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PubMed2002

Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis.

The rapid development of molecular genetic analysis tools has made it possible to analyze most biological materialfound at the scene of a crime. Evidence materials containing DNA quantities too low to be analyzed using nuclear markers can be analyzed using the highly abundant mtDNA. However, there is a shortage of sensitive nDNA and mtDNA quantification assays. In this study, an assay for the quantification of very small amounts of DNA, based on the real-time Taq-Man assay, has been developed. This analysis will provide an estimate of the total number of nDNA copies and the total number of mtDNA molecules in a particular evidence material. The quantification is easy to perform, fast, and requires a minimum of the valuable DNA extracted from the evidence materiaL The results will aid in the evaluation of whether the specific sample is suitable for nDNA or mtDNA analysis. Furthermore, the optimal amount of DNA to be used in further analysis can be estimated ensuring that the analysis is successful and that the DNA is retained for future independent analysis. This assay has significant advantages over existing techniques because of its high sensitivity, accuracy, and the combined analysis of nDNA and mtDNA. Moreover, it has the potential to provide additional information about the presence of inhibitors in forensic samples. Subsequent mitochondrial and nuclear analysis of quantified samples illustrated the potential to predict the number of DNA copies required for a successful analysis in a certain typing assay.

Cell Nucleus↗

PubMed2006

A minimally invasive method of piscine tissue collection and an analysis of long-term field-storage conditions for samples.

BACKGROUND: The acquisition of high-quality DNA for use in phylogenetic and molecular population genetic studies is a primary concern for evolutionary and genetic researchers. Many non-destructive DNA sampling methods have been developed and are used with a variety of taxa in applications ranging from genetic stock assessment to molecular forensics. RESULTS: The authors have developed a field sampling method for obtaining high-quality DNA from sunfish (Lepomis) and other freshwater fish that employs a variation on the buccal swab method and results in the collection of DNA suitable for PCR amplification and polymorphism analysis. Additionally, since the circumstances of storage are always a concern for field biologists, the authors have tested the potential storage conditions of swabbed samples and whether those conditions affect DNA extraction and PCR amplification. It was found that samples stored at room temperature in the dark for over 200 days could still yield DNA suitable for PCR amplification and polymorphism detection. CONCLUSION: These findings suggest that valuable molecular genetic data may be obtained from tissues that have not been treated or stored under optimal field conditions. Furthermore, it is clear that the lack of adequately low temperatures during transport and long term storage should not be a barrier to anyone wishing to engage in field-based molecular genetic research.

Animals↗

PubMed2003

Evaluation of 15 biparental STR loci in human identification and genetic study of the Kannada-speaking groups of India.

Thirteen tetranucleotide and 2 pentanucleotide repeat units were analyzed in 167 unrelated Kannada-speaking individuals belonging to 3 important communities, namely, Kuruva, Bhovi, and Christians, residing in different districts of Karnataka, India. Allele frequency data obtained from the analysis of 15 short tandem report (STR) markers of the subpopulation groups included in the study were observed to be similar, indicating a common ancestry or gene flow among these communities. Departures from Hardy-Weinberg equilibrium were observed in Kuruva population at locus D5S818 and D18S51 and at locus CSF1PO in the Christian community. The data of these communities were analyzed with allele frequency data of 4 other populations from Karnataka, India-Iyengar Brahmin, Gowda, Lingayat, and Muslim-to compute the combined power of discrimination, ranged from 0.962 to 0.974, with negligible difference between populations. The combined power of exclusion, however, remained constant at 0.999 for all populations evaluated in the study. Thus, the 15 markers selected for this study were found to be highly suitable in human identification and for providing information on genetic polymorphism.

Ethnicity↗

PubMed1984

[Problems and dilemmas in the testing of genetic characteristics of the blood for the purpose of determining disputed paternity (forensic hemogenetics)].

The work presents certain groups of cases selected from more than 1500 triplets (father-mother-child) we tested from 1979. to 1984., in order to indicate certain dilemmas in making definite conclusions on disputed paternity. 55 cases of the first rule exclusions, using one system only were found to be definite; one conclusion on disputed paternity exclusion using Duffy system only was found to be correctly finished, although we should not recommend it; extention of the analysis set with HLA-A, B, C products determination significantly increases exclusion percentage of misjudged fathers; in the analyzed group of 22 exclusions where HLA antigens were determined, during the second stage or simultaneously with the determination of erythrocytes, we found 7 exclusions according to erythrocyte system, also confirmed according to HLA; 12 cases with exclusions according to HLA only, 3 cases with no exclusions either according to erythrocyte system or HLA; according to Duffy system we had two cases of apparent maternity exclusions.

Blood Group Antigens↗

PubMed1993

Genetic typing of HLA class II genes in Swedish populations: application to forensic analysis.

In an attempt to determine the value of DNA based typing of HLA class II loci to forensic analysis, allele and genotype frequencies at DQA1, DQB1, DPB1, and DRB1 were determined in samples from two Swedish populations using hybridization with sequence specific oligonucleotides to PCR amplified DNA. Significant allele frequency differences were observed at the DQB1 and DRB1 loci between the two populations, as well as between one of the Swedish and a Norwegian population. The average heterozygosity varies between 0.74 to 0.91 and the power of discrimination between 0.90 to 0.98, with the highest values obtained for the DRB1 locus. The probability of genotype identity by chance differs on average 2% between the populations. When applied to a paternity case with one parent deceased and a criminal case, typing of class II loci proved in both cases informative. Analyses of DR and DQ genes does not increase the power of discrimination, due to strong linkage, but offers through the reconstruction of putative haplotypes an internal control for the consistency of the typing results at several loci. Typing of the DRB1 and DPB1 loci was found to result in an approximate combined average probability of genotype identity by chance of one in a thousand.

Alleles↗

PubMed1998

[Genetic polymorphism at D20S161 locus in Chinese populations].

OBJECTIVE: To understand the genetic relationship between different populations in China and to obtain the preliminary data on the genetic poly- morphisms of D20S161 in seven populations in China. METHODS: EDTA-blood specimens were collected from 753 healthy unrelated individuals in seven Chinese populations, including Chengdu(Han), Guangzhou(Han),Jilin(Han),Lasa (Tibetans),Dali(Bai), Nanning(Zhuang) and Hailaer(Menggu),respectively. DNA was extracted with Chelex method. The DNA samples were amplified by PCR technique, and the PAGE horizontal electrophoresis was used for typing the PCR products. RESULTS: Seven alleles at D20S161 locus were observed in six populations,while six alleles at D20S161 were observed in one population in Dali(Bai). The numbers of genotypes observed were 25, 19,21,19,16,20 and 22 for Chengdu(Han), Guangzhou(Han), Jilin(Han), Lasa(Tibetans), Dali(Bai), Nanning(Zhuang)and Hailaer(Menggu), respectively. The allele frequencies were D20S161*16:0.0220-0.0657, D20S161*17:0.1429-0.2947,D20S161*18: 0.3237-0.4835. D20S161*19:0. 0909-0.1850,D20S161*20:0.1263-0.1786,D20S161* 21: 0.0421-0.1010, D20S161*22:0-0.0250.A total of 26 genotypes were observed in 753 individuals. The heterozygosity was between 65.31% 80.41% for the seven populations. The results of test for Hardy-Weinberg equilibrium showed that the genotype distributions observed were correspondent with the expected. CONCLUSION: There are seven alleles in Chinese populations, of which D20S161*18 is most frequently observed. No significant difference in the distribution of allele frequencies at D20S161 (X2=57.9342,P>0.01) was noted among the seven Chinese populations. D20S161 may be a very useful genetic marker for both paternity test and personal identification of casework in forensic medicine and for the purpose of population genetics.

Base Sequence↗

PubMed2004

[A study of genetic polymorphism of the STR locus D7S2846, D19S400 and D18S535 in Han population in Wenzhou].

OBJECTIVE: To study genetic polymorphism of D7S2846, D19S400 and D18S535 in Han population in Wenzhou. METHODS: DNA was extracted with chelex-100 method from EDTA-blood samples of 194 unrelated individuals in Wenzhou and amplified with PCR technique. The PCR products were analyzed by PAG vertical electrophoresis and silver-stain. RESULTS: 6 alleles and 15 genotypes of D7S2846, 10 alleles and 36 genotypes of D19S400, 8 alleles and 26 genotypes of D18S535 was observed. The heterozygosities of the three loci are 0.644, 0.724 and 0.772; The power of discriminating are 0.854, 0.940 and 0.938. CONCLUSION: The heterozygosities of the three loci are high and the frequencies was in accordance with Hardy-Weinberg equilibrium (P>0.05), so the three loci can be used in forensic medicine and in other genetic researches.

Alleles↗

PubMed1997

Microsatellites in the HLA region: on overview.

Microsatellites are repeats of a DNA base motif (1-6 bp, mostly CA repeats) up to 100 times; they are distributed regularly all over the genome. Many of them are polymorphic and their high polymorphism is based upon a variable number of repeats. They are widely used for genetic mapping, linkage analysis, population genetics, evolutionary studies and in forensic medicine. Such markers have also been described in the HLA region since 1991, and a growing interest in their potential applications is being expressed. The aims of this review are: 1) to outline the presently available information from literature and molecular databases concerning 53 microsatellites in the HLA region (localization, type of repeat, number of alleles, heterozygosity, primers used for amplification); 2) to address the question of technical pitfalls when using such markers; 3) to discuss specific features such as their mutation rate (10 (-3) to 10 (-6), which is higher than that reported for HLA genes, and their linkage disequilibrium with HLA alleles; 4) to present an integrated map of microsatellites and genes of this region; and 5) to provide a synopsis of their different applications in HLA-related fields (disease studies, population genetics, recombination point studies, HLA region mapping, transplantation) along with perspectives for future use. Although some HLA region microsatellites have already been applied to the analysis of more than 10 diseases, it is now evident that their use in population genetics and the determination of genomic compatibility in bone marrow transplantation represent growing areas of application.

Animals↗

PubMed1998

Simultaneous estimation of all the parameters of a stepwise mutation model.

Minisatellite and microsatellite are short tandemly repetitive sequences dispersed in eukaryotic genomes, many of which are highly polymorphic due to copy number variation of the repeats. Because mutation changes copy numbers of the repeat sequences in a generalized stepwise fashion, stepwise mutation models are widely used for studying the dynamics of these loci. We propose a minimum chi-square (MCS) method for simultaneous estimation of all the parameters in a stepwise mutation model and the ancestral allelic type of a sample. The MCS estimator requires knowing the mean number of alleles of a certain size in a sample, which can be estimated using Monte Carlo samples generated by a coalescent algorithm. The method is applied to samples of seven (CA)n repeat loci from eight human populations and one chimpanzee population. The estimated values of parameters suggest that there is a general tendency for microsatellite alleles to expand in size, because (1) each mutation has a slight tendency to cause size increase and (2) the mean size increase is larger than the mean size decrease for a mutation. Our estimates also suggest that most of these CA-repeat loci evolve according to multistep mutation models rather than single-step mutation models. We also introduced several quantities for measuring the quality of the estimation of ancestral allelic type, and it appears that the majority of the estimated ancestral allelic types are reasonably accurate. Implications of our analysis and potential extensions of the method are discussed. SINCE the discovery that a large number of loci with tandemly repeated sequences in human and many eukaryote species are highly polymorphic because of copy number variation of the repeats in different individuals (Jeffreys 1985; Litt and Luty 1989; Weber and May 1989), allele size data from such loci are rapidly becoming the dominant source of genetic markers for genome mapping, forensic testing, and population studies. Loci with repeat sequences longer than 5 bp are generally referred to as minisatellite or variable number tandem repeat loci, and those with repeat sequences between 2 to 5 bp are referred to as microsatellite or short tandem repeat loci (Tautz 1993). Because mutations change the copy number of such loci in a stepwise fashion, rapid accumulation of population samples from minisatellite and microsatellite loci has resurrected the interest of the stepwise mutation model (SMM), which was popular in the 1970s.

Chi-Square Distribution↗

PubMed2001

The STR-based genetic profile of the population from Corsica island (France).

Short tandem repeats (STR) at loci HumFES/FPS, HumVWA, HumCSF1PO, HumTH01, HumFXIIIA01, HumTPOX, HumCD4, D3S1358 are markers of choice for population genetics and validated systems for forensic use. In this report, we analysed their allele frequency distribution in a sample of native blood donors from the two departments of Corsica island (France). Deviations from the Hardy-Weinberg rule and heterozygosity values consistently suggested a spatial differentiation of allele and genotype frequencies across the island. Pairwise comparisons showed that Corsican gene pool presents a high level of heterogeneity between departments and substantially differs from that of neighbouring and historically-related populations. The results suggest the use of local databases to calculate a priori statistics in human identity testing.

Alleles↗

PubMed2002

[Study on the construction of standard D12S391 allelic ladder and its genetic polymorphism in six populations].

OBJECTIVE: To resolve the problem of the accuracy and standardization of short tandem repeat-polymerase chain reaction (STR-PCR) typing in forensic practice, the authors have designed a new method of producing standard D12S391 allelic ladder. METHODS: Nine different PCR amplified D12S391 allelic fragments were isolated from the gel, eluted into the distilled water and re-amplified by PCR. The purified allelic fragments were then blunt-end subcloned individually into the pUC plasmid vectors and transfected into competent E.coli DH5 alpha(TM) cells. The sequencing results confirmed that the size and the structure of the inserts were correct. The recombinant plasmids DNA with 9 inserts were then used as templates for PCR re-amplification to generate D12S391 standard ladder. RESULTS: With the ladder, the authors studied the genetic polymorphisms of D12S391 locus in six populations (German, Japanese and Chinese south-western Han, northern Han, Weiwu'er and Hui populations), and the respective primary data in the six populations were obtained. D12S391 locus showed high polymorphism in all six populations, and its exclusion power and discrimination power are 0.609-0.786 and 0.940-0.952 respectively. CONCLUSION: The results demonstrate that the standard ladder generated via this method is excellent, and D12S391 locus is robust for genetic research and forensic application.

Alleles↗

PubMed2003

[Proceeding of research on X chromosome genetic markers].

The development of Human Genome Project (HGP) makes it possible and more important to reveal the variations or polymorphisms precisely between different individuals and populations. Due to the characters of their high polymorphism and value in disease-linkage analysis as well as pharmacogenomnics, genetic markers on X chromosome have attracted much more attention of current medical and forensic scientists. This report summarized the proceeding of research on X chromosome genetic markers in the clinical and forensic context.

Chromosomes, Human, X↗

PubMed2006

An isothermal method for whole genome amplification of fresh and degraded DNA for comparative genomic hybridization, genotyping and mutation detection.

Molecular genotyping has important biomedical and forensic applications. However, limiting amounts of human biological material often yield genomic DNA (gDNA) in insufficient quantity and of poor quality for a reliable analysis. This motivated the development of an efficient whole genome amplification method with quantitatively unbiased representation usable on fresh and degraded gDNA. Amplification of fresh frozen, formalin-fixed paraffin-embedded (FFPE) and DNase-degraded DNA using degenerate oligonucleotide-primed PCR or primer extension amplification using a short primer sequence bioinformatically optimized for coverage of the human genome was compared with amplification using current primers by chromosome-based and BAC-array comparative genomic hybridization (CGH), genotyping at short tandem repeats (STRs) and single base mutation detection. Compared with current primers, genome amplification using the bioinformatically optimized primer was significantly less biased on CGH in self-self hybridizations, and replicated tumour genome copy number aberrations, even from FFPE tissue. STR genotyping could be performed on degraded gDNA amplified using our technique but failed with multiple displacement amplification. Of the 18 different single base mutations 16 (89.5%) were correctly identified by sequencing gDNA amplified from clinical samples using our technique. This simple and efficient isothermal method should be helpful for genetic research and clinical and forensic applications.

Base Sequence↗

PubMedDate not supplied

[The results of the expert studies on the bone remains from the site of the burial of the family of the former Emperor Nicholas II].

Results of expert studies of bone remains found at the site of burial of the family of late Emperor Nicholas II and subjects in their attendance are presented. All expert evaluations and identification studies (forensic biological, microosteological, forensic dental, medical anthropological, molecular genetic analysis, computer photoblending of the skull and life-time photographs, plastic reconstruction, etc.) are listed. Gunshot and other injuries on bone rudiments are described. Signs of long stay of bone remains in soil are detected. Signs of exposure of some remains to aggressive chemical medium (probably inorganic acid) at the site where they were found are noted. The remains of 9 subjects from group burial near Ekaterinburg are identified as Russian Emperor Nicholas II and his family members (N. A. Romanov, A. F. Romanova, O. N. Romanova, T. N. Romanova, and A. N. Romanova) and persons in their attendance Ye. S. Botkin, A. S. Demidova, A. Ye. Troupp, and I. M. Kharitonov. Official documents of the State Commission are offered.

Bone and Bones↗

PubMed1998

[Genetic polymorphisms of FABP2 and F13A1 loci in Han population].

OBJECTIVE: To find more STR loci usable in forensic medicine and understand the distribution of the genetic polymorphisms of two STR loci FABP2 and F13A1 in the Han population in Chengdu. METHODS: EDTA-blood specimens were collected from 115 healthy unrelated Han individuals in Chengdu, DNA was extracted using Chelex method. The DNA samples were amplified by PCR technique, and the PAGE horizontal electrophoresis was used for typing of the PCR products. RESULTS: The allele frequencies were FABP2*1:0.513,FABP2*2:0.096, FABP2*3:0.330, FABP2*4:0.052, FABP2*5:0.009, and 10 genotypes were observed in 115 individuals for FABP2; while for F13A1, the allele frequencies were F13A1*1:0.128, F13A1*2: 0.053, F13A1*3:0.288, F13A1*4:0.527, F13A1*5:0.004 and 10 genotypes were observed in 113 individuals. The result of test for Hardy-Weinberg equilibrium showed that the genotype distribution observed at FABP2 locus was correspondent with the expected. CONCLUSION: FABP2 may be a useful marker for paternity test or personal indentification of biological stain. On the other hand, more studies need to be done to understand the polymorphism at F13A1 locus in Chinese population because a deviation from Hardy-Weinberg equilibrium has been observed in this Han population.

Carrier Proteins↗

PubMed2002

Molecular stability of DNA typing short tandem repeats in the mammary tree of patients with breast cancer.

Archival pathologic specimens are a rich source for the studies of hereditary diseases, cancer genetics, and identification cases in forensic science. In this study, the intraindividual consistency of eight identifying microsatellite polymorphisms (i.e., HMTH01, vWFA31, F13A, MITMH26, FES-FPS, CD4, TPOX, CSF1PO)in a cohort of 40 patients with invasive breast carcinoma were analyzed. Nests of cancer and adjacent morphologically normal ductal-lobular structures (TDLUs) were microdissected as discrete regions from hematoxylin-eosin-stained slides. As controls for each case, DNA templates were prepared from TDLUs located in nontumor quadrants and from unaffected breast skin. Over 1,400 carefully controlled PCR reactions were reviewed, and no evidence was found for microsatellite mismatches among intraindividual cancer and control DNAs. The negative results, supported by validation experiments, strongly argue that alterations of simple repeats are rare somatic events during the onset and progression of breast cancer. This study suggests that PCR artifacts may be a relevant cause of misdiagnosis of microsatellite instability in human sporadic cancer.

Adult↗

PubMed2002

Restriction fragment length polymorphism and polymerase chain reaction: HLA-DQA1 and polymarker analysis of blood samples from transfusion recipients.

The effect of blood transfusion on DNA profiles of an individual is a significant issue in the forensic context. In the present study, the effects of blood transfusion in 5 recipients were studied by performing restriction fragment length polymorphism and polymerase chain reaction HLA-DQA1 and Polymarker (LDLR, GYPA, HBGG, D7S8, and GC) assays (Roche Molecular Systems, Branchburg, NJ) on serial posttransfusion blood samples. Pretransfusion and posttransfusion DNA profiles of all 5 recipients were consistent with no evidence of the donor genetic material. Currently used DNA profiling techniques in forensic science are reliable and informative for paternity and identity purposes in situations involving transfusion of 1 or 2 U of blood up to 24 hours posttransfusion.

Blood Transfusion↗

PubMed1999

Y-chromosomal polymorphic loci DYS19, DYS390, DYS393 in a population sample from northern Poland.

Short tandem repeats (STR) are presently of particular use in the field of forensic science, evolution and anthropology. Y-chromosomal STR systems are widely used for population genetics, population history, and for male identification in forensic cases. Here we present an examination of DYS19, DYS390 and DYS393 allele frequencies in a northern Polish population sample. The calculated indices reflect the potential of these markers for application in forensic casework. Statistically significant differences were observed between most western European populations and the Polish cohort when comparing homogeneity of distribution of DYS19 and DYS390 alleles. For three analyzed loci in a sample of 176 males, 43 haplotypes were observed. The studies revealed some rare alleles and a new allele, allele 16, in the DYS393 system. Sequencing by capillary electrophoresis (PE ABI 310) showed the presence of 16 GATA repetitive elements, confirming results obtained after capillary electrophoresis of the DNA fragment. Additionally, sequencing revealed the presence of a novel transversion (A->C) in the analyzed sample.

Alleles↗