Informativeness of the CODIS STR loci for admixture analysis

Population admixture (or ancestry) is used as an approach to gene discovery in complex diseases, particularly when the disease prevalence varies widely across geographic populations. Admixture analysis could be useful for forensics because an indication of a perpetrator's ancestry would narrow the pool of suspects for a particular crime. The purpose of this study was to use Fisher's information to identify informative sets of markers for admixture analysis. Using published founding population allele frequencies we test three marker sets for efficacy for estimating admixture: the FBI CODIS Core STR loci, the HGDP-CEPH Human Genome Diversity Cell Line Panel and the set of 39 ancestry informative SNPS from the Shriver lab at Pennsylvania State University. We conclude that the FBI CODIS Core STR set is valid for admixture analysis, but not the most precise. We recommend using a combination of the most informative markers from the HGDP-CEPH and Shriver loci sets.     

Third molar development according to chronological age in populations from Spanish and Magrebian origin

Spain is frequently the entrance country into the European Union for undocumented immigrants, especially those from the Magreb (Northern Africa). Forensic age estimates for these persons are difficult because systematic studies of dental maturity are lacking. Three different populations were analyzed to determine the pattern of development of third molars as a tool for age estimation in people of different ethnic and geographic origin. Orthopantomograms from two different populations of Spanish origin (Galicia in northwestern continental Spain, and Ceuta, a Spanish province in Northern Africa) were compared to radiographs of molars from a Magrebian population (Northern Africa) resident in Ceuta. Orthopantomograms were obtained from a private dental clinic (n=344) in Galicia and from the Public Oral Health Services (n=228) in Ceuta. We looked for differences in third molar mineralization (determined with the Demirjian scale) that might serve as age indicators (older versus younger than 18 years). Differences in maturation patterns were found between sexes and populations of origin. Mineralization of tooth 38 was more advanced in males than females among subjects 18 years of age and older in all three populations. Moreover, mineralization of tooth 38 in subjects aged 18 years and older was significantly slower in the Spanish-Galicia population than in the Magrebian-Ceuta population. We found no significant differences between Magrebian and Spanish individuals from Ceuta. We conclude that differences in tooth 38 mineralization may be related more with socio-geographical than ethnic origin (ancestry), and thus constitute evidence of the relevance of socio-geographic rather than genetic factors in third molar development. We used ROC analysis to determine the accuracy of the examiner's ability to correctly estimate age as younger or older than 18 years. The results suggest that Demirjian stage for tooth 38 can be considered a good indicator of age in all three populations.     

Sex determination from the talus of Koreans by discriminant function analysis

The aims of this study were to investigate the sex discriminating potential of the talus in Koreans and compare this with other analyses in different populations. Statistical analyses were performed using data from nine measurements acquired from 140 tali (70 men, 70 women). The talus of Koreans is dimorphic between sexes in all measurements (p < 0.01). Discriminant function equations were generated by univariate, multivariate, and stepwise methods with a range of accuracy from 67.1 to 87.1%. Stepwise equations of other populations did not discriminate the sex of the Korean sample as accurately as each equation's own accuracies. The variables with high accuracy in this study are useful for sex determination of Koreans on the basis of confirmation of population specificity.     

STR data for the AmpFℓSTR Identifiler loci from Swedish population in comparison to European, as well as with non-European population

The modern Swedish population is a mixture of people that originate from different parts of the world. This is also the truth for the clients participating in the paternity cases investigated at the department. Calculations based on a Swedish frequency database only, could give us overestimated figures of probability and power of exclusion in cases including clients with a genetic background other than Swedish. Here, we describe allele frequencies regarding the markers in the Identifiler-kit. We have compared three sets of population samples; Swedish, European and non-European to investigate how these three groups of population samples differ. Also, all three population sets were compared to data reported from other European and non-European populations.Swedish allele frequencies for the 15 autosomal STRs included in the Identifiler kit were obtained from unrelated blood donors with Swedish names. The European and non-European frequencies were based on DNA-profiles of alleged fathers from our paternity cases in 2005 and 2006.     

Self-destructing prophecies: Long-term forecasting of municipal correctional bed need

Although municipal jails consume a significant amount of resources and the number of inmates housed in such facilities exploded in the 1990s, the literature on forecasting jail populations is sparse. Jail administrators have available discussions on jail crowding and its causes, but do not have ready access to applications of forecasting techniques or practical demonstrations of a jail inmate population forecast. This article argues that the underlying reason for this deficiency is the inherent unpredictability of local long-term correctional population levels. The driving forces behind correctional bed need render local jail population forecasts empirically valid only for a brief time frame. These inherent difficulties include the volatile nature of jail populations and their greater sensitivity when compared with prison populations to local conditions; the gap between the data needed for local correctional population forecasting and what is realistically available to forecasters; the lack of reliable lead variables for long-term local correctional population forecasts; the clash of the mathematics of forecasting and the substantive issues involved in the interpretation of forecast models; and the significant political and policy impacts of forecasts on local criminal justice systems and subsequent correctional population trends.The differences between the accuracy of short-term versus long-term jail bed need forecasts means that forecasting local correctional bed need is empirically valid for, at best, one to two years. As the temporal cast is extended, longer-term forecasts quickly become error prone. Except for unique situations where jails exist in highly stable local political, social, and criminal justice environments, long-term forecasts of two years or greater are fatally flawed and have little empirical accuracy. Long-term forecasts of local jail bed needs are useful, though, as policy catalysts to encourage policymakers to consider possible long-term impacts of current decisions, but forecasts should be thought of and presented as one possible future scenario rather than a likely reality. Utilizing a demonstration of a local jail forecast based upon two common empirical forecasting approaches, ARIMA and autoregression, this article presents a case study of the inherent difficulties in the long-term forecasting of local jail bed need.     

Estimating stature from tibia length: a comparison of methods

Most forensic and biological anthropological studies use the stature-estimation formulae developed by Trotter and Gleser. In recent decades, studies of morphological differences between populations have indicated that population-specific formulae are necessary to obtain accurate estimates. A number of equations have been devised for the Turkish population. Previously, we introduced a "general formula" and three "stature-group-specific formulae" based on tibial length. The purpose of the present study was to determine whether formulae in the literature are suitable for estimating height in the Turkish population. To make this assessment, we compared the accuracy of formulae designed for Turkish people to the accuracy of formulae devised for other populations. We also evaluated the accuracy in short, medium, and tall height groupings. The formulae were tested on 110 healthy Turkish male adults, with estimated height compared to true height in each case. Analysis showed that the Trotter-Gleser formula for Mongoloids was most accurate for estimating stature in the study group as a whole. The formulae of Sa?ir for the Turkish population and our previously published "general formula" were the next most accurate methods, respectively. When the 110 subjects were categorized as short (1652 mm and below), medium (1653 to 1840 mm), and tall (1841 and above), the stature-group-specific formulae calculated in the present study were more accurate than all other equations for subjects at the height extremes. The results of this study indicate that stature-group-specific formulae are more reliable for forensic cases.     

D8S384基因座的遗传多态性及其在法医物证检验中的应用

揭示人类自然群体中D8S384基因座的基因型频率,评估D8S384基因座在法医物证中的应用价值,以及建立D8S384基因座的分型方法。用不同基因型PCR产物混合的方法,制备了D8S384等位基因分型标准物,并按照国际法医血液遗传学会DNA委员会推荐的原则命名了等位基因。采用PCR扩增、电泳分析、银染显色的方法,调查了世界3大人种11个群体1103名个体的D8S384基因型。D8S384基因座共有8个等位基因,群体内基因型分布符合Hardy－Weinberg平衡,群体间基因型构成有显著性差异。利用群体数据估计了D8S384基因座的法医学理论应用价值,计算得出D8S384基因座的期望杂合度为0．704±0．014,个人识别机率为0．864。D8S384基因座是一个较好的法医学STR遗传标记。     

Data for 10 autosomal STR markers in South Tunisian population

Allele frequencies, together with some parameters of forensic interest for 10 STRs (D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA) were estimated from 201 unrelated individuals originating from southern Tunisia. Significant deviation from Hardy-Weinberg equilibrium was observed for only one marker. Comparative analyses between our population data and other populations showed that only markers D3S158, vWA and FGA were homogenous among populations. The combination of these 10 STR loci provide a powerful tool for forensic identification in Tunisian population.     

Genetic polymorphism revealed by 13 tetrameric and 2 pentameric STR loci in four Mongoloid tribal population

The short tandem repeat allelic profiles at to 15 autosomal polymorphic loci were analyzed in four tribal populations of Mizoram (India). The analysis was performed on 354 unrelated healthy individuals belonging to Mongoloid races. All the samples were subjected to sex test (Amelogenin marker) besides the STR typing and in all instances; it has shown no deviation from expectation. The allele frequencies for all the analyzed loci in the studied populations are within expected range in comparison to the populations from same racial background. No significant deviation from the Hardy-Weinberg Equilibrium was observed for all the populations. In no cases the observed heterozygosity is less than that of expected values and it varied from 0.978 (Penta E) to as low as 0.425 (THO1). The discriminatory power and exclusion probability values for all the analyzed markers are significantly high and thus reveal high forensic significance. There is no evidence for association of alleles among the 15 studied loci. This allele frequency data will be useful for human identity testing in Mizo population.     

Genetic polymorphism of 30 autosomal InDel loci in Chinese Hainan Li population

A novel genetic marker, Insertion/Deletion polymorphism (InDel) shows remarkable potential for forensic DNA applications. Hainan Island is the southernmost and the second largest island in China, of which the Li ethnic group is regarded as the original inhabitants. In this study, 207 individual samples of Li ethnic group from Hainan were genotyped using Investigator DIPplex kit which contains 30 autosomal InDels and Amelogenin. Allele frequency and forensic parameters were calculated for these loci. Several deviations from Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) may indicate founder effect in the Li ethnic group. The combined power of discrimination (CPD) and the cumulative probability of exclusion (CPE) reached 0.99999999992912 and 0.9861, respectively. These results suggested that the kit was effective for personal identification in Hainan Li population. The population comparisons through the Nei’s standard genetic distance (R_st), phylogenetic tree, multidimensional scaling analysis (MDS), principal component analysis (PCA), and STRUCTURE analyses along continental divisions manifested that the 30 InDels panel had a certain intercontinental differentiation ability.     

Population data on the forensic genetic markers: phosphoglucomutase-1, esterase D, erythrocyte acid phosphatase and glyoxylase I

Blood specimens from white and black sample populations from Baltimore, Maryland, were analyzed for the four most forensically important, polymorphic red cell enzyme systems-phosphoglucomutase-1, esterase D, erythrocyte acid phosphatase and glyoxalase I. The distributions of the phenotypes for each marker in each racial group were in Hardy-Weinberg equilibrium. The population data were similar to previously reported data for Whites and Blacks from different geographical locations within the United States.     

Sexual variation in bucco-lingual dimensions in Turkish dentition

Sexual differences in the human skeleton have been well studied in many populations. Odontometric analysis of the human sexual variation has been less investigated and mostly derived from the dentition of extinct populations. Turkey is situated in a unique location where populations from different regions mixed with each other and created a rich gene pool. One might anticipate that modern Turkish population is composed of genes from the Balkans, Caucasus, Middle East, Iran and further as well as from ancient Romans, Byzantines, Arabs and Asiatic Turks. It is clear that contemporary Turks are a mixture of these extant and extinct people and ideal to consider it a representative study population. The purpose of this study is to analyze dental dimensions and sexual variation in living Turks and develop forensic techniques to identify human remains from the teeth when any other technique is not available or not reliable. The study is composed of Ankara University dental students (50 male and 50 female casts, average age of 21 years). Bucco-lingual breadths from 14 teeth (I1 through M2 of the maxilla and mandible) are taken from the left side and analyzed using the discriminant function statistics. An intraobserver error test did not indicate any statistically significant difference between any two measurements. Results of the study revealed that males exceeded females significantly (P<0.001) in dimensions. Coefficient of variation was most obvious in I1s and I2s of both jaws in both sexes. Stepwise discriminant function statistics suggested that upper C, and lower C and M2 are the most contributory teeth to the function. Additional formulae were calculated for situation in which only one or a fragmented jaw is available for identification. Overall accuracy of sex diagnosis ranged from 73 to 77%. In conclusion this research supports earlier studies that sexual dimorphism is population specific. While dental difference between the sexes in several human populations has been found highly dimorphic, it was not found so in Turks and accuracy of classification remained low at about 77%. The difficulty or the lack of dimorphism comes from male subjects.     

The single most polymorphic STR Locus: SE33 performance in U.S. populations

The STR locus SE33 (ACTBP2) located on chromosome 6 (6q14) is arguably the most polymorphic marker examined thus far by the forensic community with a heterozygosity of >0.95 in some populations. Three different primer sets were utilized in this study in order to assess the possibilities of primer binding site mutations. Population variation was measured in 460 U.S. Caucasian, 445 African American, 336 Hispanic, and 202 Asian samples along with mutation rates from almost 400 father–son pairs. In addition, the 10 genomic DNA components in NIST Standard Reference Material SRM 2391b were sequenced and found to exhibit a variety of additional base changes, insertions, and deletions outside of the SE33 repeat region.     

中国汉族与日本群体DYFl55S1基因座的遗传多态性

目的探讨Y染色体DYF155S1基因座的遗传多态性及群体间差异。方法 应用MVR-PCR、荧光显谱及DNA序列分析技术,对来自中国群体(北方汉族,64例)和日本群体(43例)男性个体的DYF155S1基因座进行初步分析。结果107例样本共检出了5种重复序列类型,包括新的命名为6型的重复序列,它是在1型的基础上T22A置换所形成,仅存在于日本群体,可作为民族特征性遗传标记。2群体重复序列的排列方式以3134顺序为主,在中国和日本群体中各占73.44％和67.44％,是黄种人的特点。134顺序在中国群体中占第二位,为17.19％,6134排列占日本群体的16.28％。3’端的4型重复序列的平均数目在日本群体为8.8条,明显低于中国群体的12.5条。结论DYF155S1基因座具有非常高的遗传多态性和明显的群体差异。     

DNA typing in populations of mule deer for forensic use in the Province of Alberta

The present study involves the development of forensic DNA typing tests and databases for mule deer in the Province of Alberta. Two multiplex PCR reactions interrogating 10 loci were used to analyze samples from three populations of mule deer. Additionally, an amelogenin based sex-typing marker was used to determine the gender of samples. Results show that the tests and databases are appropriate for use in forensic applications. Additionally, the results indicate that there is little population structure in mule deer in Alberta and that no changes to management of this game species are suggested.     

Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: an expanded Korean population database

We have analyzed variation of the mitochondrial DNA (mtDNA) hypervariable segments I and II (HVS-I and HVS-II) in 185 randomly chosen individuals from Korea to provide an expanded and reliable Korean database. Combined sequence comparison of HVS-I and HVS-II led to the identification of 167 different haplotypes characterized by 154 variable sites. One hundred and fifty-one of the haplotypes were individual-specific, 14 were found in two individuals and 2 were found in three individuals. A pairwise comparison of the 185 HVS-I/II sequences found an average of 10.11 +/- 4.63 differences between individuals. The random match probability and gene diversity for the combined hypervariable regions were estimated at 0.66% and 0.9988, respectively. Analyzing the expanded database including three previously reported data sets and the present data using haplogroup-based comparisons and comparison with closely related sequences allowed errors to be detected and eliminated, thus considerably improving data quality. Sample division comparisons based on PhiST genetic distance measures revealed no significant population differentiation in the distribution of mtDNA sequence variations between the present data set and a database in The Scientific Working Group on DNA Analysis Methods (SWGDAM), but did indicate differences from other sets of data. Based on the results of mtDNA profiles, almost all of the mtDNA types studied here could be classified into subsets of haplogroups common in east Asia, and show that the Koreans possess lineages from both the southern and the northern haplogroup complexes of east Asian populations. The new data, combined with other mtDNA sequences, demonstrate how useful comparison with closely related mtDNA sequences can be for improving database quality, as well as providing haplotype information for forensic and population genetic analyses in the Korean population.     

Sex determination from the distal part of the femur in a French contemporary population

Until now, determining the sex of a recently deceased individual using the measurement of the bicondylar breadth of the femur (also known as condylar width, epicondylar breadth and distal epiphyseal breadth) raised some concerns as to accuracy because no sample of contemporary French subjects was available. In this study, a sample of 88 female and male femurs taken from recently deceased elderly French people was studied. The bones were collected from subjects who had donated their bodies to the Medical School of Nice. The mean value of the male bicondylar breadth was found to be greater than that of females (84.3mm versus 74.8mm), confirming the sexual dimorphism of this parameter. Furthermore, the results showed a 95.4% accuracy rate for sexing individuals. To date, in the French population, as in some other samples, epicondylar breadth is the single most accurate measurement of sex determination, ahead even of head diameter. A discriminant function is presented to allow sex determination from remains of the distal femur. With regard to the data available in the literature, sexual dimorphism is probably the result of both genetic and environmental factors. The comparison of our results with those of other populations shows that there are inter-population variations of the bicondylar breadth, and also intra-population variations that account for the differences in the accuracy rate of this variable for the purposes of sex determination. These findings underscore the need to re-evaluate bone measurements within various contemporary populations.     

Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America

A total of 2443 male individuals, previously typed for the 13 CODIS STR loci, distributed across the five North American population groups African American, Asian, Caucasian, Hispanic, and Native American were typed for the Y-STR loci DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 using the PowerPlex Y System. All population samples were highly polymorphic for the 12 Y-STR loci with the marker DYS385a/b being the most polymorphic across all sample populations. The Native American population groups demonstrated the lowest genetic diversity, most notably at the DYS393 and DYS437 loci. Almost all of the 12-locus haplotypes observed in the sample populations were represented only once in the database. Haplotype diversities were greater than 99.6% for the African Americans, Caucasians, Hispanics, and Asians. The Native Americans had the lowest haplotype diversities (Apaches, 97.0%; Navajo, 98.1%). Population substructure effects were greater for Y-haplotypes, compared with that for the autosomal loci. For the apportionment of variance for the 12 Y-STRs, the within sample population variation was the largest component (>98% for each major population group and approximately 97% in Native Americans), and the variance component contributed by the major population groups was less than the individual component, but much greater than among sample populations within a major group (11.79% versus 1.02% for African Americans/Caucasians/Hispanics and 15.35% versus 1.25% for all five major populations). When each major population is analyzed individually, the R(ST) values were low but showed significant among group heterogeneity. In 692 confirmed father-son pairs, 14 mutation events were observed with the average rate of 1.57x10(-3)/locus/generation (a 95% confidence bound of 0.83x10(-3) to 2.69x10(-3)). Since the Y-STR loci reside on the non-recombining region of the Y chromosome, the counting method is one approach suggested for conveying an estimate of the rarity of the Y-haplotype. Because the Y-STR loci are not all in disequilibrium to the same extent, the counting method is a very conservative approach. The data also support that autosomal STR frequencies can be multiplied by the upper bound frequency estimate of a Y-haplotype in the individual population group or those pooled into major population groups (i.e., Caucasian, African American, Hispanic, and Asian). These analyses support use of the haplotype population data for estimating Y-STR profile frequencies for populations residing in North America.     

Population genetics of Y-chromosomal microsatellites in Baltic males

Y-chromosomal microsatellites (STRs) are potentially useful in forensic practice but, in contrast to autosomal systems, large and diverse population databases are required in order to facilitate the statistical evaluation of donor-stain matches. Since appropriate data from the Baltic region have so far been lacking, blood samples were obtained from 430 males originating from one of the three Baltic states and these samples were genotyped using a previously described "extended core set" of nine Y-STR marker systems. Allele frequency distributions and discrimination indices were calculated, and the three populations were tested for genetic differences by means of analysis of molecular variance (AMOVA). A larger genetic difference became apparent between Estonian and both Lithuanian and Latvian males than between the latter two, non-Finno-Ugric speaking populations. The haplotype data reported here have been included into the Y-STR database maintained at the Institute of Legal Medicine, Humboldt University, Berlin.     

STR data for the power plex-16 loci in a population from Central Poland

The allele frequencies for the 13 CODIS core loci and two recently developed but not extensively validated in Central European populations pentanucleotide STRs (Penta E and D) were determined using the Power Plex-16 (Promega) kit in a sample of 430 unrelated individuals born in Central Poland. The calculated parameters of polymorphism showed Penta E to be the most valuable marker from the studied set. The obtained distribution of Penta E and D alleles was statistically significantly different from that previously reported for a population of Southern Poland. Analysis of Hardy-Weinberg equilibrium revealed a deviation for the D5S818 locus which may reflect presence of a null allele.