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PubMed1993

Physical properties of VNTR data, and their impact on a test of allelic independence.

In this article we describe the physical properties of VNTR data, as well as their effects on the two-dimensional distribution of fragment pairs. Tests of independence of alleles at a locus may confound those physical properties with allele independence. A recently proposed test by Geisser and Johnson is an example. We show that alleles can be strictly independent, yet the proposed test suggests large violations of allele independence because it is sensitive to well-known electrophoretic phenomena.

Alleles↗
PubMed1993

Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing.

We have developed a new method for forensic identification of individuals, in which a panel of biallelic DNA markers are amplified by the PCR, and the variable nucleotides are detected in the amplified DNA fragments by the solid-phase minisequencing method. A panel of 12 common polymorphic nucleotides located on different chromosomes with reported allele frequencies close to .5 were chosen for the test. The allele frequencies for most of the markers were found to be similar in the Finnish and other Caucasian populations. We also introduce a novel approach for rapid determination of the population frequencies of biallelic markers. By this approach we were able to determine the allele frequencies of the markers in the Finnish population, by quantitative analysis of three pooled DNA samples representing 3,000 individuals. The power of discrimination and exclusion of the solid-phase minisequencing typing test with 12 markers was similar to that of three VNTR markers that are routinely used in forensic analyses at our institute. The solid-phase minisequencing method was successfully applied to type paternity and forensic case samples. We also show that the quantitative nature of our method allows typing of mixed samples.

Adult↗
PubMed1996

[A method to calculate the probability of paternity between relatives--a paternity case where the putative father was a deceased granduncle].

To test paternity in a case where the putative father was a deceased uncle of mother (plaintiff's granduncle), we designed a new method to calculate the probability of paternity likelihood. The putative father's genotypes of red cell antigens, HLA and short tandem repeat (STR) polymorphism were estimated from those of mother and sister of the plaintiff. When the probability was calculated from the frequencies in the unrelated individuals (the standard method), a significant bias might be introduced since the putative father and the plaintiff were likely to have the same alleles come from their common ancestry. Therefore, we designed a new method to calculate the likelihood ratio from the frequencies in the group of mother's uncles estimated from mother's genotypes. The probability (0.9299) calculated with our method was found to be lower than that (0.9992) done with the standard method indicating that the new method could remove the bias introduced from the incest.

Adult↗
PubMed1996

Population data on the loci LDLR, GYPA, HBGG, D7S8, and GC in three southwest European populations.

Three Southwest European populations: Galicia (NW Spain), a mixed Spanish population from the rest of Spain (outside Galicia), and a population sample from the Coimbra area (Centre of Portugal) have been studied for the Low Density Lipoprotein Receptor (LDLR), Glycophorin A (GYPA), Hemoglobin G Gammaglobin (HBGG), D7S8 and Group Specific Component (GC). The allele and genotype frequencies found have been compared with other previously published data. All loci meet Hardy-Weinberg expectations in the three sampled populations. There was no evidence of association in any of the three population samples, between the five loci studied. No significant differences were found with Caucasian populations, nevertheless, significant differences were observed between our three population studies and the US SW Hispanic and African populations. The AmpliType PM DNA test greatly facilitates DNA testing in forensic laboratories, providing quick results and a good discrimination power from a single test.

DNA↗
PubMed1997

Population study of the HUMTH01, HUMVWA31A, HUMF13A1, and HUMFES/FPS STR polymorphisms in the north of Portugal.

Allele and genotype frequencies of four short tandem-repeat loci were determined in a population sample from the North of Portugal using the polymerase chain reaction (PCR). After denaturing PAGE, 6 alleles were identified for HUMTH01 (n = 419), 9 alleles for HUMVWA31A (n = 376), 12 alleles for HUMF13A1 (n = 232), and 5 alleles for HUMFES/FPS (n = 409). No deviation from Hardy-Weinberg equilibrium was found. The allele frequencies observed are similar to those of the European populations compared. The combined power of discrimination is 0.999.

Alleles↗
PubMed1997

United States population data on the multiplex short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--and the variable number tandem repeat locus D1S80.

Allele frequencies for three tetrameric short tandem repeat (STR) loci HUMTHO1, TPOX, and CSF1PO and a variable number tandem repeat locus D1S80 were determined in United States Caucasian, African American, and Hispanic sample populations. All loci, except the TPOX locus in the Caucasian sample population, meet Hardy-Weinberg expectations. There is no evidence for association of alleles among the four loci. The allelic frequency data are similar to other comparable data within the same major population group.

Black People↗
PubMed1998

Chilean population data on ten PCR-based loci.

Allele frequencies for ten PCR-based loci LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, D1S80, CSF1PO, TPOX and THO1 were determined in unrelated Chileans from Santiago. All loci except HBGG and THO1 meet Hardy-Weinberg expectations. There is little evidence for association of alleles among the ten loci. Only 3 out of 45 pairwise comparisons demonstrated departures from independence. The allelic frequency data are similar to other comparable data.

Alleles↗
PubMed1997

Basic issues in forensic DNA typing.

DNA analysis has become the standard method in forensic stain typing (termed DNA profiling). In contrast to conventional serological methods, any human tissue or body fluid can be analysed by DNA profiling as long as it contains nucleated cells. The majority of genetic systems studied at the DNA level are derived from "non-coding" portions from the human genome, and are located either in the vicinity of expressed (coding) genes or in stretches of DNA sequences interspersing with the genes. The typing results are usually recorded as DNA fragment lengths or "alleles" indicating the number of core repeat elements for short tandem repeat systems. These typing results do not contain any useful information which might reveal genetic traits or predispositions for inherited disease about the individual studied. Typing systems for DNA profiling are predominantly selected according to criteria related to the robustness for typing of (potentially degraded) forensic specimens, the degree of genetic polymorphism (which influences the chance to exclude a wrongfully accused person), and the amenability to standardisation as a basis to obtain reproducible results.

Alleles↗
PubMedDate not supplied

Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci.

Tetrameric short tandem repeat (STR) polymorphisms are widely used in population genetics, molecular evolution, gene mapping and linkage analysis, paternity tests, forensic analysis, and medical applications. This article provides allelic distributions of the STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TPOX, TH01, and D16S539 in 143 Mestizos from Northeastern Mexico, estimates of contributions of genes of European (Spanish), American Indian and African origin in the gene pool of this admixed Mestizo population (using 10 of these loci); and a comparison of the genetic admixture of this population with the previously reported two polymorphic molecular markers, D1S80 and HLA-DQA1 (n = 103). Genotype distributions were in agreement with Hardy-Weinberg expectations (HWE) for almost all 13 STR markers. Maximum likelihood estimates of admixture components yield a trihybrid model with Spanish, Amerindian, and African ancestry with the admixture proportions: 54.99% +/- 3.44, 39.99% +/- 2.57, and 5.02% +/- 2.82, respectively. These estimates were not significantly different from those obtained using D1S80 and HLA-DQA1 loci (59.99% +/- 5.94, 36.99% +/- 5.04, and 3.02% +/- 2.76). In conclusion, Mestizos of Northeastern Mexico showed a similar ancestral contribution independent of the markers used for evolutionary purposes. Further validation of this database supports the use of the 13 STR loci along with D1S80 and HLA-DQA1 as a battery of efficient DNA forensic markers in Northeastern Mestizo populations of Mexico.

Genetic Markers↗
PubMed2004

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing.

The development of new methodologies for high-throughput SNP analysis is one of the most stimulating areas in genetic research. Here, we describe a rapid and robust assay to simultaneously genotype 17 mitochondrial DNA (mtDNA) coding region SNPs by minisequencing using SNaPshot. SNaPshot is a methodology based on a single base extension of an unlabeled oligonucleotide with labeled dideoxy terminators. The set of SNPs implemented in this multiplexed SNaPshot reaction allow us to allocate common mitochondrial West Eurasian haplotypes into their corresponding branch in the mtDNA skeleton, with special focus on those haplogroups lacking unambiguous diagnostic positions in the first and second hypervariable regions (HVS-I/II; by far, the most common segments analyzed by sequencing). Particularly interesting is the set of SNPs that subdivide haplogroup H; the most frequent haplogroup in Europe (40-50%) and one of the most poorly characterized phylogenetically in the HVS-I/II region. In addition, the polymorphic positions selected for this multiplex reaction increase considerably the discrimination power of current mitochondrial analysis in the forensic field and can also be used as a rapid screening tool prior to full sequencing analysis. The method has been validated in a sample of 266 individuals and shows high accuracy and robustness avoiding both the use of alternative time-consuming classical strategies (i.e. RFLP typing) and the need for high quantities of DNA template.

DNA Primers↗
PubMed2004

A genetic basis for anomalous band patterns encountered during DNA STR profiling.

Since 1995 the Forensic Science Service (FSS) has carried out DNA profiling of reference samples for the UK National DNA Database and in forensic casework using two multiplex STR profiling systems. During this period, profiles with anomalous banding patterns, although comparatively rare, have been encountered regularly. The FSS has collected instances of triallelic patterns and aberrant diallelic patterns. A systematic examination of these patterns has provided insight into their underlying genetic cause. The triallelic patterns could be classified into two types based on the relative intensities of their component alleles. In the Type 1 pattern the alleles were of uneven intensity, whereas in the Type 2 pattern, all three alleles were of even intensity. Evidence is presented that the more frequent Type 1 pattern is the result of somatic mutation at a heterozygous locus, and the Type 2 pattern is the result of a localized chromosomal rearrangement at a heterozygous locus. Directly from the Type 1 pattern, it was possible to deduce the size difference between the progenitor and mutated allele. All mutational changes were found to be multiples of four nucleotides, suggesting the loss or addition of one or more tetrameric repeat units. Aberrant diallelic patterns were identified by analysts due to an unexpectedly large difference in intensity between alleles at a heterozygous locus. While some of these diallelic patterns are likely caused by the same genetic phenomena described above occurring at a homozygous locus, others are demonstrated to be caused by a mutation in the primer binding sequence, leading to a reduction in amplification efficiency of one allele. It is concluded that based on a visual inspection of a profile, it is possible to infer a likely genetic basis directly from the triallelic pattern. By contrast, the aberrant diallelic patterns can be due to any one of a number of possible genetic effects.

Child↗
PubMed2005

Forensic evaluation of the QIAshredder/QIAamp DNA extraction procedure.

The potential to recover genetic profiles from evidence samples has substantially increased since robust and sensitive amplification kits are commercially available. Nevertheless, even the best amplification kits cannot succeed when the extracted DNA is of poor quality. In this study we compared the efficiency of silica (QIAamp DNA Mini Kit), Chelex and Phenol-Chloroform (PC) based protocols to recover DNA from different categories of samples (blood and saliva on cotton swabs, muscles, cigarette butts, saliva on foods and epidermal cells on clothes). The efficiency of the QIAamp system was improved when samples were treated with QIAshredder homogenizing columns. Overall, conventional Chelex or PC protocols allowed to recover conclusive SGM Plus profiles for 61% of the samples considered in this study. Contrastingly, 82% of them were successfully genotyped after being treated with a combination of QIAshredder and QIAamp systems. Our results further suggested that the QIAshredder/QIAamp protocol was particularly helpful to analyze evidence samples with few DNA and/or that were collected on substrates containing PCR inhibitors.

Blood Chemical Analysis↗
PubMed1992

Conserved, extended MHC haplotypes.

Extended major histocompatibility complex (MHC) haplotypes are fixed conserved regions of the short arm of the sixth human chromosome defined by their HLA-B, complotype (BF, C2, C4A, C4B), HLA-DR alleles. The regions of conservation may extend further. At least a third of normal MHC haplotypes in Caucasians are extended, and they are largely responsible for previously observed linkage disequilibrium in the region. They are relatively population-specific. Their presence has major implications for tissue transplantation, and particularly for the identification of unrelated donor-recipient pairs, since matching for extended haplotypes probably optimizes engraftment in individuals who have them. Even for those who do not, extended haplotypes provide the means for identifying likely MLR-I-negative donor-recipients, and for identifying the genes involved in this function. Extended haplotypes provide most of the markers for HLA-associated autoimmune diseases; like the MHCs of inbred and inbred recombinant strains of mice, they have aided in the analysis of the contribution of specific genes in this region to disease susceptibility and immune functions, particularly the antibody response. Finally, extended haplotypes must be taken into account when considering population genetic questions and when using HLA markers to identify individuals in forensic applications.

Asthma↗
PubMed2000

Genetic analysis of the Utah population: a comparison of STR and VNTR loci.

Genetic data are reported for nine short tandem repeat (STR) loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820) and six variable number of tandem repeat (VNTR) loci (D2S44, D10S28, D4S139, D1S7, D5S110, and D17S79) in samples of Utah African Americans, European Americans, and Hispanics. Little evidence of departures from Hardy-Weinberg equilibrium or gametic equilibrium was found in these populations. Because of their relatively higher mutation rates, the VNTR loci exhibited higher average heterozygosity and lower FST levels than did the STR loci. Genetic distance analysis showed congruence between the two types of systems, and a genetic distance analysis of the STR data showed that the three Utah populations are genetically similar to the same ethnic groups in other parts of the United States. In addition, this analysis showed that the African American population is the most genetically divergent, with greater similarity between the Hispanic and European American populations. This analysis demonstrates a high degree of consistency for population designations commonly used in forensic analysis.

Evolution, Molecular↗
PubMed2006

Genetic polymorphisms of 15 STR loci of Chinese Dongxiang and Salar ethnic minority living in Qinghai Province of China.

Fifteen autosomal STRs loci were analyzed from two samples of 178 healthy unrelated autochthonous individuals of Chinese Dongxiang and Salar ethnic minority groups using a multiplex PCR system. Allele frequencies distribution and statistical parameters for all STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA, were determined by the AmpFISTR Identifiler Kit. The observed genotype frequencies and expected of genotype frequencies were evaluated by chi(2)-test and the Fisher exact tests. chi(2)-test showed that the agreement with Hardy-Weinberg equilibrium (p>0.05) was for all studied STR loci of two populations. The data in the present study can be used greatly for routine forensic application in the region, and enrich Chinese ethnical genetic informational resources.

Alleles↗