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PubMed2006

CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.

BACKGROUND: Genotyping may be carried out by a number of different methods including direct sequencing and polymorphism analysis. For a number of reasons, PCR-based polymorphism analysis may be desirable, owing to the fact that only small amounts of genetic material are required, and that the costs are low. One popular and cheap method for detecting polymorphisms is by using cleaved amplified polymorphic sequence, or CAPS, molecular markers. These are also known as PCR-RFLP markers. RESULTS: We have developed a program, called CapsID, that identifies snip-SNPs (single nucleotide polymorphisms that alter restriction endonuclease cut sites) within a set or sets of reference sequences, designs PCR primers around these, and then suggests the most parsimonious combination of markers for genotyping any individual who is not a member of the reference set. The output page includes biologist-friendly features, such as images of virtual gels to assist in genotyping efforts. CapsID is freely available at http://bbc.botany.utoronto.ca/capsid. CONCLUSION: CapsID is a tool that can rapidly provide minimal sets of CAPS markers for molecular identification purposes for any biologist working in genetics, community genetics, plant and animal breeding, forensics and other fields.

Computational Biology↗
PubMed2004

[Polymorphism of STR loci D12S391/D18S865 in Wenzhou Han population].

OBJECTIVE: To investigate the polymorphism and forensic efficiency values of STR loci D12S391/D18S865 METHODS: Population studies on D12S391 and D18S865 were carried out in a sample of 454 unrelated Wenzhou Han individuals using PCR followed by PAGE and silver stain detection. RESULTS: 11/7 alleles and 50/21 genotypes of D12S391/D18S865 were respectively observed among the 454 unrelated individuals. The genotype frequency matched the Hardy-Weinberg equilibrium, The heterozygotes (H) in D12S391/D18S865 were 0.7974/0.7379, Power of Exclusion were 0.9566/0.9077, polymorphism information content (PIC) were 0.8260/0.7279 respectively. CONCLUSION: D12S391 and D18S865 were high polymorphic loci and the frequencies were in accordance with Hardy-Weinberg equilibrium (P>0.5), so the two loci can be used in forensic medicine and in other genetic research areas.

Alleles↗
PubMed1998

Population analysis of the collagen type IIalpha1 3' variable number of tandem repeat polymorphism by heteroduplex genotyping.

The AT-rich variable number of tandem repeat (VNTR) marker at the 3' end of the collagen type IIalpha1 (COL2A1) gene has been shown to have a complex structure with extensive sequence variations among repeat units. We analyzed this VNTR polymorphism in a large population of 972 Caucasian individuals with a genotyping procedure involving heteroduplex analysis of PCR products using polyacrylamide gel electrophoresis. Seven size alleles were identified, combining to 19 different homoduplex genotypes (heterozygosity = 0.64). These could be further dissected by analysis of heteroduplexes into 85 different heteroduplex genotypes (heterozygosity = 0.84). By systematically heteroduplexing homozygous and heterozygous individuals in vitro, characteristic heteroduplex doublet bands were generated of known allelic composition. A comparison of these doublets with heteroduplex patterns observed in the population allowed us to identify 29 alleles. The degree of correspondence with a different COL2A1 VNTR genotyping system, based on size separation of single-strand VNTR alleles [1], was investigated by the analysis of samples typed with both methods, including samples from reference CEPH pedigrees. This revealed improved genetic resolution by the heteroduplex method including discrimination of frequent alleles considered identical by the single-strand analysis. Our findings demonstrate heteroduplex analysis of the COL2A1 VNTR to be a robust and highly informative genetic marker system. The documented increased genetic variability has important implications in forensic and paternity testing, as well as in linkage and association studies relating genetic variation at this locus to disease endpoints.

Aged↗
PubMedDate not supplied

[Genetic expertise and the penal process].

The author reflects on the major forensic biology issues related to human genome analysis. He also discusses, from the comparative law perspective, the extent to which genetic test evidence is binding on judges. He concludes with a discussion of the influence of genetic research on people's fundamental rights.

Bioethics↗
PubMed2000

Short Tandem Repeat loci analysis in forensic casework.

The development of polymerase chain reaction typing method has enhanced the possibilities of genetic identification of biological evidence samples for forensic caseworks. The authors report the use of multiplex amplification reactions associating several short tandem repeat loci. These amplification systems produce reliable results and a sufficient incrimination power to send the cases before the court.

Chromosome Mapping↗
PubMedDate not supplied

[Identification of blood stains and fetal tissue using genetic fingerprinting].

Two cases from practical forensic serological investigations which could not be clarified by means of conventional serological methods, but could be resolved on the basis of the DNA finger print technique with oligonucleotide probes are presented. Both the comparison of the identity of the blood sample which had been stored for a long time and the determination of paternity in fetal material in a case of incest demonstrate the enormous possibilities of this method. However, some problems which still have not been resolved at least at present with regard to the evaluation and appraisal of the band patterns are also discussed.

Accidents, Traffic↗
PubMed1994

A non-excluded set method for the calculation of paternity probability.

Forensic judgment of paternity depends on genetic and nongenetic evidence. Sometimes genetic marker tests can provide clear evidence to exclude a falsely accused man, but they do not always succeed. On the other hand, if the accusation is true, the alleged father will not ever be excluded by genetic marker tests. When a nonexclusion case occurs after one or more marker tests, a report of paternity probability is required in the court. The current methods for calculating the paternity probability are the "paternity index method" and the "nonexclusion method." A number of recent articles have openly debated the fallacies, validity and utility of both methods. This paper briefly reviews the two methods and proposes a non-excluded set method along with examples for illustrating the various patterns of paternity probabilities of the three methods.

Forensic Medicine↗
PubMed1995

[Evaluation of allele frequency of the hypervariable locus D17S30 in a sample of populations of European origin from a number of Siberian regions].

Frequencies of alleles of the polymorphic locus D17S30 were estimated in a sample of 121 unrelated Siberian inhabitants of European origin. The main method of study was polymerase chain reaction (PCR). The consecutive use of two pairs of primers allowed increasing of the specificity and sensitivity of the amplification reaction. The results of this study may be of theoretical interest for studies in population genetics. They may also find practical application in forensic medical examination and in the diagnosis of some genetic abnormalities.

Alleles↗
PubMed2006

Noninvasive genotyping of 9 Y-chromosome specific STR loci using circulatory fetal DNA in maternal plasma by multiplex PCR.

BACKGROUND: Human Y-Chromosome specific STR (Y-STR) has now become a useful loci in casework. However, noninvasive genotyping of multiple Y-STR loci and its application in prenatal genetic diagnosis haven't been reported. The purpose of this study is to develop a Y-STR multiplex PCR amplification system that is suitable for the amplification of short-sized templates of circulatory male fetal DNA and use the established multiplex in noninvasive prenatal genetic diagnosis and its further applications in forensic casework. METHODS: On the basis of the characteristic of circulatory fetal DNA in maternal plasma, we selected 9 Y-STR loci in which the allele size was less than 180 bp in length and developed two multiplexes that allowed fluorescent genotyping of 9 Y-STR loci simultaneously. These Y-STR loci include two trinucleotide repeats (DYS426 and DYS388) and seven tetranucleotide repeats (DYS393, DYS460, H4; DYS391, DYS389 I, DYS456 and DYS458). Sixty-four pairs of plasma DNA samples from pregnant women and genomic DNA samples from their husbands were detected by our method. RESULTS: As a result, an average of 7.3 Y-STR specific alleles was detected in each of the 30 plasma DNA samples from pregnancies with male fetuses. However, none of these 9 Y-STR specific alleles was detected in 34 plasma samples from pregnant women carrying female babies. The chances of detecting Y-STR alleles ranged from 66.7 to 93.3%. Fifty-eight haplotypes were detected in 64 unrelated Chinese male individuals; haplotype diversity was 0.9966. This highly polymorphic Y-STR multiplex has greatly improved the chances of detecting the Y-STR allele. CONCLUSIONS: This assay provides a sensitive, accurate and efficient method for noninvasive prenatal genetic diagnosis and forensic casework.

Alleles↗
PubMedDate not supplied

Frequencies of salivary genetic marker systems in the Japanese population and their application to forensic medicine.

Seven salivary polymorphic systems were studied using whole and parotid saliva from random Japanese individuals. The gene frequencies obtained were: Pa+ = 0.212, Pb1 = 1.000, Pb2 = 0, Pr1 = 0.763, Pr2 = 0.237, Db+ = 0.051, Pm+ = 0.409, Ph+ = 0.026 and Amy1v = 0.013, respectively. Based on these gene frequencies, the chances for exclusion of falsely alleged fathers were calculated. The chance of exclusion on the basis of five salivary polymorphic systems was 0.305. The combined chance of exclusion utilizing only blood, serum and red-cell enzyme polymorphic systems among the Japanese population was 0.919; however, by applying salivary polymorphic systems to the calculation, the total exclusion rose to 0.944.

Black People↗
PubMed2002

[The polymorphism of four Y-STR loci and its application in forensic medicine].

We have obtained the alleles and haplotype distribution of 100 unrelated males from the Chinese Han and Zhuang populations at the four Y chromosome-specific loci A10, C4, A7.1, A7.2 by fluorescent primers and with 377 DNA sequencer. We observed 7, 6, 6, 6 alleles in loci A10, C4, A7.1, A7.2 respectively, the gene diversity (GD) values are 0.7776/0.629, 0.773/0.732, 0.5978/0.7272, 0.6664/0.6458 (Zhuang/Han). 114 haplotypes were found in 200 males, haplotype diversity (HD) values are 0.9786, 0.9772 (Zhuang/Han). We have confirmed the core repeats and its repeating number of these alleles by sequencing. A tetraplex PCR system consisting of the A10, C4, A7.1 and A7.2 loci was set up and it is of good specificity. We investigated the validation at these four Y-STRs loci in forensic application such as the male specificity, genetic stability and the sensitivity. In conclusion, the four Y-STRs loci are very suitable to forensic medicine analysis and paternity test.

Alleles↗
PubMed1995

Frequency distribution of hypervariable VNTRs in Apo B, HVR-Ig and COL2A1 loci in Taiwan: forensic application.

By use of a simple, rapid and reliable polymerase chain reaction (PCR)-based method, we analyzed three hypervariable tandem repeats in the 3'-Apo B, 5'-HVR-Ig and 3'-COL2A1 loci. As accurate data of allele frequency of genetic markers is a prerequisite for forensic application, the allele frequency distribution of the three variable number of tandem repeats (VNTR) among the Chinese population in Taiwan were studied. In a total of 123 unrelated Chinese subjects, the Apo B VNTR demonstrated a heterozygosity of 68.2% with 9 alleles, 0.85 of the power of discrimination (PD) value and 0.74 of the allelic diversity (h) value. In a sample of 103 unrelated Chinese subjects, the COL2A1 VNTR showed 49.0% heterozygosity with six alleles, 0.79 of the PD value and 0.74 of the h value. In 106 unrelated subjects, the HVR-Ig VNTR showed 47.4% heterozygosity with seven alleles, 0.79 of the PD value and 0.59 of the h value. The data obtained in this study are not only useful for forensic identification, but will also be helpful for paternity testing, genetic linkage studies and the identification of the three VNTR loci associated with human genetic diseases. Some verifying examinations for the validity and reliability of the three VNTR were performed. The high sensitivity and inexpensive nature of this approach make it superior to the traditional method of DNA fingerprinting for forensic typing. With the use of this PCR-VNTR system, many forensic cases have been successfully identified. The value of this system is illustrated in the investigation of a rape and murder case.

Adolescent↗
PubMedDate not supplied

[A population genetics study of the allelic polymorphism in the hypervariable region of the apolipoprotein B gene in the population of different regions of Ukraine].

The allelic variation of the hypervariable locus from 3'-untranslated region of apolipoprotein B gene in healthy volunteers from different regions of Ukraine was analysed. Among 396 DNA samples studied, 13 allelic variants were identified with the number of repeats ranging from 29 to 53. The frequency of alleles varied from 0.0013 to 0.3575 with the mean heterozygosity index 77.9%. The investigation of the genetic differences between 4 populations of different regions of Ukraine has been performed. A high level of the polymorphism and a heterozygosity index of APOB locus allow to recommend this polymorphic system as an informative marker for study of genetic structure population and to forensic medical analysis.

Alleles↗
PubMed1992

Reporting of highly individual genetic typing results: a practical approach.

This paper considers the interpretation of serological typing data as a problem in forensic science, as opposed to a problem in population genetics or statistics. Controversies arising in this area are partly due to an overly narrow perspective that ignores basic forensic science principles. After an initial discussion of the special problem that deoxyribonucleic acid (DNA) blood typing poses to forensic science, the three difficulties common to all the proposed interpretive methods are discussed. These are: predicting genotype incidence from allele frequencies, predicting frequencies for the joint occurrence of genotypes in a number of different genetic marker systems, and determining the appropriate population to use to measure the frequencies. The inability to test assumptions that are inherent in our routine methods is noted. This is a procedural weakness that unnecessarily limits the admissibility of DNA typing evidence in court. A practical solution to this problem is offered that begins with minimal assumptions. Initially a statement is made based on (1) how many reference samples the laboratory has typed and (2) how many of these samples show genotypes corresponding to the case samples. The second stage of the presentation begins with a statement that additional assumptions are necessary to fully interpret the evidence and that although these assumptions are scientifically very reasonable, they cannot be absolutely proven. The presentation can then proceed, if desired, to consideration of the specific assumptions and frequency estimates of any of the methods that have been proposed to date. To follow this approach population data must be kept in a form that allows the simple first-stage statement to be made. This means that each individual's record would include typing results in each genetic marker system. Although this method of data storage differs from that used in most forensic science laboratories, it is exceptionally versatile, and allows great flexibility in data analysis.

Alleles↗
PubMed2006

Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in forensic and ancient DNA studies.

We evaluate the usefulness of a commercially available microchip CE (MCE) device in different genetic identification studies performed with mitochondrial DNA (mtDNA) targets, including the haplotype analysis of HVR1 and HVR2 and the study of interspecies diversity of cytochrome b (Cyt b) and 16S ribosomal RNA (16S rRNA) mitochondrial genes in forensic and ancient DNA samples. The MCE commercial system tested in this study proved to be a fast and sensitive detection method of length heteroplasmy in cytosine stretches produced by 16 189T>C transitions in HVR1 and by 309.1 and 309.2 C-insertions in HVR2. Moreover, the quantitative analysis of PCR amplicons performed by LIF allowed normalizing the amplicon input in the sequencing reactions, improving the overall quality of sequence data. These quantitative data in combination with the quantification of genomic mtDNA by real-time PCR has been successfully used to evaluate the PCR efficiency and detection limit of full sequencing methods of different mtDNA targets. The quantification of amplicons also provided a method for the rapid evaluation of PCR efficiency of multiplex-PCR versus singleplex-PCR to amplify short HV1 amplicons (around 100 bp) from severely degraded ancient DNA samples. The combination of human-specific (Cyt b) and universal (16S rRNA) mtDNA primer sets in a single PCR reaction followed by MCE detection offers a very rapid and simple screening test to differentiate between human and nonhuman hair forensic samples. This method was also very efficient with degraded DNA templates from forensic hair and bone samples, because of its applicability to detect small amplicon sizes. Future possibilities of MCE in forensic DNA typing, including nuclear STRs and SNP profiling are suggested.

Animals↗
PubMed2000

Analysis of eight polymorphic human genetic markers in a well-defined Greek population.

The use of DNA in forensic science has become a basic tool for person identification or parentage testing. The use of polymorphic markers permits the formation of a unique profile for each individual. The knowledge of allele frequencies in a given population allows the scientist to estimate the probability of a particular allele combination. For this task, allele databanks are essential. In this report, the authors estimate the frequencies of eight polymorphic markers (namely, HumFES, HumF13A1, HumTHO1, HumVWA, HumFABP2, HumLIPOL, D1S80, and D17S5) in a randomly selected sample from Crete, Greece. The allele profile of all markers, with the exception of D17S5 and HumFABP2, concurs with previous reports and international data.

Alleles↗