Statistical analysis of data for three British ethnic groups from a new STR multiplex

Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity

Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 244 human groups. We find higher false inclusion rates for mixtures with more contributors, and for groups with lower genetic diversity. Even for two-contributor mixtures where one contributor is known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 56 out of 244 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.

Population data for 23 autosomal STR loci in White British population

We report allele frequencies and standard population genetics parameters for 23 forensic autosomal STR loci tested among White British population. In addition, we use generated allele frequency data to compare the extent of genetic variation with 19 other European populations.

Fitting the Balding-Nichols model to forensic databases

Large forensic databases provide an opportunity to compare observed empirical rates of genotype matching with those expected under forensic genetic models. A number of researchers have taken advantage of this opportunity to validate some forensic genetic approaches, particularly to ensure that estimated rates of genotype matching between unrelated individuals are indeed slight overestimates of those observed. However, these studies have also revealed systematic error trends in genotype probability estimates. In this analysis, we investigate these error trends and show how they result from inappropriate implementation of the Balding-Nichols model in the context of database-wide matching. Specifically, we show that in addition to accounting for increased allelic matching between individuals with recent shared ancestry, studies must account for relatively decreased allelic matching between individuals with more ancient shared ancestry.

Population genetic study in two Transylvanian populations using forensically informative autosomal and Y-chromosomal STR markers

Our study provides population genetic data on two population samples collected in a Hungarian speaking region of Transylvania, Romania. Allele frequency and profile databases were generated on 17 autosomal STR loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, VWA, FGA, TH01, TPOX, CSF1PO, Penta E and Penta D) as well as at the 12 European Y-STR extended haplotype loci (DYS19, DYS389-I/II, DYS390, DYS391, DYS392, DYS393, DYS385 loci, DYS437, DYS438 and DYS439). Data were compared to a Central Hungarian (Budapest region) population sample [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27] that was used as a reference group of the Hungarian population. Calculating the F(ST) indices and with the pairwise comparisons of interpopulation molecular variance (AMOVA) the two populations from Transylvania could be fit into the Hungarian population data showing less substructuring effects as compared to the previous findings in Hungary [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27; B. Egyed, S. Füredi, M. Angyal, I. Balogh, L. Kalmar, Z. Padar, Analysis of the population heterogeneity in Hungary using fifteen forensically informative STR markers, Forensic Sci. Int. 158 (2005) 244-249].

Race and genetics: Controversies in biomedical, behavioral, and forensic sciences

Among biomedical scientists, there is a great deal of controversy over the nature of race, the relevance of racial categories for research, and the proper methods of using racial variables. This article argues that researchers and scholars should avoid a binary-type argument, in which the question is whether to use race always or never. Researchers should instead focus on developing standards for when and how to use racial variables. The article then discusses 1 context, criminology, in which the use of racial variables in behavioral genetics research could be particularly problematic. If genetic studies of criminalized behavior use forensic DNA databanks or forensic genetic profiles, they will be confounded by the many racial biases of the law enforcement and penal system.

A method for distinguishing consanguinity and population substructure using multilocus genotype data

We use the patterns of homozygosity at multiple loci to distinguish between excess homozygosity caused by consanguineous mating and that due to undetected population subdivision (the Wahlund effect). Clarification of the underlying causes of excess homozygosity is of practical importance in explaining the occurrence of recessive genetic disorders and in forensic match probability calculations. We calculated a likelihood surface for two parameters: C, the proportion of the population practicing consanguinity, and theta, the genetic correlation due population subdivision. To illustrate the method, we applied it to multilocus genotypic data of two U.K. Asian populations, one practicing a high frequency of cousin marriage, and another in which caste endogamy was suspected. The method was able to successfully distinguish the different patterns of relatedness. The method also returned accurate estimates of C and theta using simulated data sets. We show how our method can be extended to allow for degrees of inbreeding closer than cousin unions, including selfing. With closer inbreeding, the relatedness of recent ancestors beyond the parents becomes an issue.

Inferring ethnic origin by means of an STR profile

We report the use of DNA profiles from six STR loci for inferring the ethnic origin of a crime stain and discuss how such inference may be used as intelligence information to reduce the expected number of interviews to resolve a case. To enable this work, databases have been created for five British ethnic groups (Caucasians, Afro-Caribbeans, Indian sub-continentals, Southeast Asians and Middle Easterners) that together comprise 99.7% of the UK population.

Sequenced allelic ladders and population genetics of a new STR multiplex system

The advent of PCR technology and use of short tandem repeat (STR) loci improves throughput and reduces costs whilst a high level of discrimination can be achieved. A new system, comprising seven STRs, was developed to compliment the existing systems. This paper describes the preparation of allelic ladders of the most commonly observed alleles of a new STR multiplex system (third generation; TGM multiplex); all alleles have been sequenced. Meioses studies estimated a mutation rate of 0-0.4% across loci. Statistical independence was investigated by employing exact tests; chi(2)-tests and excess homozygosity tests. The results demonstrated that the allele proportions do not differ from those expected and that there was no consequential dependence between loci. The discriminating power of the system was examined using 295 Caucasian, 140 Afro-Caribbean and 212 Asian unrelated samples, and was found to be approximately 1 in 50 million, 1 in 85 million and 1 in 20 million for each of these groups, respectively.

Genetic differentiation within and between four UK ethnic groups

In previous papers [L.A. Foreman, J.A. Lambert, I.W. Evett, Regional genetic variation in Caucasians, Forensic Sci. Int. 95 (1998) 27-37; L.A. Foreman, Analyses to investigate appropriate measures of differentiation between European Caucasian populations using short tandem repeat (STR) data, FSS Research Report FSS-RR-804 (1999)], we have carried out detailed investigations of the level of regional and national variation in STR characteristics exhibited within white Caucasian populations. The studies described here extend our earlier work to the black African/Caribbean and Asian (Indo-Pakistani) populations of the UK, routinely considered in casework calculations at the Forensic Science Service (FSS). In addition, estimation of allele distributions and database comparisons are carried out for two further populations, i.e. those classified as containing individuals of Oriental and Arabic appearance.

Human autosomal short tandem repeat types in Jat Sikhs from North India

This study provides Jat Sikhs population data in North India for nine short tandem repeat (STR) loci.

Analysis of eight STR loci in two Hungarian populations

A collection of eight STR loci (D3S1358, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) was used to generate allele frequency databases for two Hungarian population samples, Caucasians from the Budapest area and Romanies from Baranya county. During the analysis two intermediate sized alleles and a sequence variant allele were observed at the D7S820 locus. All three types of allelic variants were found to have modification (deletion, insertion, transversion) in the same block of a (T)(9) stretch located within the 3' flanking region of each allele, which may indicate a possible higher mutation rate of this (T)(9) block. For the loci D3S1358 and D7S820 the Romany population database showed departures from Hardy-Weinberg equilibrium. The forensic efficiency values for the Romany population were slightly different from those found in the Hungarian Caucasian population. Comparing the allele frequency values by G-statistic, calculating the F(st) indices and with the pairwise comparisons of inter-population variance, the two Hungarian populations could be distinguished using data of the eight STR loci.

Microsatellite variation in Central Africa: an analysis of intrapopulational and interpopulational genetic diversity

As a part of a research project on molecular variation in Central Africa, we have analyzed 10 microsatellites (CD4, CSFO, D3S1358, D18S51, D21S11, F13A1, FES, TH01, TPOX, and VWA) in the Bamileke and Ewondo from Cameroon and the Sanga and Mbenzele Pygmies from the Central African Republic (a total of 390 chromosomes). A statistically significant trend towards heterozygote deficiency was detected in the Mbenzele Pygmies. This was established through the use of powerful exact tests for the Hardy-Weinberg equilibrium. A certain degree of isolation and a small effective size may explain this finding. However, the lack of any substantial reduction in allelic diversity in the Mbenzele does not support the possibility that this group has a smaller effective size in evolutionary terms. A possible explanation based on ethnographic studies suggests that the gene flow from non-Pygmies to Pygmies could have been interrupted only in relatively recent times. The analysis of association between genotypes at pairs of independent loci indicates that the level of subheterogeneity is markedly lower in the Bamileke than in other sampled populations. This may be explained by the combined effect of larger population size, more rigid respect of clanic exogamy, and higher matrimonial mobility of the Bamileke. Finally, we have analyzed interpopulational relationships among our sampled populations and other Central African populations. The results are consistent with a previous study of protein loci (Spedini et al. 1999), which suggests the recent history of the Bamileke and Ewondo has led them to aquire a substantial genetic similarity. Furthermore, the Mbenzele Pygmies diverge from Biaka Pygmies, despite their common origin and geographical proximity. This is probably due to the differentiating effect of genetic drift, which is enhanced by the small effective size of Pygmy populations.

DNA evidence, probabilistic evaluation and collaborative tests

Forensic scientists working in 12 state or private laboratories participated in collaborative tests to improve the reliability of the presentation of DNA data at trial. These tests were motivated in response to the growing criticism of the power of DNA evidence. The experts' conclusions in the tests are presented and discussed in the context of the Bayesian approach to interpretation. The use of a Bayesian approach and subjective probabilities in trace evaluation permits, in an easy and intuitive manner, the integration into the decision procedure of any revision of the measure of uncertainty in the light of new information. Such an integration is especially useful with forensic evidence. Furthermore, we believe that this probabilistic model is a useful tool (a) to assist scientists in the assessment of the value of scientific evidence, (b) to help jurists in the interpretation of judicial facts and (c) to clarify the respective roles of scientists and of members of the court. Respondents to the survey were reluctant to apply this methodology in the assessment of DNA evidence.

When can a DNA profile be regarded as unique?

The probability that a defendant's DNA profile is unique in a population of untyped individuals is shown to be bounded below by one minus twice the sum of the match probabilities over the population. This bound assumes that the possibility of laboratory or handling error can be neglected, and applies only when there is no non-DNA evidence in favour of the defendant. There cannot be a completely general lower bound: if there is overwhelming non-DNA evidence that the defendant is not the source of the crime stain, then that is also overwhelming evidence of non-uniqueness. Application to k-locus short tandem repeat (STR) profiles is discussed, and illustrated with calculations based on the 6-STR-locus system used in current UK casework. However, because of the problem of the non-DNA evidence, there seems to be no satisfactory way for an expert witness to address the question of uniqueness in court.

Population distribution of six PCR-amplified loci in Madeira Archipelago (Portugal)

Frequency data of the short tandem repeat (STR) loci HUMTH01, HUMVWA31/A, HUMF13A1, HUMFES/FPS, D12S391 and HUMFIBRA/FGA were determined in blood stains obtained from a population of unrelated individuals from the Madeira Archipelago. The observed genotype distribution showed no significant deviation from the Hardy-Weinberg equilibrium and there was no evidence for association of alleles among the six loci. Population data showed a combined discrimination power of 0.9999998 and a chance of exclusion of 0.99597. The frequencies are similar to those of other compared caucasian populations but significant differences were found between the Madeira population and Japanese, Chinese, Greenland Eskimos and Quechua Amerindians. The six loci studied, together proved to be highly discriminating and valuable for forensic cases.

Analysis of the short tandem repeat (STR) locus HumVWA in a Qatari population

Polymerase chain reaction (PCR), amplified DNA fragments and denaturing polyacrylamide gel electrophoresis were used to investigate the STR locus HumVWA in a Qatari population sample (n = 200). Seven alleles were identified with frequencies ranging from 0.0125 to 0.3175. The distribution of genotypes fits the Hardy-Weinberg equilibrium. The HumVWA system shows a power of discrimination of 0.9290 and a chance of paternity exclusion of 60.1% in the population studied.

Regional genetic variation in Caucasians

When evaluating DNA evidence, the necessary calculations are often carried out using databases drawn from broad populations; for example, the Forensic Science Service (FSS) maintains genetic databases for the 3 major racial groups of England and Wales--Caucasian, Afro-Caribbean and Asian (from the Indian subcontinent). The resulting figures may be challenged in court on the premise that they are not based on data from the population of most relevance in the particular case under consideration. One important factor might be the location of the crime. Since the recent establishment of a National DNA Intelligence Database, data have been made available from a wide range of geographical regions in England and Wales. This paper gives details of analyses conducted to measure the differentiation between white caucasian populations from these regions and from other areas of the UK and abroad using a Bayesian approach.

Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat

In 10,844 parent/child allelic transfers at nine short-tandem-repeat (STR) loci, 23 isolated STR mismatches were observed. The parenthood in each of these cases was highly validated (probability >99.97%). The event was always repeat related, owing to either a single-step mutation (n=22) or a double-step mutation (n=1). The mutation rate was between 0 and 7 x 10(-3) per locus per gamete per generation. No mutations were observed in three of the nine loci. Mutation events in the male germ line were five to six times more frequent than in the female germ line. A positive exponential correlation between the geometric mean of the number of uninterrupted repeats and the mutation rate was observed. Our data demonstrate that mutation rates of different loci can differ by several orders of magnitude and that different alleles at one locus exhibit different mutation rates.

Polymerase chain reaction typing of D21S11 short tandem repeat polymorphism by capillary electrophoresis. Allele frequencies and sequencing data in a population sample from central Italy

Blood samples were collected from 100 individuals living in Central Italy and analysed for STR locus D21S11 by capillary electrophoresis on an ABI Prism 310 genetic analyzer. For fragment sizing, PCR amplification products, obtained using a 6-FAM 5'-labeled reverse primer and an unlabeled forward primer, were run with an internal size standard labeled with TAMRA dye and typed using the local reciprocal method. An allele ladder consisting of a mix of sequenced amplified products was also prepared. An Italian population database was established. No deviation from Hardy-Weinberg equilibrium was observed. The result of statistical analysis were highly informative (PD = 0.94; mean exclusion change = 0.66). DNA sequencing was performed on a set of representative alleles by Taq cycle sequencing using dye terminator labeling chemistry. A new structural variant was found.