Characterisation of novel and rare Y-chromosome short tandem repeat alleles in self-declared South Australian Aboriginal database

Y-chromosome short tandem repeats (Y-STRs) are used in forensic science laboratories all over the world, as their application is wide and often vital in solving casework. Analysis of an in-house database of South Australian self-declared Aboriginal males held by Forensic Science South Australia (FSSA) using the Applied Biosystem’s AmpF?STR® Yfiler? PCR Amplification Kit revealed 43 variant Y-STR alleles at 6 of the 17 loci. All variant alleles were sequenced to determine the exact repeat structure for each. As a high level of admixture has previously been found within the SA Aboriginal database, samples were haplogrouped using Y-SNPs to determine their likely geographical origin. Although a number of variant alleles were associated with non-Aboriginal Y-haplogroups, a high frequency was observed within the Australian K-M9 lineage. Detailed knowledge of these variant alleles may have further application in the development of new DNA markers for identification purposes, and in population and evolutionary studies of Australian Aborigines.     

Predicting biogeographical ancestry in admixed individuals – values and limitations of using uniparental and autosomal markers

When microsatellite profiles generated from crime scene samples do not match a known person, or eye-witness information is unreliable, highly informative uniparental and autosomal markers can help unveil biogeographical ancestry. However, as genetic admixture is becoming increasingly common in cosmopolitan societies, concern arises with their accuracy and suitability when dealing with samples from admixed individuals. Here we assess the ability to detect biogeographical ancestry in 85 individuals from self-declared Asian and European admixed families using a set of uniparental (Y and mitochondrial DNA) and autosomal single nucleotide polymorphisms, specifically selected to distinguish between these two biogeographical ancestries. Haplogroups and autosomal genotypes were investigated using STRUCTURE to detect levels of admixture. All haplogroups were characteristic of self-declared populations of origin. Overall, the autosomal markers inferred biogeographical ancestry more accurately in admixed individuals, showing no significant differences between observed and expected contribution from each population studied according to level of admixture, although some outliers were observed. We suggest a panel of highly informative autosomal and uniparental markers should be employed to infer biogeographical ancestry of an individual to help detect admixed ancestries.     

An investigation of admixture in an Australian Aboriginal Y-chromosome STR database

Y-chromosome specific STR profiling is increasingly used in forensic casework. However, the strong geographic clustering of Y haplogroups can lead to large differences in Y-STR haplotype frequencies between different ethnicities, which may have an impact on database composition in admixed populations. Aboriginal people have inhabited Australia for over 40,000 years and until ～300 years ago they lived in almost complete isolation. Since the late 18th century Australia has experienced massive immigration, mainly from Europe, although in recent times from more widespread origins. This colonisation resulted in highly asymmetrical admixture between the immigrants and the indigenes. A State jurisdiction within Australia has created an Aboriginal Y-STR database in which assignment of ethnicity was by self-declaration. This criterion means that some males who identify culturally as members of a particular ethnic group may have a Y haplogroup characteristic of another ethnic group, as a result of admixture in their paternal line. As this may be frequent in Australia, an examination of the extent of genetic admixture within the database was performed. A Y haplogroup predictor program was first used to identify Y haplotypes that could be assigned to a European haplogroup. Of the 757 males (589 unique haplotypes), 445 (58.8%) were identified as European (354 haplotypes). The 312 non-assigned males (235 haplotypes) were then typed, in a hierarchical fashion, with a Y-SNP panel that detected the major Y haplogroups, C-S, as well as the Aboriginal subgroup of C, C4. Among these 96 males were found to have non-Aboriginal haplogroups. In total, ～70% of Y chromosomes in the Aboriginal database could be classed as non-indigenous, with only 169 (129 unique haplotypes) or 22% of the total being associated with haplogroups denoting Aboriginal ancestry, C4 and K* or more correctly K(xL,M,N,O,P,Q,R,S). The relative frequencies of these indigenous haplogroups in South Australia (S.A.) were significantly different to those seen in samples from the Northern Territory and Western Australia. In S.A., K* (～60%) has a much higher frequency than C4 (～40%), and the subgroup of C4, C4(DYS390.1del), comprised only 17%. Clearly admixture in the paternal line is at high levels among males who identify themselves as Australian Aboriginals and this knowledge may have implications for the compilation and use of Y-STR databases in frequency estimates.     

Use of subpopulation data in Australian forensic DNA casework

DNA profiling evidence presented in court should be accompanied by a reliable estimate of its evidential weight. In calculating such statistics, allele frequencies from commonly employed autosomal microsatellite loci are required. These allele frequencies should be collected at a level that appropriately represents the genetic diversity that exists in the population. Typically this occurs at broadly defined bio-geographic categories, such as Caucasian or Asian. Datasets are commonly administered at the jurisdictional level. This paper focuses on Australian jurisdictions and assesses whether this current practice is appropriate for Aboriginal Australian and Caucasian populations alike. In keeping with other studies we observe negligible differences between Caucasian populations within Australia when segregated geographically. However segregation of Aboriginal Australian population data along contemporary State and Territory lines appears to mask the diversity that exists within this subpopulation. For this reason datasets collated along more traditional lines may be more appropriate, particularly to distinguish the most genetically differentiated populations residing in the north of the continent.     

Use of subpopulation data in Australian forensic DNA casework

DNA profiling evidence presented in court should be accompanied by a reliable estimate of its evidential weight. In calculating such statistics, allele frequencies from commonly employed autosomal microsatellite loci are required. These allele frequencies should be collected at a level that appropriately represents the genetic diversity that exists in the population. Typically this occurs at broadly defined bio-geographic categories, such as Caucasian or Asian. Datasets are commonly administered at the jurisdictional level. This paper focuses on Australian jurisdictions and assesses whether this current practice is appropriate for Aboriginal Australian and Caucasian populations alike. In keeping with other studies we observe negligible differences between Caucasian populations within Australia when segregated geographically. However segregation of Aboriginal Australian population data along contemporary State and Territory lines appears to mask the diversity that exists within this subpopulation. For this reason datasets collated along more traditional lines may be more appropriate, particularly to distinguish the most genetically differentiated populations residing in the north of the continent.     

Australian population data for the twenty Promega PowerPlex 21 short tandem repeat loci

This paper describes the analysis of population data typed using the Promega PowerPlex 21 multiplex for the three major sub populations within Australia. Samples from 1427 declared Australian Aboriginal, 546 Pure Aboriginals from the Northern Territory, 990 Asian, and 1707 Caucasian individuals representing were analysed. Departures from Hardy–Weinberg equilibrium (HWE) and linkage equilibrium (LE) were assessed using exact tests. The Aboriginal populations were shown to display significant departures from equilibrium. All four subpopulation databases are of suitable size for the purpose of estimating allele frequencies.     

Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region

The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations. A sensitive multiplex assay, termed Pacifiplex, was developed and optimized in a small-scale test applicable to forensic analyses. The Pacifiplex assay comprises 29 ancestry-informative marker SNPs (AIM-SNPs) selected to complement the 34-plex test, that in a combined set distinguish Africans, Europeans, East Asians and Oceanians. Nine Pacific region study populations were genotyped with both SNP assays, then compared to four reference population groups from the HGDP-CEPH human diversity panel. STRUCTURE analyses estimated population cluster membership proportions that aligned with the patterns of variation suggested for each study population’s currently inferred demographic histories. Aboriginal Taiwanese and Philippine samples indicated high East Asian ancestry components, Papua New Guinean and Aboriginal Australians samples were predominantly Oceanian, while other populations displayed cluster patterns explained by the distribution of divergence amongst Melanesians, Polynesians and Micronesians. Genotype data from Pacifiplex and 34-plex tests is particularly well suited to analysis of Australian Aboriginal populations and when combined with Y and mitochondrial DNA variation will provide a powerful set of markers for ancestry inference applied to modern Australian demographic profiles. On a broader geographic scale, Pacifiplex adds highly informative data for inferring the ancestry of individuals from Oceanian populations. The sensitivity of Pacifiplex enabled successful genotyping of population samples from 50-year-old serum samples obtained from several Oceanian regions that would otherwise be unlikely to produce useful population data. This indicates tests primarily developed for forensic ancestry analysis also provide an important contribution to studies of populations where useful samples are in limited supply.     

The golden gene (SLC24A5) differentiates US sub-populations within the ethnically admixed Y-SNP haplogroups

Y-SNPs are currently being investigated for their potential to predict the ethnogeographic origin of the donor of a crime scene sample. Unfortunately, due to the presence of genetically admixed individuals within ethnic sub-populations within a particular haplogroup (hg), it is sometimes difficult to predict the ethnogeographic ancestry of an individual using only Y-SNPs. In the present work we determine the feasibility of using a combination of the golden pigmentation gene (SLC24A5) SNP and recently described high resolution Y-SNP markers to distinguish some of the different ethnic groups within particular Y-SNP hgs. Four hundred twenty-four individuals (128 African, 206 European, 50 Hispanic/Latin, 20 Pakistan, 20 E.Asian/Indian) were typed for a SNP within the golden gene. The Y-SNP hg was determined for all males and it was found that many of the European derived hg possessed a significant amount of ethnic admixture, with R1b3 having the most. We show the use of the golden gene, in combination with more informative Y-SNPs (U152, U106, and M222) and those that define the major hg, can differentiate between most of the African vs. European and African vs. E. Asian members of these heterogeneous populations.     

Comparison of the genetic background of different Colombian populations using the SNPforID 52plex identification panel

Various strategies for analysing SNP markers and genotyping have been published with the goal of obtaining informative profiles from biological samples that contain only small amounts of template and/or degraded DNA. In this study, a multiplex assay of 52 autosomal single-nucleotide polymorphisms (SNPs) was used to analyse 438 individuals from urban populations from different regions of Colombia, as well as a sample of 50 Native American individuals of the Pastos ethnic group from Nariño. To determine if significant differences in these 52 SNPs exist between the distinct regions of Colombia, genetic distance and admixture analyses were performed based on the available data for 17 different Colombian population groups and for population groups from Africa, Europe and America. The results demonstrate significant differences between the populations from the Southwest Andean, Central-West Andean, Central-East Andean, Orinoquian and northern Colombian Pacific Coast regions. Most of the regions exhibited a European and Native American admixture. One exception is the population from the region of Chocó (on the northern Pacific Coast), which exhibits a high proportion of African admixture (54 %). From the observed genetic backgrounds, it is possible to conclude that a single reference database for the entire country would not be suitable for forensic purposes. The allele frequencies and the forensically relevant parameters were calculated for all of the markers in each Colombian region with significant values for the combined matching probability (power of discrimination ≥0.99999999999999990) and the combined probability of exclusion (≥0.9990) in trios that were obtained from all of the population groups.     

Haplotype data for 23 Y-chromosome markers in four U.S. population groups

The PowerPlex Y23 kit contains 23 Y-chromosomal loci including all 17 of the markers in the Yfiler Y-STR kit plus six additional markers: DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643. We have typed 1032 unrelated population samples from four self-declared US groups: African Americans, Asians, Hispanics, and Western European Caucasians. An analysis of the population genetic parameters and the improvement of adding additional Y-STR markers to the dataset are described.     

MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania

Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.     

Typing of Amerindian Kichwas and Mestizos from Ecuador with the SNPforID multiplex

A total of 119 unrelated individuals from two of the major ethnic groups in Ecuador were typed for 49 of the autosomal single nucleotide polymorphisms (SNPs) in the SNPforID 52plex using the SNapShot(?) assay. Of the above, 42 samples originated from Mestizos (an admixed population) and the remaining 77 were from Native Amerindian Kichwas. We obtained full SNP profiles in all individuals and concordance of duplicated analyses. No deviation from Hardy-Weinberg equilibrium (HWE) was observed for any SNP in the Mestizo and Kichwa populations and only one and four pairs of loci, respectively showed significant linkage disequilibrium. A relatively low genetic diversity and global positive F(IS) value was observed in Kichwas. A statistically significant global F(ST) value was obtained when the two Ecuadorian populations were compared with populations in Spain, Portugal, Argentina, Denmark, Greenland, China, Somalia and Mozambique. All pairwise F(ST) values were statistically significant. A multi-dimensional scaling based on pairwise F(ST) values showed that the Kichwa population differed from all other populations investigated and that the Mestizos had an intermediate position between Kichwas and Europeans. An admixture analysis indicated that the greater contributor to the Mestizo population was the Kichwas (71.2%) compared to the European contribution. The combined mean match probability and mean paternity exclusion probability were 3.3 × 10(-17) and 0.998, respectively, for the Mestizo population and 3.3 × 10(-14) and 0.993, respectively, for the Kichwa population.     

Characteristics of asphyxial deaths in adolescence

Review of 69 cases of lethal asphyxia in individuals aged from 10 to 18 years was undertaken in South Australia. There were 62 cases of suicide due to hanging (89.9%) (age range 10-18 years; mean?=?16.6 years; M:F?=?3.4:1), 4 accidents (5.8%) (3 crush asphyxias in motor vehicle rollovers, and 1 positional asphyxia associated with marked alcohol intoxication) and 3 homicides (4.3%). In the suicide group, there were 46 whites (74.2%), 12 Aboriginal (19.4%), 3 Asians (4.8%) and 1 African (1.6%). There were no deaths due to sexual asphyxia or the "choking game". However, the percentage of Aboriginal victims was disproportionately high compared to the percentage of the population aged 10-19 years listed as Aboriginal (approximately 3%). Thus, constant monitoring of local trends in mortality will identify if new activities such as the "choking game" have emerged, and also characterize specific problems that may exist in particular communities or cultural groups.     

Allelic frequencies and statistical data obtained from 48 AIM INDEL loci in an admixed population from the Brazilian Amazon

Allelic frequencies of 48 informative insert-delete (INDEL) loci were obtained from a sample set of 130 unrelated individuals living in Macapá, a city located in the northern Amazon region, in Brazil. The values of heterozygosity (H), polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), matching probability (MP) and typical paternity index (TPI) were calculated and showed the forensic efficiency of these genetic markers. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 50%, 21% and 29%. Comparing these allele frequencies with those of other Brazilian populations and the parental populations, statistically significant distances were found. The interpopulation genetic distance (F(ST) coefficients) to the present database ranged from F(ST)=0.0431 (p<0.00001) between Macapá and Belém to F(ST)=0.266 (p<0.00001) between Macapá and the Native American group.     

Indel markers: genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material

Aiming to evaluate the usefulness of 38 non-coding bi-allelic autosomal indels in genetic identification and kinship testing, three Brazilian population samples were studied: two from Rio de Janeiro (including a sample of individuals with self-declared African ancestry) and one Native American population of Terena from Mato Grosso do Sul. Based on the observed allele frequencies, parameters of forensic relevance were calculated. The combined power of discrimination of the 38 indels was high in all studied groups (PD≥0.9999999999997), although slightly lower in Native Americans. Genetic distance analysis showed significant differences between the allele frequencies in the Rio de Janeiro population and those previously reported for Europeans, Africans and Asians explained by its intermediate position between Europeans and Africans. As expected, the Terena sample was significantly different from all the other populations: Brazilians from Rio de Janeiro general population and with self-declared African ancestry, Europeans, Africans and East Asians. Finally, the performance of the 38-indel multiplex assay was tested in post-mortem material with positive results, supporting the use of short amplicon bi-allelic markers as an additional tool to STR analysis when DNA molecules are degraded.     

Age estimation and the medial clavicular epiphysis: analysis of the age of majority in an Australian population using computed tomography

This study was designed in order to assess the suitability of clavicular development in discriminating whether or not an individual has reached the age of 18 years. The development of the medial clavicular epiphysis was examined in an Australian population using computed tomography as the imaging modality. The sample consisted of individuals who were admitted to the Victorian Institute of Forensic Medicine, Melbourne, Australia, for the purposes of medico-legal death investigation. Comparisons were made with similar studies conducted on different populations in other countries, which revealed that the Australian population reaches maturity earlier, and the level of left/right asymmetry is higher than in other studies. The high degree of variation in fusion times is discussed, and the consequent effect upon the ability to use this epiphysis as a tool for determining if an individual has reached the age of 18 years is analysed. If an individual in this population has completely fused clavicles at stage 5, then for males they will be at least 18 years of age, with a 99% certainty of being at least 21, and for females they will be at least 20 years old. If at stage three then an individual of either sex will be at least 17 years of age.     

Haplotype data for 16 Y-chromosome STR loci in Aboriginal and Caucasian populations in South Australia

Y-STR haplotype data was obtained using the AmpFlSTR^® YFiler? PCR Amplification Kit (Applied Biosystems, Foster City, CA) for 1079 Caucasian and 766 Australian Aboriginal individuals. Haplotype diversity was similar in both populations, however discrimination capacity was higher in Caucasians than Aborigines (0.946 compared to 0.692). Locus DYS385, which was considered as a single locus, was the most diverse marker in both populations (0.836 in Caucasians and 0.905 in Aborigines).PopulationThe South Australian Aboriginal and Caucasian databases were compiled from casework reference profile information held on the South Australian Criminal, Reference and Evidence DNA Database (SACREDD). Ethnicity was assigned based on self-declaration.     

The interaction of death, sorcery and coronial/forensic practices within traditional indigenous communities

The investigation of death in traditional indigenous communities often involves 'men of high degree' performing rituals and procedures to ascertain whether sorcery has been involved. If this is the case then the perpetrator must be identified and suitable retribution or compensation sought. In Central Australia investigations into such deaths occur in 'sorry camps' which consist of temporary meeting camps distant from facilities and amenities. Delays in the issuing of autopsy reports may unnecessarily prolong the time that tribal members have to spend in these camps, and wording of standard autopsy reports may not assist tribal concerns over matters such as sorcery. An initiative in South Australia, following discussions with Aboriginal elders in the Anangu Pitjantjatjara tribal lands, has been to issue a one page provisional report as soon as possible after completion of the autopsy, listing the likely cause of death. This is sent to Aboriginal authorities through local health clinics. In addition, a statement that 'no sticks, stones, bones or other foreign objects were found within the body that would implicate another person in the death' is also included to inform tribal members that no physical evidence of magical interference with the body has been detected. Relatively minor alterations in standard forensic/coronial reporting practices may significantly assist certain groups whose cultural requirements may be under-appreciated and incompletely understood by investigating authorities.     

Variability of mitochondrial DNA in a population sample from Iceland

Over the past decade investigations of human mitochondrial DNA (mtDNA) have considerably contributed to our knowledge about human evolution and migration. The genome of the Icelandic population is of special interest since Iceland has been genetically isolated for centuries. The sequence of the hypervariable regions HVS-I and HVS-II of the mtDNA control region was generated for 100 Icelandic individuals. A total of 75 different mtDNA sequences were observed, of which 19 sequences were shared by more than one individual, 16 sequences were shared by two individuals and two sequences were shared by three individuals; the most frequent haplotype (16129 A, 16239 T, 00263 G and 00315.1 C) was found six times. Both the genetic diversity (0.9925+/-0.0031) and the average number of pairwise nucleotide differences (7.371) were comparable with most of the other European populations. However, we found a smaller number of distinct mitochondrial lineages, suggesting that founder effects and genetic drift may have exerted a visible influence on the Icelandic genetic diversity. We compared these data with 1400 other European sequences from the D-Loop-BASE database. The paper discusses the evolutionary relationship between Icelandic and Central European mtDNA under due consideration of the historical context. Finally, our study has been aimed at increasing the number of mtDNA sequences available throughout the world and contributing to human genome investigations.     

Is Obesity a Factor in Sudden Asthmatic Deaths?

To determine whether there could be an association between obesity and acute fatal asthmatic episodes the autopsy files at Forensic Science SA, Australia, were searched over a 10-year period from 2007 to 2016 for cases where the cause of death was acute asthma. Thirty-three cases were identified (M:F = 1.2:1; age range 34-56yrs). BMIs ranged from 18.4-46.7 (mean 28.2). The nine cases with normal weights accounted for 27.3% of the total, compared to the South Australian coronial autopsy population of 32.1% and the general population of 35%; conversely the obese cases accounted for 33.3% compared to the South Australian coronial autopsy population of 27.2% and to the general population of 27.8%. This study demonstrates that individuals who present to medicolegal autopsy having died suddenly and unexpectedly during an asthmatic attack are likely to weigh more than individuals from the forensic autopsy and general populations. Calculation of BMI is an important part of the evaluation of such cases.