Detection of sequence variation in the HVII region of the human mitochondrial genome in 689 individuals using immobilized sequence-specific oligonucleotide probes

We have developed a rapid, immobilized probe-based assay for the detection of sequence variation in the hypervariable segment II (HVII) of the mitochondrial DNA (mtDNA) control region. Using a panel of 17 sequence-specific oligonucleotide (SSO) probes immobilized on nylon membrane strips, we typed 689 individuals from four population groups. The genetic diversity value for each population was calculated from the frequency data, and the frequencies of distinct "mitotypes" in each group were determined. We performed DNA sequence analysis of 129 samples to characterize the sequences associated with "blanks" (absence of probe signals) and weak probe signals. Out of 689 samples, we observed five heteroplasmic samples (excluding the variable C-stretch beginning at position 303) using the immobilized SSO probe panel. The SSO probe strips were used for the analysis of shed hairs and bloodstains from several criminal cases in Sweden, one of which is described here. We conclude that this mtDNA typing system is useful for human identification and significantly decreases casework turnaround time.     

Belgian canine population and purebred study for forensics by improved mitochondrial DNA sequencing

In canine population studies for forensics, the mitochondrial DNA is profiled by sequencing the two hyper variable regions, HV1 and HV2 of the control region.In a first effort to create a Belgian population database some samples showed partially poor sequence quality. We demonstrated that a nuclear pseudogene was co-amplified with the mtDNA control region. Using a new combination of primers this adverse result was no longer observed and sequencing quality was improved. All former samples with poor sequence data were reanalyzed. Furthermore, the forensic canine population study was extended to 208 breed and mixed dogs. In total, 58 haplotypes were identified, resulting in an exclusion capacity of 0.92. The profile distribution of the Belgian population sample was not significantly different from those observed in population studies of three other countries.In addition to the total population study 107 Belgian registered pedigree dogs of six breeds were profiled. Per breed, the obtained haplotypes were supplemented with those from population and purebred studies. The combined data revealed that some haplotypes were more or less prominent present in particular dog breeds. The statistically significant differences in haplotype distribution between breeds and population sample can have consequences on mtDNA databasing and matching probabilities in forensics.     

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.     

Examination of Y-STR mutations in sex chromosomal abnormality in forensic cases

The Y-STR typing was carried out on eight DNA samples (three from criminal cases) demonstrating Klinefelter's syndrome. STR types in the X chromosome were randomly distributed. However, some Y-STR markers were distributed within the normal range but restricted to only one or two specific alleles, that is, some specific haplotypes were found in Klinefelter's syndrome. In addition, a single nucleotide polymorphism in DYS390 (transversion of G to A at the 28th position downstream of tandem repeats) was detected in Klinefelter samples. This Y-STR polymorphism and restricted Y-STR alleles in Klinefelter's syndrome is not known, but it might be related to the genesis of Klinefelter's syndrome. We also found that extended standard haplotypes of these samples are extremely rare in the normal population, according to the Y-STR haplotype reference database (YHRD). The extended standard haplotype database in a Japanese population is also reported. In 100 unrelated Japanese, 89 haplotypes were observed, and the haplotype diversity was calculated to be 0.9866.     

Y-chromosomal STR haplotypes in a Gypsy population from Portugal

We analyzed 17 Y-chromosomal STR loci in a population sample of 126 unrelated Portuguese Gypsies. Fifty three different haplotypes were found, three represented with considerable high frequencies (≥8.7%). The percentage of unique haplotypes (71.2%) was rather low as well as haplotype diversity (94.37%). In the comparison with available Portuguese population data and with those from other Gypsy and general population samples from Bulgaria, Lithuania and Spain, our sample showed significant differences in comparison with the general population data from Portugal, Spain and Bulgaria. Significant differences were observed with Bulgarian Gypsies, but not with the Spanish or Lithuanian groups. The Gypsy populations from Portugal, Spain and Bulgaria were found to be more closely related to each other than with the general population from their own countries.     

Comparative analysis of two indel-based ancestry informative multiplex PCR typing kits

Two different insertion/deletion (indel) multiplexes have been used to analyse a subset of the CEPH Human Genome Diversity Panel as well as several additional populations collected locally in order to compare the effectiveness of the marker sets in differentiating the populations on a continental level. We show that both marker sets by themselves are able to achieve full continental population differentiation and combining all 67 markers leads to considerably higher accuracy of classification. While differentiation of the European and Middle Eastern population groups remains impossible, surprisingly high accuracy is achieved in assigning Central South Asian samples.     

Exploring the Justice of Punishments: Framing, Expressiveness, and the Just Prison Sentence

This paper examines views about the justice of punishments for offenders convicted of five major types of offenses—drug, violent, corporate, property, and victimless crimes. We focus on the just punishment and the just dispersion in the punishment distribution, together with observers' framing and expressiveness; and we test for interrespondent differences. Data are drawn from six U.S. samples interviewed in 1982, a probability sample of the adult population of a major city and samples of five special groups, prison inmates, police officers, law-school and high-school students, and Job Corps trainees. Respondents' judgments were obtained using Rossi's factorial survey method. Fictitious offenders were constructed by randomly combining offender, offense, and victim characteristics; and respondents used a line-matching technique to rate the justice of punishments randomly assigned to fictitious offenders. Analysis is guided by the framework for empirical justice analysis, which provides an integrated set of procedures for estimation and testing. Results indicate that respondents in all samples save one disagree with each other on the just punishment; and the six samples yield four distinct average orderings of just prison sentences. However, large majorities in all six samples find the dispersion in the punishments experimentally put into the vignette world to be too small relative to the just dispersion. More broadly, comparing the results obtained here from the probability sample of a major city with results from a comparable study on the justice of earnings, we find two interesting symmetries—approximately 1% of the general population is contrarian, regarding earnings as a bad and time in prison as a good; and approximately 92% to 94% of the population regard earnings inequality as too high and prison-time inequality as too low. Finally, this study provides additional evidence that the general population in the United States exhibits independence of mind informing their ideas about what constitutes the just earnings and the just punishment.     

Evaluating population structure of Ecuador for forensic STR markers

The continuous admixture events among Europeans, Native Americans, and Africans occurred differently throughout the Ecuadorian territory, creating a diversified genetic composition. Therefore, to evaluate how the genetic diversity is partitioned along the country for 15 STRs, 842 admixed-population samples were analyzed. We also evaluated the effect of applying an adjustment for population structure when estimating LRs using a national database. The results showed that to accurately assess forensic evidence, the use of a national database may be justified with the application of an appropriate adjustment for population structure.     

Understanding (Mis)classification Trends of Latin Americans in Fordisc 3.1: Incorporating Cranial Morphology,Microgeographic Origin,and Admixture Proportions for Interpretation

Assigning correct population affinity to a skeleton can contribute important information to an investigation—yet recent work highlights high error rates when classifying Latinos with a traditional tool, Fordisc 3.1 (FD3). Our study examines whether misclassification trends exist, and whether these can be used to infer population affinity. We examine the relationships among ancestry, geography, and FD3 misclassifications of Latinos using canonical variate analysis and unsupervised model‐based clustering of craniometrics. Northern Mexicans appear more strongly associated with FD3 references samples with elevated amounts of European ancestry (e.g., American Blacks and Whites), while Southern Mexicans are more strongly associated with FD3 reference samples with reduced amounts of European ancestry (e.g., Guatemalans and Native Americans). FD3 classifications revealed that Latinos exhibited lower posterior probabilities when compared to other common case demographics (Whites and African Americas), even when the classification was “correct.” We make recommendations for practitioner interpretation of FD3 reports for casework.     

Gene and genotype frequencies for HLA-DQA1 in Caucasians and Mulattoes in Brazil.

Gene and genotype frequencies of the HLA-DQA1 locus were determined in a sample of 197 unrelated individuals (144 Caucasians and 53 Mulattoes), living in the city of S?o Paulo, Brazil. The Mulatto group consisted of mixed individuals who presented at least one negroid physical characteristic or declared themselves to be of mixed ancestry. A total of six different alleles were identified with frequencies ranging from 0.087 to 0.316 in the Caucasian population and from 0.066 to 0.330 in the Mulatto population. We observed an increased frequency of allele 1.2 among Mulattoes in relation to Caucasians. The sample heterozygote frequency was 0.722 among Caucasians and 0.736 among Mullatoes. No significant deviations from Hardy-Weinberg equilibrium were found either in the Caucasian or in the Brazilian Mullato population samples.     

A comprehensive population survey on the distribution of STR frequencies in Belarus

This work develops a detailed STR database from 11 population samples and samples from paternity analyses from different districts of Belarus. The combined data on 2020 individuals form a total database for the country, with the exclusion power of 99.987% based on 11 STR loci. Possible differentiation in allele frequencies between population samples, small in terms of F-statistics and undetectable by standard statistical tests, is discussed.     

4个miniSTR基因座复合扩增体系及应用

目的构建D6S474、D20S482、D4S2408、D6S1017等4个miniSTR基因座复合扩增体系,评价其对腐败检材的应用价值,调查4个基因座在汉族人群中的遗传多态性。方法采用不同荧光标记4个miniSTR基因座上游引物,构建复合扩增体系。用分子克隆方法制备等位基因分型标准物。采用上述体系对135份汉族无关个体血样进行检测,并计算群体遗传学参数。比较该体系与ID试剂盒在降解检材分析中的成功率。结果采用本文复合扩增体系检测,汉族人群中4个基因座基因型频率分布均符合Hardy-Weinberg平衡定律,累积个人识别能力为0.999 666,累积非父排除率为0.914 902。本文体系较ID试剂盒对自然腐败检材的分型成功率更高。结论 4个miniSTR基因座复合扩增体系对法庭科学实践,特别是对腐败检材的检测有应用价值。     

Characterization of new miniSTR loci to aid analysis of degraded DNA

A number of studies have demonstrated that successful analysis of degraded DNA specimens from mass disasters or forensic evidence improves with smaller sized polymerase chain reaction (PCR) products. We have scanned the literature for new STR loci, unlinked from the CODIS markers, which can generate amplicons less than 125 bp in size and would therefore be helpful in testing degraded DNA samples. New PCR primers were designed and tested for the STR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045, arranged into two miniSTR triplexes. All loci show a moderate degree of polymorphism among 474 U.S. population samples tested and were reliable and sensitive to at least 100 pg of DNA template under controlled laboratory conditions and pristine DNA samples. The utility of these new loci were confirmed in comparing the success of the miniSTR assays for typing degraded bone samples while partial profiles were observed with the majority of the samples using a commercial STR kit.     

Sequence polymorphism in the human melanocortin 1 receptor gene as an indicator of the red hair phenotype.

We describe a minisequencing protocol for screening DNA samples for the presence of 12 mutations in the human melanocortin 1 receptor gene (MC1R), eight of which are associated with the red hair phenotype. A minisequencing profile which shows homozygosity for one of these mutations or the presence of two different mutations would strongly indicate that the sample donor is red haired. The absence of any red hair causing mutations would indicate that the sample donor does not have red hair. We report the frequencies of MC1R variants in the British red haired population.     

Misclassifications of Hispanics Using Fordisc 3.1: Comparing Cranial Morphology in Asian and Hispanic Populations

It has been brought to the attention of the authors of Fordisc 3.1 that Hispanic samples will often misclassify as Japanese when Asian population samples are included. This study examined this problem in an effort to better document the occurrence and deduce possible causes via comparative analyses. Asian and Hispanic samples were first compared utilizing the existing samples from the University of Tennessee's Forensic Data Bank. Additional modern Japanese, Thai, and Korean samples collected by the first author that have previously not been utilized in analyses were subsequently included. Results of this study confirm frequent rates of misclassification among Hispanic and Japanese groups. Furthermore, a close morphological relationship is identified through further group comparisons and the addition of data used in conjunction with Fordisc samples. Similarities identified among Hispanic and Japanese crania may stem from similar population histories reflected in ancestral Native American and East Asian populations.     

The atlas of dialkylphosphates; assessment of cumulative human organophosphorus pesticides' exposure

Organophosphorus pesticides (OPs) are a group of chemicals with significant health interest, due to their wide spectrum of action and their excessive use both indoors (household) and outdoors (occupationally). The non-specific metabolites of OPs, dialkylphosphates (DAPs), are the most commonly used indicators for the assessment of cumulative OP exposure in humans. This review presents studies on human biomonitoring of OPs in the general population and in occupationally exposed humans. Furthermore, cases of OP intoxication determined by the measurement of DAP metabolites in various biological samples are included. In many studies, urine samples from both the general population and exposed populations have been analyzed mainly in Europe and America, while other matrices such as amniotic fluid, meconium, hair and blood have been less studied. A variety of analytical techniques were used for the determination of DAPs in these matrices. In studies measuring DAPs in urine samples, the detected concentrations ranged from 18 to 830ppb for the general population, while the corresponding values for exposed populations ranged from 29 to 1370ppb. Studies on amniotic fluid indicated DAP levels of 0.3-2.8ppb. Studies on meconium samples showed a concentration range of 0.5-16,000ppb. DAP levels in hair samples ranged from 40 to 165ppb for the general population and from 181.7 to 812.9ppb for the exposed population. Each matrix provides specific information on OP exposure, namely acute, long-term, chronic or prenatal. Meconium and hair can indicate cumulative exposure, while amniotic fluid is an indicator of fetal exposure to xenobiotics. Thus, various biological samples provide a more comprehensive view of OP exposure. In general, dimethylphosphate (DMP) and diethylphosphate (DEP) levels were higher in mainly urine samples, than other methyl and ethyl phosphates. In addition, results in the existing literature are sufficient to demonstrate the difference in levels of DAPs in general and occupationally exposed populations, mainly in urine and hair samples. However, more studies are needed to measure DAP levels in matrices such as amniotic fluid, meconium and hair to add to the literature and confirm existing data.     

Utility of the Y-STR typing systems Y-PLEX 6 and Y-PLEX 5 in forensic casework and 11 Y-STR haplotype database for three major population groups in the United States

The Y-PLEX 6 and Y-PLEX 5 systems enable analysis for 11 Y-STR loci. We present here the utility of these systems in forensic casework. A total of 188 samples, including 127 evidence samples, were analyzed using either or both of the systems. The evidence sample types included fingernail scrapings, sperm or seminal fluid, epithelial cells, blood and other tissues. The Y-STR typing systems provided useful probative results in difficult cases. A reference database for Caucasian (n = 517), African American (n = 535), and Hispanic (n = 245) population groups within the United States was generated for estimating the haplotype frequency in forensic casework. Among the individuals profiled, 311 Caucasians, 412 African Americans, and 194 Hispanics provided unique profiles in their respective population datasets. This is the first report describing the haplotype database for the set of 11 Y-STR loci recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Linkage analysis reveals that the frequencies from forensically important autosomal loci can be multiplied with the Y-STR haplotype frequency. The results from Y-PLEX systems have been accepted in courts in the United States.     

Allele frequencies of 15 tetrameric short tandem repeats (STRs) in Andalusians from Huelva (Spain)

The allele frequency distribution of 15 short tandem repeat (STR) loci contained in the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems), was determined in 114 individuals from Andalusia (province of Huelva), in the southernmost part of the Iberian Peninsula. After Bonferroni's correction, no deviations from the Hardy-Weinberg equilibrium were observed for all samples at the 15 STR loci. All loci are highly polymorphic. The aim of the study was to obtain accurate allele frequencies relevant for applications in forensics and population genetics. Comparative analyses between our population data and other population samples gathered from the literature are also presented.     

Population genetic data for 17 non-CODIS STR loci for the Saudi Arabian population using the SureID®23comp Human Identification Kit

Our previous work focused on validation the SureID 23comp Human Identification Kit (Health Gene Technologies, China), following the minimum criteria for validation recommended by the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) using 500 samples from the population of Saudi Arabia. The kit genotypes 22 STRs, 17 of which are non-CODIS, and Amelogenin. The validation tests showed that it has the potential to increase the power of testing in complex cases.In this paper, the allele frequency data, common forensic parameters for the 17 non-CODIS STR loci are presented. We found the majority of loci had an excess of homozygosity in the data set, which is most likely explained by the relatively high levels of consanguinity in the population of Saudi Arabia.     

Implications for DNA identification arising from an analysis of Australian forensic databases

Previous analyses of Australian samples have suggested that populations of the same broad racial group (Caucasian, Asian, Aboriginal) tend to be genetically similar across states. This suggests that a single national Australian database for each such group may be feasible, which would greatly facilitate casework. We have investigated samples drawn from each of these groups in different Australian states, and have quantified the genetic homogeneity across states within each racial group in terms of the "coancestry coefficient" F(ST). In accord with earlier results, we find that F(ST) values, as estimated from these data, are very small for Caucasians and Asians, usually <0.5%. We find that "declared" Aborigines (which includes many with partly Aboriginal genetic heritage) are also genetically similar across states, although they display some differentiation from a "pure" Aboriginal population (almost entirely of Aboriginal genetic heritage).