating in the African-Jordanian subpopulation.

Africa↗
PubMed2005

Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis.

To test for human population substructure and to investigate human population history we have analysed Y-chromosome diversity using seven microsatellites (Y-STRs) and ten binary markers (Y-SNPs) in samples from eight regionally distributed populations from Poland (n = 913) and 11 from Germany (n = 1,215). Based on data from both Y-chromosome marker systems, which we found to be highly correlated (r = 0.96), and using spatial analysis of the molecular variance (SAMOVA), we revealed statistically significant support for two groups of populations: (1) all Polish populations and (2) all German populations. By means of analysis of the molecular variance (AMOVA) we observed a large and statistically significant proportion of 14% (for Y-SNPs) and 15% (for Y-STRs) of the respective total genetic variation being explained between both countries. The same population differentiation was detected using Monmonier's algorithm, with a resulting genetic border between Poland and Germany that closely resembles the course of the political border between both countries. The observed genetic differentiation was mainly, but not exclusively, due to the frequency distribution of two Y-SNP haplogroups and their associated Y-STR haplotypes: R1a1*, most frequent in Poland, and R1*(xR1a1), most frequent in Germany. We suggest here that the pronounced population differentiation between the two geographically neighbouring countries, Poland and Germany, is the consequence of very recent events in human population history, namely the forced human resettlement of many millions of Germans and Poles during and, especially, shortly after World War II. In addition, our findings have consequences for the forensic application of Y-chromosome markers, strongly supporting the implementation of population substructure into forensic Y chromosome databases, and also for genetic association studies.

Chromosomes, Human, Y↗
PubMed2005

Forensic interpretation of Y-chromosomal DNA mixtures.

The mathematical concept previously introduced for the forensic interpretation of DNA mixtures using non-associated genetic markers has been adapted to the assessment of haplotypes. Such calculus is required, for example, when Y-chromosomal markers are used in forensics. In addition to outlining the general mathematical framework, we devise two approaches to its practical computational implementation, involving either the inclusion-exclusion principle of probability theory or a recursion in the number of unknown contributors invoked. The two approaches scale differently, depending upon the complexity of the case and the diversity of the markers used. The performance of Y-chromosomal microsatellites (Y-STRs) as a means of trace donor discrimination has been assessed by simulation, using the derived formulas. Based upon data from the Y-chromosomal Haplotype Reference Database (YHRD), the exclusion chance of a non-contributor is shown to vary between 95% in the case of two contributors, and 70% for five contributors. With only one additional contributor, half of all contributing suspects would yield a log-likelihood ratio in favour of donorship of 1.61 or higher, although the median drops to 0.66 with four additional contributors. It must be emphasised that these estimates of the discriminatory power of Y-STRs are likely to be conservative since the simulations involved only haplotypes known to occur in YHRD.

Chromosomes, Human, Y↗
PubMed2001

Mutations at Y-STR loci: implications for paternity testing and forensic analysis.

Knowledge about mutation rates and the mutational process of Y-chromosomal short-tandem-repeat (STR) or microsatellite loci used in paternity testing and forensic analysis is crucial for the correct interpretation of resulting genetic profiles. Therefore, we recently analysed a total of 4999 male germline transmissions from father/son pairs of confirmed paternity (probability > or = 99.9%) at 15 Y-STR loci which are commonly applied to forensics. We identified 14 mutations. Locus specific mutation rate estimates varied between 0 and 8.58 x 10(-3), and the overall average mutation rate estimate was 2.80 x 10(-3) (95% CIL 1.72 x 10(-3)-4.27 x 10(-3)). In two confirmed father/son pairs mutation at two Y-STRs were observed. The probability of two mutations occurring within the same single germline transmission was estimated to be statistically not unexpected. Additional alleles caused by insertion polymorphisms have been found at a number of Y-STRs and a frequency of 0.12% was estimated for DYS19. The observed mutational features for Y-STRs have important consequences for forensic applications such as the definition of criteria for exclusions in paternity testing and the interpretation of genetic profiles in stain analysis. In order to further enrich our knowledge of Y-STR mutations we suggest the establishment of a Y-STR mutation database and ask the forensic community for data contribution.

Autoradiography↗
PubMedDate not supplied

[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.

Alleles↗
PubMed1999

Allele frequencies of six STR loci in Argentine populations.

Allele frequencies of six short tandem repeat (STR) loci were determined in a Caucasian urban sample of La Plata city and three Amerindian sample populations of Argentina. Allele frequencies showed differences between urbans and Amerindians, and among Amerindians as well. The degree of genetic differentiation of subpopulations was mainly due to the Amerindian contribution. Mapuche, Mocovi, and pooled Amerindian populations showed little evidence of HW disequilibrium, and association of alleles. In the urban sample, there is no evidence of population substructuring. Forensic probabilities of exclusion and matching showed high differences between the population groups. Finally, La Plata sample did not show differences with Caucasians from other geographic regions.

Adult↗
PubMed2002

High resolution Y chromosome typing: 19 STRs amplified in three multiplex reactions.

Nineteen Y-specific short tandem repeat (STR) loci have been amplified in 768 samples from the Iberian Peninsula in order to evaluate their usefulness in forensic casework. Two previously published multiplex reactions by Thomas et al. [Hum. Genet. 6 (1999) 577] (MS1, modified here: DYS19, DYS388, DYS390, DYS391, DYS392 and DYS393) and by Ayub et al. [Nucl. Acids Res. 28 (2000) e8] (CTS: DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439) plus a novel one reported here (EBF: DYS385, DYS389, DYS460, DYS461, DYS462 and amelogenin) have been used. DYS385, DYS439 and DYS391 were the most informative loci with allele diversities of 0.7997, 0.6683 and 0.5940, respectively. A total of 635 different haplotypes were observed, of which 573 (90.24%) were found in single individuals. The overall haplotype diversity was 0.9988 and that obtained by each multiplex system was 0.9812 for EBF, 0.9292 for MS1 and 0.9089 for CTS.

Base Sequence↗
PubMed2006

[Genetic polymorphism of 15 STR loci in a Lhasa Tibetan population].

The polymorphism distributions of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were investigated in a Lhasa Tibetan population by multiplex PCR amplification using five fluorochromes (6FAM, VIC, NED, PET, LIZ). Gene frequency, discrimination power (DP), heterozygosity (H), polymorphism information content (PIC) and probability of paternity exclusion (EPP) were calculated, and all loci were tested for Hardy-Weinberg equilibrium. Results indicate that the gene frequency of these 15 STR loci is in Hardy-Weinberg equilibrium. The DP is at 0.7515 - 0.9599, H is at 0.5576 - 0.8538, PIC is at 0.5455 - 0.8458, and EPP is at 0.37550.8520. Cumulative DP of the 15 STR is 0.99999999, and cumulative EPP is 0.999999997. Therefore, these 15 STR loci can be used as genetic markers of in Lhasa Tibetan populations in anthropological studies, linkage analysis of genetic diseases, individual identification and paternity testing in forensic medicine.

Ethnicity↗
PubMed2004

DNA polymorphisms in the tyrosine hydroxylase and GNB3 genes: association with unexpected death from acute myocardial infarction and increased heart weight.

Sudden and unexpected death from myocardial infarction (MI) is one of the most commonly observed findings in forensic medicine. To investigate the biochemical and genetic background of this disease we investigated the genotypes for two polymorphisms associated with hypertension: TH01, a tetrameric microsatellite in the tyrosine hydroxylase gene and the single nucleotide polymorphism C825T in the GNB3 gene in 116 sudden deaths from MI (78 males, 38 females) and in a control group of 137 deaths from natural causes other than MI (52 males, 85 females). For TH01 no correlation with the prevalence of MI was found. For C825T, results were different. While for the male individuals allelic frequencies and genotype distributions were similar in both groups, T-homozygosity was significantly more common in female fatalities from MI than in the female control group (24% versus 7%; Relative Risk 2.29). Nevertheless, neither for TH01 nor for C825T an association with heart weight was found. Thus our results demonstrate that the C825T polymorphism may play a role in the development of myocardial infarctions, at least in females. They also demonstrate that the genetic component in complex diseases like MI may depend on the gender of the patients. As the influence of this polymorphism on arterial blood pressure appears to be relatively small, and G-proteins are involved in numerous intracellular signal cascades it can be speculated that T-homozygosity at this locus might influence the incidence or mortality of cardiovascular disease via hitherto unknown mechanisms.

Adult↗
PubMed2001

[Allele sequences and population genetics of pentanucleotide tandem repeat D6S957].

OBJECTIVE: Pentanucleotide tandem repeat loci are useful markers of short tandem repeat (STR) for genetic analysis. We focused on the analysis of the DNA sequence for each allele at the pentanucleotide STR locus D6S957 in order to understand their structures in the human genome and to construct human allelic ladder, which is necessary for forensic DNA typing. In order to evaluate the forensic applicability of D6S957, we investigated the genotype distributions and allele frequencies in major ethnic groups. METHODS: A total of 230 samples from unrelated individuals were analyzed by PCR. Allele determination was carried out by comparison with a sequenced human allelic ladder made in-house. An example of each allele was sequenced on an ABI 377 automated sequencer. RESULTS: This pentanucleotide STR exhibited a minimal amount of stutter and provided easily interpretable results. Eight alleles were found in these populations. No evidence of deviation from Hardy-Weinberg equilibrium was observed. In 64 confirmed father/mother/child triplets no mutation events were observed. The mutation rate was indirectly estimated at 2.5 x 10(-5) using a maximum likelihood method. CONCLUSION: D6S957 is a useful marker for forensic casework and paternity analysis.

Alleles↗
PubMed2004

[A genetic study of 15 STR loci in Chinese E Wen-ke population].

OBJECTIVE: To investigate the genetic polymorphisms of 15 STRs loci in Chinese E Wen-ke population. METHODS: DNA samples from 99 unrelated individuals in Chinese E Wen-ke population were screened by Power Plex 16 System and ABI3100 Genetic Analyzer. RESULTS: The genotype frequencies of these 15 STR loci meet the Hardy-Weinberg expectation. The Matching probability of 15 STRs loci were between 0.0205-0.1733, discriminating power (DP) at 0.8267-0.9795, heterozygosity (Ho) at 0.6061-0.9091, power of exclusion (PE) at 0.4038-0.7690, polymorphism information content (PIC) at 0.5985-0.8734. The total DP of 15 STRs loci is 0.9999999999998. CONCLUSION: Our results showed that the 15 STRs loci of Power Plex 16 System are valuable STR loci genetic marker system having high DP and are useful in forensic case work in Chinese E Wen-ke population.

Alleles↗
PubMed1991

Genetic studies of human apolipoproteins. XIX. Apolipoproteins E and A-IV phenotyping from whole blood and blood stains.

Apolipoproteins E and A-IV reveal common, genetically determined, structural polymorphisms, which can be detected in serum or plasma, using isoelectric focusing and immunoblotting techniques. In the present study, we have investigated the possibility of detecting the gene products of these two polymorphic loci in whole blood and blood stains. A total of 68 plasma samples and their corresponding whole blood samples were screened. Phenotypic patterns obtained in whole blood were identical to those obtained in plasma for both the APO E and APO A-IV polymorphisms. The signal-to-noise ratio in the APO E patterns was higher in whole blood than in fresh plasma. The gene products of both the APO E and APO A-IV were found to be very stable in several months old blood stains. The detection of apolipoprotein polymorphisms in whole blood and blood stains signifies their potential applications, on a wider scale, to several areas including forensic serology, paternity testing, clinical and population genetic studies.

Apolipoproteins A↗
PubMed2006

Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the software methods.

Automation↗
PubMed1995

Allele-specific HLA-DRB1 amplification of forensic evidence samples with mixed genotypes.

A major problem in analyzing forensic casework samples is the presence of genetic material from more than one individual in the material evidence. For instance, in sexual assault cases the evidence (vaginal swabs) usually contains a majority of vaginal epithelial cells and varying amounts of sperm cells from the perpetrator. Samples with mixed genotypes are also common among other biological evidence materials such as nail scrapes and mixed bloodstains. We have developed an allele-specific amplification system for the highly polymorphic HLA class II DRB1 locus that permits the detection of individual alleles in a sample with mixed genotypes, independent of the initial frequency of the alleles. Using a set of eight allele-specific amplification primers and typing the amplified fragments with sequence-specific probes, most of the 60 DRB1 alleles can be resolved. The method is highly specific and sensitive, with the potential for amplifying 15 copies of a particular allele in a background of 3 x 10(5) copies of other alleles. The method was successfully applied to three forensic cases, where the material evidence consisted of sperm stains on panties, nail scrapes and bloodstains on skin. Thus the DRB1 allele-specific amplification system can be employed for the unambiguous determination of the presence of individual alleles in materials suspected to contain mixed genotypes, even when the alleles of interest constitute only a small fraction of the total DNA.

Alleles↗
PubMed1999

Validation of highly polymorphic fluorescent multiplex short tandem repeat systems using two generations of DNA sequencers.

Validation studies are a crucial requirement before implementation of new genetic typing systems for clinical diagnostics or forensic identity. Two different fluorescence-based multiplex DNA profiling systems composed of amelogenin, HumD21S11 and HumFGA (referred to as multiplex 1A), and HumD3S1358, HumD21S11 and HumFGA (multiplex 1B) have been evaluated for use in forensic identification using the Applied Biosystems Model 373A and Prism 377 DNA Sequencers, respectively. Experiments were aimed at defining the limit of target DNA required for reliable profiling, the level of degradation that would still permit amplification of the short tandem repeat (STR) loci examined, and the robustness of each locus in the multiplexes after samples were exposed to environmental insults. In addition, the specificity of the multiplexes was demonstrated using nonhuman DNAs. Forensically relevant samples such as cigarette butts, chewing gum, fingernails and envelope flaps were processed using both an organic extraction procedure and a QIAamp protocol. DNAs and resultant multiplex STR profiles were compared. The validation of the triplex STR systems was extended to include over 140 nonprobative casework specimens and was followed with a close monitoring of initial casework (over 300 exhibits). Our results document the robustness of these multiplex STR profiling systems which, when combined with other multiplex systems, could provide a power of discrimination of approximately 0.9999.

Animals↗
PubMedDate not supplied

[Use of polymerase chain reaction of the HLA-DQ alpha system in forensic trace analysis].

The polymerase chain reaction (PCR) can be used for genetic typing of minute amounts of biological stains. This is achieved by in vitro amplification of a well-defined and genetically polymorphic human genomic DNA sequence. Using the HLA-DQ alpha system, a population study was carried out among 212 unrelated individuals of German origin. The usefulness of this system is discussed by presenting examples of its application in forensic casework, i.e. the analysis of mixed (male/female) body fluids as well as segregation studies on embryonic and paraffin-embedded tissue samples.

Alleles↗