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PubMed1995

A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity.

A method is proposed for allowing for the effects of population differentiation, and other factors, in forensic inference based on DNA profiles. Much current forensic practice ignores, for example, the effects of coancestry and inappropriate databases and is consequently systematically biased against defendants. Problems with the 'product rule' for forensic identification have been highlighted by several authors, but important aspects of the problems are not widely appreciated. This arises in part because the match probability has often been confused with the relative frequency of the profile. Further, the analogous problems in paternity cases have received little attention. The proposed method is derived under general assumptions about the underlying population genetic processes. Probabilities relevant to forensic inference are expressed in terms of a single parameter whose values can be chosen to reflect the specific circumstances. The method is currently used in some UK courts and has important advantages over the 'Ceiling Principle' method, which has been criticized on a number of grounds.

Alleles↗
PubMed2001

Allelic structure and distribution of two STR loci, D8S580 and D22S442, in the Japanese population.

The allelic frequency and structural characteristics of two STR loci D8S580 and D22S442 were investigated using blood samples from 143 unrelated healthy Japanese individuals. Thirty-eight alleles in D8S580 locus and 13 alleles in D22S442 locus were identified. The discrimination power, heterozygosity, and the polymorphic information content of those loci displayed high values (0.98, 0.88, and 0.87 in D8S580 and 0.97, 0.86 and 0.85 in D22S442), and their frequency distributions met Hardy-Weinberg equilibrium expectations. The allelic pattern of D8S580 was complex and differentiated into three groups (group I: alleles 184-194bp; group II: alleles 203-223, 235, 239, 243, 252 and 255bp; group III: alleles 227-286bp). Most of their alleles contained five categories of repeat units (A: aaaag; B: aaag; C: aagg; D: caag; E: agaa). On the other hand, D22S442 contained only two types of repeat units (A: agga; B: aggg). The present study, hence, proves that both D8S580 and D22S442 are highly polymorphic and represent stable genetic markers applicable to forensic investigations.

Alleles↗
PubMed2000

Forensic validation of a multiplex containing nine STRs--population genetics in northern Poland.

This paper presents the allele frequency distributions for the nine loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) present in the commercially available Profiler Plus kit. DNA samples of 202 individuals from Northern Poland were amplified in a multiplex reaction with subsequent automatic detection using capillary electrophoresis. All loci met the Hardy-Weinberg equilibrium conditions. The calculated probability of identity was 2.26 x 10(-11) giving an average probability of identity of 1 in 44 billion. Considerable improvement of analysis precision was observed after substituting the GeneScan 500 for the fluorescent ladder 60-400 bp. The influence of DNA concentration on stutter and artefact formation and the ratio of heterozygote alleles was analysed.

DNA Fingerprinting↗
PubMed1989

The polymerase chain reaction.

The polymerase chain reaction (PCR) is a powerful new method for 'in vitro cloning'. It can selectively amplify a single molecule of template DNA several millionfold in a few hours and has made possible new approaches to problems in molecular genetics, evolutionary biology, and development.

Biological Evolution↗
PubMed1989

BstEII restriction fragment alleles and haplotypes of the human IGHG genes with reference to the BamHI/SacI RFLPs and to the Gm polymorphism.

In previous studies, we have described, for each of the five human immunoglobulin IGHG (C gamma) genes, BamHI, SacI and BamHI/SacI allelic restriction fragments. Further, we have determined BS (BamHI/SacI) linkage groups of alleles for the whole of the IGHG loci and we have demonstrated correlation with the Gm alleles and haplotypes. In this paper we characterize more precisely the polymorphism of the IGHG genes and, consequently, the structure and evolution of this multigene family, using the restriction enzyme BstEII and two different probes, a IGHG (C gamma) probe and a G3 (C gamma 3) specific probe. Alleles and haplotypes of the BstEII restriction fragments have been defined with reference to the BS alleles and haplotypes. New RFLPs of the IGHG genes are described and unambiguous correlations have been established with most of the Gm alleles and haplotypes. Thus, the IGHG gene RFLPs strengthen the Gm polymorphisms as powerful tools for the characterization of populations, disease and genetic marker linkage analyses, forensic medicine and evolution of these IGHG genes.

Alleles↗
PubMed1997

Validation studies for the genetic typing of the D1S80 locus for implementation into forensic casework.

A series of validation experiments were designed to evaluate, according to the Technical Working Group on DNA Analysis Methods (TWGDAM) guidelines, the analysis of the D1S80 locus for casework implementation. Approximately 400 samples from three different populations (Minnesota Caucasian, Minnesota African Americans, and Minnesota Native Americans) were typed to determine allele frequencies. Simulated forensic type specimens (blood, saliva, hair and semen, or vaginal secretions) were typed to demonstrate that deoxyribonucleic acid (DNA) extracted from various tissues of an individual yield the same D1S80 type. Dilution studies were performed and it was determined that a wide range of input DNA (0.5 ng to 40.0 ng) will consistently yield typeable results. The evaluation of DNA from various animals showed that the D1S80 locus is specific to human DNA within the limits of the parameters tested. The reproducibility of the system was tested by duplicate analysis of approximately 200 population samples. Duplicate samples were analyzed on both horizontal and vertical gel systems. In addition, simulated forensic specimens were analyzed by two independent laboratories: the Minnesota Forensic Science Laboratory (MFSL) and the Roche Biomedical Laboratories (RBL). All analyses, including extraction, quantitation, amplification and typing, were performed independently. All typing results for both laboratories were in agreement. By the analysis of mixtures from various simulated casework type mixtures, it was demonstrated that the D1S80 typing system is suitable for analyzing mixtures. In addition to the simulated casework, evidentiary samples from several adjudicated cases previously analyzed by restriction fragment length polymorphism (RFLP) analysis and/or DQA1 were typed at the D1S80 locus. The D1S80 results were consistent with previous RFLP and/or DQA1 results regarding inclusions/exclusions.

Alleles↗
PubMed1997

Genetic variations at four tetrameric tandem repeat loci in Korean population.

Allele and genotype frequencies for four tetrameric short tandem repeat (STR) loci, HumFES/FPS, HumFOLP23, HumGABRB15, and HumCYAR04, have been determined by polymerase chain reaction (PCR) amplification and subsequent polyacrylamide gel electrophoresis from approximately 200 genetically unrelated Koreans. This method allows a single base pair resolution and rapid typing with silver staining. The allele and genotype distributions satisfy Hardy-Weinberg expectation. Also, these STR loci have proven to be useful for forensic analyses and paternity tests in which the variable number of tandem repeat (VNTR) loci have some limitations.

Alleles↗
PubMed1998

[Determination of the presence of traces of biological material using molecular genetics].

Polymerase chain reaction is often used for molecular genetic human identification in forensic medicine today. In this study, the possibilities are demonstrated, which are provided by the method in such cases, where it is necessary to determine, if the biological traces are of animal or human origin. The method is rapid and well performed in a molecular genetic laboratory with standard equipment. Eleven samples of DNA isolated from different animals and birds were examined. In all cases, it was possible to distinguish these samples according to the results of reaction from simultaneously examined human DNA.

Animals↗
PubMed1993

The use of polymorphic Alu insertions in human DNA fingerprinting.

We have characterized several Human Specific (HS) Alu insertions as either dimorphic (TPA25, PV92, APO), slightly dimorphic (C2N4 and C4N4) or monomorphic (C3N1, C4N6, C4N2, C4N5, C4N8) based on studies of Caucasian, Asian, American Black and African Black populations. Our approach is based upon: 1) PCR amplification using primers complementary to the unique DNA sequences that flank the site of insertion of the different Alu elements studied; 2) gel electrophoresis and scoring according to the presence or absence of an Alu insertion in one or both homologous chromosomes; 3) allele frequencies determined by gene counting and compared to Hardy-Weinberg expectations. Our DNA fingerprinting procedure using PCR amplification of diallelic polymorphic (dimorphic) Human Specific Alu insertions, may be used as a tool for genetic mapping, to characterize populations, study human migrational patterns, and track the inheritance of human genetic disorders.

DNA Fingerprinting↗
PubMed2001

Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca) and their usefulness in other spruce species.

Microsatellite DNA/simple-sequence-repeat (SSR) loci were identified, isolated and characterized in white spruce (Picea glauca) by screening both a non-enriched partial genomic library and a partial genomic library enriched for (AG/TC)n-containing clones. Inheritance and linkage of polymorphic SSR loci were determined in F1 progeny of four controlled crosses. We also assessed the compatibility and usefulness of the P. glauca microsatellite DNA markers in five other Picea species. Twenty-four microsatellites were identified by sequencing 32 clones selected from screens of 5,400 clones from the two libraries. The (AG/TC)n microsatellites were the most abundant in the non-enriched library. Eight microsatellite DNA loci were of the single-copy type, and six of these were polymorphic. A total of 87 alleles were detected at the six polymorphic SSR loci in 32 P. glauca individuals drawn from several populations. The number of alleles found at these six SSR loci ranged from 2 to 22, with an average of 14.5 alleles per locus, and the observed heterozygosity ranged from 0.48 to 0.91, with a mean of 0.66 per locus. Parents of the controlled crosses were polymorphic for five of the six polymorphic SSR loci. Microsatellite DNA variants at each of these five SSR loci followed a single-locus, codominant, Mendelian inheritance pattern. Joint two-locus segregation tests indicated complete linkage between PGL13 and PGL14, and no linkage between any of the remaining SSR loci. Each of the 32 P. glauca individuals examined had unique single or two-locus genotypes. With the exception of non-amplification of PGL12 in P. sitchensis, P. mariana, and P. abies and the monomorphic nature of PGL7 in P. mariana, primer pairs for all six polymorphic SSR loci successfully amplified specific fragments from genomic DNA and resolved polymorphic microsatellites of comparable sizes in P. engelmanni, P. sitchensis, P. mariana, P. rubens, and P. abies. The closely related species P. mariana and P. rubens, and P. glauca and P. sitchensiss could be distinguished by the PGL12 SSR marker. The microsatellite DNA markers developed and reported here could be used for assisting various genetics, breeding, biotechnology, tree forensics, genome mapping, conservation, restoration, and sustainable forest management programs in spruce species.

Base Sequence↗
PubMed2003

Characterisation of variant alleles at the HumD21S11 locus implies unique Australasian genotypes and re-classification of nomenclature guidelines.

Several variant alleles of the HumD21S11 locus have only been reported in Australasian population samples. Fifteen such alleles were observed in Caucasian and Australian Aborigine sub-population databases compiled from residents of the state of Western Australia. Each variant was sequenced to authenticate the allelic designation and determine the structural conformation. Nine novel structural variants are described. The structure of the repeat region of these rare alleles combined with the STR designation brings aspects of the HumD21S11 nomenclature guidelines into question, in particular the designation of common incomplete repeats (or "0.2's"). The conformation of the sequences provides evidence in support of a genetic relationship between the Australian Aborigine and the Papuan people.

Alleles↗
PubMed2000

Why genes don't count (for racial differences in health).

There is a paradoxical relationship between "race" and genetics. Whereas genetic data were first used to prove the validity of race, since the early 1970s they have been used to illustrate the invalidity of biological races. Indeed, race does not account for human genetic variation, which is continuous, complexly structured, constantly changing, and predominantly within "races." Despite the disproof of race-as-biology, genetic variation continues to be used to explain racial differences. Such explanations require the acceptance of 2 disproved assumptions: that genetic variation explains variation in disease and that genetic variation explains racial variation in disease. While the former is a form of geneticization, the notion that genes are the primary determinants of biology and behavior, the latter represents a form of racialization, an exaggeration of the salience of race. Using race as a proxy for genetic differences limits understandings of the complex interactions among political-economic processes, lived experiences, and human biologies. By moving beyond studies of racialized genetics, we can clarify the processes by which varied and interwoven forms of racialization and racism affect individuals "under the skin."

Bias↗
PubMed2006

[The genetic polymorphism of 9 short tandem repeat loci in Yi ethnic group of Yunnan in China].

OBJECTIVE: To study the short teadem repeat(STR) genetics structure of a Chinese Yunnan Yi racial group. METHODS: Genetic distributions for nine STR loci were determined based on STR gene scan marked by fluorescence. RESULTS: Sixty-nine alleles and 164 kinds of genotypes were detected and identified from 84 unrelated Yi racial individuals. The corresponding gene and genotype frequencies were in 0.0060-0.5060 or 0.0119-0.4167 respectively. The expected and observed genotype frequencies of nine STR loci were in accordance with the Hardy-Weinberg equilibrium(P>0.05). The statistical analyses of nine STR loci showed that PIC was distributed in 0.5804-0.8777, H was in 0.6507-0.8002, DP was in 0.7976-0.9558, EPP was in 0.5207-0.8386, except TPOX and THO1 loci. CONCLUSION: Above research data enrich the Chinese genetic database, and play an important role in Chinese genetic study and in forensic application.

Asian People↗
PubMed1998

Turkish population data on the HLA-DO alpha, LDLR, GYPA, HBGG, D7s8, and GC loci.

We have determined the allele and genotype frequencies of six PCR-based genetic markers HLA-DQ alpha, LDLR, GYPA, HBGG, D7S8 and GC in the Turkish population (n = 361 for HLA-DQ alpha, and n = 260 for PM). All loci meet Hardy-Weinberg expectations. The frequency data can be used in forensic analyses in the Turkish population.

Alleles↗
PubMed2001

The human Y chromosome: function, evolution and disease.

The human Y chromosome is strictly paternally inherited and, in most of its length, does not recombine during male meiosis. These features make the Y a very useful genetic marker for different purposes. In the last decade, the Y has been increasingly used to investigate the evolution, migrations and range expansions of modern humans. The possibility to construct highly informative Y chromosome haplotypes has also had a significant impact in forensic studies and paternity testing. All these studies assume that the Y chromosome markers used are selectively neutral. However, recent experimental and statistical analyses suggest that both positive and negative selection are acting on the Y chromosome and, consequently, may influence Y chromosome haplotype distribution in the general population. Current data suggest that the effects of selection on patterns of Y chromosome distribution are minimal, however as interest focuses on biological functions of the Y chromosome which have a major impact on male fitness such as fertility, these assumptions may be challenged. This review briefly describes the genes and biological functions of the human Y chromosome and its use in disentangling the origin and history of human populations. An overview of the role of selection acting on the Y chromosome from the perspective of human population histories and disease is given.

Congenital Abnormalities↗