The forensic DNA implications of genetic differentiation between endogamous communities

Forensic genetics and genomics: Much more than just a human affair

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.

Outlining the Ancestry Landscape of Colombian Admixed Populations

The ancestry of the Colombian population comprises a large number of well differentiated Native communities belonging to diverse linguistic groups. In the late fifteenth century, a process of admixture was initiated with the arrival of the Europeans, and several years later, Africans also became part of the Colombian population. Therefore, the genepool of the current Colombian population results from the admixture of Native Americans, Europeans and Africans. This admixture occurred differently in each region of the country, producing a clearly stratified population. Considering the importance of population substructure in both clinical and forensic genetics, we sought to investigate and compare patterns of genetic ancestry in Colombia by studying samples from Native and non-Native populations living in its 5 continental regions: the Andes, Caribe, Amazonia, Orinoquía, and Pacific regions. For this purpose, 46 AIM-Indels were genotyped in 761 non-related individuals from current populations. Previously published genotype data from 214 Colombian Natives from five communities were used for population comparisons. Significant differences were observed between Native and non-Native populations, among non-Native populations from different regions and among Native populations from different ethnic groups. The Pacific was the region with the highest African ancestry, Amazonia harboured the highest Native ancestry and the Andean and Orinoquían regions showed the highest proportion of European ancestry. The Andean region was further sub-divided into 6 sub-regions: North East, Central West, Central East, West, South West and South East. Among these regions, the South West region showed a significantly lower European admixture than the other regions. Hardy-Weinberg equilibrium and variance values of ancestry among individuals within populations showed a potential stratification of the Pacific population.

Northern Slavs from Serbia do not show a founder effect at autosomal and Y-chromosomal STRs and retain their paternal genetic heritage

Studies on Y-chromosomal markers revealed significant genetic differentiation between Southern and Northern (Western and Eastern) Slavic populations. The northern Serbian region of Vojvodina is inhabited by Southern Slavic Serbian majority and, inter alia, Western Slavic (Slovak) and Eastern Slavic (Ruthenian) minorities. In the study, 15 autosomal STR markers were analysed in unrelated Slovaks, Ruthenians and Serbs from northern Serbia and western Slovakia. Additionally, Slovak males from Serbia were genotyped for 17 Y-chromosomal STR loci. The results were compared to data available for other Slavic populations. Genetic distances for autosomal markers revealed homogeneity between Serbs from northern Serbia and Slovaks from western Slovakia and distinctiveness of Serbian Slovaks and Ruthenians. Y-STR variation showed a clear genetic departure of the Slovaks and Ruthenians inhabiting Vojvodina from their Serbian neighbours and genetic similarity to the Northern Slavic populations of Slovakia and Ukraine. Admixture estimates revealed negligible Serbian paternal ancestry in both Northern Slavic minorities of Vojvodina, providing evidence for their genetic isolation from the Serbian majority population. No reduction of genetic diversity at autosomal and Y-chromosomal markers was found, excluding genetic drift as a reason for differences observed at autosomal STRs. Analysis of molecular variance detected significant population stratification of autosomal and Y-chromosomal microsatellites in the three Slavic populations of northern Serbia, indicating necessity for separate databases used for estimations of frequencies of autosomal and Y-chromosomal STR profiles in forensic casework. Our results demonstrate that regarding Y-STR haplotypes, Serbian Slovaks and Ruthenians fit in the Eastern European metapopulation defined in the Y chromosome haplotype reference database.

Forensic analysis of polymorphism and regional stratification of Y-chromosomal microsatellites in Belarus

Nine loci defining minimal haplotypes and four other Y-chromosomal short tandem repeats (Y-STRs) DYS437, DYS438, DYS439 and GATA H4.1 were analysed in 414 unrelated males residing in four regions of Belarus. Haplotypes of 328 males were further extended by 7 additional Y-STRs: DYS388, DYS426, DYS448, DYS456, DYS458, DYS460 and DYS635. The 13-locus haplotype diversity was 0.9978 and discrimination capacity was 78.7%, indicating presence of identical haplotypes among unrelated males. Seven additional Y-STRs enabled almost complete discrimination of undifferentiated 13-locus haplotypes, increasing haplotype diversity to 0.9998 and discrimination capacity to 97.9%. Analysis of molecular variance of minimal haplotypes excluded the use of a Y-STR database for Belarusians residing in northeastern Poland as representative for the Belarusian population in forensic practice, and revealed regional stratification within the country. However, four additional markers (DYS437, DYS438, DYS439 and GATA H4.1) were shown to eliminate the observed geographical substructure among Belarusian males. The results imply that in case of minimal and PowerPlex Y haplotypes, a separate frequency database should be used for northern Belarus to estimate Y-STR profile frequencies in forensic casework. In case of Yfiler haplotypes, regional stratification within Belarus may be neglected.

A simple and improved correction for population stratification in case-control studies

Population stratification remains an important issue in case-control studies of disease-marker association, even within populations considered to be genetically homogeneous. Campbell et al. (Nature Genetics 2005;37:868-872) illustrated this by showing that stratification induced a spurious association between the lactase gene (LCT) and tall/short status in a European American sample. Furthermore, existing approaches for controlling stratification by use of substructure-informative loci (e.g., genomic control, structured association, and principal components) could not resolve this confounding. To address this problem, we propose a simple two-step procedure. In the first step, we model the odds of disease, given data on substructure-informative loci (excluding the test locus). For each participant, we use this model to calculate a stratification score, which is that participant's estimated odds of disease calculated using his or her substructure-informative-loci data in the disease-odds model. In the second step, we assign subjects to strata defined by stratification score and then test for association between the disease and the test locus within these strata. The resulting association test is valid even in the presence of population stratification. Our approach is computationally simple and less model dependent than are existing approaches for controlling stratification. To illustrate these properties, we apply our approach to the data from Campbell et al. and find no association between the LCT locus and tall/short status. Using simulated data, we show that our approach yields a more appropriate correction for stratification than does principal components or genomic control.

The appropriate use of subpopulation corrections for differences in endogamous communities

Zhivotovsky et al. [L.A. Zhivotovsky, S. Ahmed, W. Wang, A. Bittles, The forensic DNA implications of genetic differentiation between endogamous communities, Forensic Sci. Int. 119 (2001) 269-272] gave an estimate of 0.13 for the coancestry coefficient, theta in three co-resident Pakistani communities. Wang et al. [W. Wang, S.G. Sullivan, S. Ahmed, D. Chandler, L.A. Zhivotovsky, A.H. Bittles, A genome-based study of consanguinity in three co-resident endogamous Pakistan communities, Ann. Hum. Genet. 94 (2000) 41-49] explain that the sampling is from extended families but conclude that "the present findings show that differentiation resulting from genetic stratification by genetic relatedness can be very pronounced in specific populations and thus be important in the evaluation of forensic DNA evidence." In this paper we present simulation results that show that sampling from families will be expected to produce high values of theta regardless of the population value for theta. A theta value estimated in this way cannot be used in formulae suggested by NRC II [NRC II, National Research Council Committee on DNA Forensic Science, The Evaluation of Forensic DNA Evidence, National Academy Press, Washington, DC, 1996] (Eqs. (1) and (2)) to estimate the match probability for a DNA profile in a subpopulation. Whilst it may have some application to estimating the match probability from the pedigree itself there are superior methods for assigning match probabilities for relatives.

Genetic Structure Among 38 Populations from the United States Based on 11 U.S. Core Y Chromosome STRs*

A DNA database consisting of the 11 Y chromosome short-tandem-repeat (Y-STR) recommended by the Scientific Working Group on DNA Analysis Methods is constructed for 2517 individuals from 38 populations in the United States. The population samples derive from five ethnic groups currently living in 10 states. A multidimensional scaling (MDS) plot places the populations into four discrete clusters (African Americans (AA), European Americans (EA), Hispanic Americans (HA), and Asian Americans (SA)) and one dispersed cluster of Native Americans. An analysis of molecular variance (AMOVA) indicates that a large proportion of the total genetic variance is partitioned among ethnic groups (24.8%), whereas only a small amount (1.5%) is found among-populations within ethnic groups. Separate AMOVA analyses within each ethnic group show that only the NA sample contains statistically significant among-population variation. Pair wise population differentiation tests do uncover heterogeneity among EA and among HA populations; however, this is due to only a single sample within each group. The analyses support the creation of AA, EA, HA, and Asian American databases in which samples from different geographic regions within the United States are pooled. We recommend that separate databases be constructed for different NA groups.

Endogamy, consanguinity and community disease profiles

Considerable attention is paid to the role of consanguineous marriage as a causative factor in the prevalence of genetic disorders. At the same time, the potential influence of community endogamy on overall levels of homozygosity and disease profiles remains largely under-investigated. With the ongoing global epidemiological transition from infectious to non-communicable disease, the impact of genetic disorders will become increasingly important and a thorough understanding of the determinants of human population-genetic structure will be all the more necessary. In particular, the genetic components of adult-onset diseases will become more obvious and assume greater significance. Similarly, refinements of study design to incorporate intercommunity genetic variation appear to be an essential prerequisite in pharmacogenetic research if the concept of individualized treatments is to achieve reality, with equivalent subject-control comparison difficulties also predicted in forensic genetics.

STR polymorphisms of "forensic loci" in the northern Han Chinese population

A preliminary Chinese DNA database has been constructed by the analysis of samples from 2,211 Han Chinese in Liaoyang City, northeast China. Thirteen autosomal tetranucleotide short tandem repeats (STRs) widely used in forensic identification were selected for the DNA profiling, together with the X-Y homologous gene Amelogenin for sex determination. Only one of the 13 autosomal loci showed significant deviation from Hardy-Weinberg equilibrium in the individuals genotyped. The cumulative discrimination power and power of exclusion of the 13 loci were greater than 0.999999999 and 0.9999888, respectively, giving an average match probability of 5.5 x 10(-15) for the population. Allelic distributions at the vWA, TH01, D13S317, and D16S539 loci differed from African-Americans and US Caucasians, and more detailed population data at these four loci may be needed to ensure their applicability for forensic purposes in Chinese populations. Previously unreported alleles were detected at several loci (some at relatively high frequencies), suggesting the need for their inclusion in the reference allelic ladder to meet the practical standard of forensic profiling in certain Chinese ethnic sub-populations. The preliminary DNA database provides base-line information applicable to the construction of a National Index System for criminal DNA profiling in PR China.

What is the magnitude of the subpopulation effect?

The effect of population subdivision on estimated match probabilities has been raised [Nature 339 (1989) 501; Am. J. Hum. Genet. 48 (1991) 819; Science 254 (1991) 1921]. Previous work [J. Forensic Sci. 39 (1994) 319; J. Forensic Sci. 39 (1994) 988; Am. J. Hum. Genet. 55 (1994) 533] has compared product rule estimates from differing databases and found that the "subpopulation" error may be of the order of a factor of 10. This approach compares an estimate with an estimate. This paper uses simulation to extend these studies by allowing a comparison to a 'true match probability' and supports the conclusion that subpopulation effects are mild. In addition the performance of recommendations 4.1 and 4.2 of NRC II [National Research Council and C.O.D.F. Science, The Evaluation of Forensic DNA Evidence, National Academy Press, Washington, DC, 1996].