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Forensic Science International: Genetics

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Articles of Interest

Micro and Macro Geographical Analysis of Y-Chromosome Lineages in South Iberia

Journal: Forensic Science International: Genetics | Year: 2017

Abstract:

In this study, we intend to identify the evolutionary footprints of the South Iberian population focusing on the Berber and Arab influence, which has received little attention in the literature. Analysis of the Y-chromosome variation represents a convenient way to assess the genetic contribution of North African populations to the present-day South Iberian genetic pool and could help to reconstruct other demographic events that could have influenced on that region. A total of 26 Y-SNPs and 17 Y-STRs were genotyped in 144 samples from 26 different districts of South Iberia in order to assess the male genetic composition and the level of substructure of male lineages in this area. To obtain a more comprehensive picture of the genetic structure of the South Iberian region as a whole, our data were compared with published data on neighboring populations. Our analyses allow us to confirm the specific impact of the Arab and Berber expansion and dominion of the Peninsula. Nevertheless, our results suggest that this influence is not bigger in Andalusia than in other Iberian populations.

Peoples: Portuguese and Spanish | Places: Iberian Peninsula | Topics: | DNA Type: Y-DNA

Updating the African human mitochondrial DNA tree: relevance to forensic and population genetics

Journal: Forensic Science International: Genetics | Year: 2017

Abstract:

Analysis of human mitochondrial DNA variation plays an important role in forensic genetic investigations, especially in degraded biological samples and hair shafts. There are many issues of the mtDNA phylogeny that are of special interest to the forensic community, such as haplogroup classification or the post hoc investigation of potential errors in mtDNA datasets. We have analyzed >2200 mitogenomes of African ancestry with the aim of improving the known worldwide phylogeny. More than 300 new minor sub-clades were identified, and the Time to the Most Recent Common Ancestor (TMRCA) was estimated for each node of the phylogeny. Phylogeographic details are provided which might also be relevant in forensic genetics. The present study has special interest for forensic investigations because current analysis and interpretation of mtDNA casework rest on a solid worldwide phylogeny, as is evident from the role that phylogeny plays in popular resources in the field (e.g. Phylotree), software (e.g. Haplogrep 2), and databases (e.g. EMPOP). Apart from this forensic genetic interest, we also highlight the impact of this research in anthropological studies, such as those related to the reconstruction of the transatlantic slave trade.

Peoples: Africans | Places: Africa | Topics: TMRCA | DNA Type: mtDNA

Biohistorical materials and contemporary privacy concerns—The forensic case of King Albert I

Journal: Forensic Science International: Genetics | Year: 2016

Abstract:

The rapid advancement of technology in genomic analysis increasingly allows researchers to study human biohistorical materials. Nevertheless, little attention has been paid to the privacy of the donor’s living relatives and the negative impact they might experience from the (public) availability of genetic results, even in cases of scientific, forensic or historical relevance. This issue has become clear during a cold case investigation of a relic attributed to Belgian King and World War I-hero Albert I who died, according to the official version, in a solo climbing accident in 1934. Authentication of the relic with blood stains assigned to the King and collected on the place where his body was discovered is recognised as one of the final opportunities to test the plausibility of various conspiracy theories on the King’s demise. While the historical value and current technological developments allow the genomic analysis of this relic, publication of genetic data would immediately lead to privacy concerns for living descendants and relatives of the King, including the Belgian and British royal families, even after more than 80 years. Therefore, the authentication study of the relic of King Albert I has been a difficult exercise towards balancing public research interests and privacy interests. The identification of the relic was realised by using a strict genetic genealogical approach including Y-chromosome and mitochondrial genome comparison with living relatives, thereby limiting the analysis to genomic regions relevant for identification. The genetic results combined with all available historical elements concerning the relic, provide strong evidence that King Albert I was indeed the donor of the blood stains, which is in line with the official climbing accident hypothesis and contradicts widespread ‘mise-en-scène’ scenarios. Since publication of the haploid data of the blood stains has the potential to violate the privacy of living relatives, we opted for external and independent reviewing of (the quality of) our data and statistical interpretation by external forensic experts in haploid markers to guarantee the objectivity and scientific accuracy of the identification data analysis as well as the privacy of living descendants and relatives. Although the cold case investigation provided relevant insights into the circumstances surrounding the death of King Albert I, it also revealed the insufficient ethical guidance for current genomic studies of biohistorical material.

Peoples: | Places: Belgium | Topics: King Albert I and Privacy | DNA Type: mtDNA and Y-DNA

Complete mitochondrial genome sequences for 265 African American and U.S. “Hispanic” individuals

Journal: Forensic Science International: Genetics | Year: 2008

Abstract:

Entire mitochondrial genome (mtGenome) sequences of 265 unrelated African American and U.S. “Hispanic” individuals were generated.

Peoples: African Americans and Hispanic Americans | Places: | Topics: | DNA Type: mtDNA

Concordance and Reproducibility of a Next Generation mtGenome Sequencing Method for High-Quality Samples using the Illumina MiSeq

Journal: Forensic Science International: Genetics | Year: 2016

Abstract:

Sanger-type sequencing (STS) of mitochondrial DNA (mtDNA), specifically the control region (CR), is routinely employed in forensics in human identification and missing persons scenarios. Yet next-generation sequencing (NGS) has the potential to overcome some of the major limitations of STS processing, permitting reasonable paths forward for full mitochondrial genome (mtGenome) sequencing, while also offering higher-throughput and higher sensitivity capabilities. To establish the accuracy and reproducibility of NGS for the development of mtDNA data, 90 DNA extracts that were previously used to generate forensic quality full mtGenomes using STS were sequenced using Nextera XT library preparation and the Illumina MiSeq. Using the same amplicon product, replicate library sets were generated and sequenced at different laboratories, and analysis was performed in replicate using the CLC Genomics Workbench. Both sequencing sets resulted in 99.998% of positions with greater than 10X coverage when 96 samples (including controls) were multiplexed. Overall, 99.9996% concordance was observed between the NGS data and the STS data for the full mtGenome. The only “discordant” calls involved low level point heteroplasmies, with the differences resulting from stochastic variation and/or the increased sensitivity of NGS. Higher sensitivity also allowed for the detection of a mixed sample previously not detected with STS. Additionally, variant calls were reproducible between sequencing sets and between software analysis versions with the variant frequency only differing by 0.23% and 0.01%, respectively. Further validation studies and specialized software functionality tailored to forensic practice should facilitate the incorporation of NGS processing into standard casework applications. The data herein comprise the largest, and likely most thoroughly examined, complete mtGenome STS-NGS concordance dataset available.

Peoples: - | Places: - | Topics: Illumina MiSeq, Next-generation sequencing, and Sanger-type sequencing | DNA Type: mtDNA

Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping

Journal: Forensic Science International: Genetics | Year: 2015

Abstract:

The colonization of Americas is thought to have occurred 15–20 thousand years ago (Kya), with little or no subsequent migration into South America until the European expansions beginning 0.5 Kya. Recently, however, haplogroup C3* Y chromosomes were discovered in two nearby Native American populations from Ecuador. Since this haplogroup is otherwise nearly absent from the Americas but is common in East Asia, and an archaeological link between Ecuador and Japan is known from 6 Kya, an additional migration 6 Kya was suggested. Here, we have generated high-density autosomal SNP genotypes from the Ecuadorian populations and compared them with genotypes from East Asia and elsewhere to evaluate three hypotheses: a recent migration from Japan, a single pulse of migration from Japan 6 Kya, and no migration after the First Americans. First, using forward-time simulations and an appropriate demographic model, we investigated our power to detect both ancient and recent gene flow at different levels. Second, we analyzed 207,321 single nucleotide polymorphisms from 16 Ecuadorian individuals, comparing them with populations from the HGDP panel using descriptive and formal tests for admixture. Our simulations revealed good power to detect recent admixture, and that ≥5% admixture 6 Kya ago could be detected. However, in the experimental data we saw no evidence of gene flow from Japan to Ecuador. In summary, we can exclude recent migration and probably admixture 6 Kya as the source of the C3* Y chromosomes in Ecuador, and thus suggest that they represent a rare founding lineage lost by drift elsewhere.

Peoples: Ecuadorians | Places: Ecuador and Japan | Topics: Gene flow | DNA Type: Autosomal DNA and Y-DNA

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

Journal: Forensic Science International: Genetics | Year: 2012

Abstract:

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.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Genetic polymorphism of 17 STR loci in Chinese population from Hunan province in Central south China

Journal: Forensic Science International: Genetics | Year: 2012

Abstract:

We selected 586 unrelated healthy individuals (338 males and 248 females) whose ancestors lived in Hunan Province for at least three generations. After informed consent in compliance with the ethical norms set by Chinese legislation was acquired, we obtained bloodstains from each of the subjects. The study was approved by the ethics committee of the Third Xiangya Hospital of Central South University, and was carried out following the guidelines for publication of population data required by the journal [1] and according to the International Society of Forensic Genetics (ISFG) recommendations [2].

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

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

Journal: Forensic Science International: Genetics | Year: 2012

Abstract:

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.

Peoples: - | Places: - | Topics: - | DNA Type: mtDNA

Population data of the AmpFISTR® NGM™ STR loci in a North of Portugal sample

Journal: Forensic Science International: Genetics | Year: 2012

Abstract:

The AmpF?STR® NGM™ PCR Amplification Kit includes 15 STRs loci and 12 of them (D3S1358, VWA, D8S1179, D21S11, D18S51, TH01, FGA, D1S1656, D2S441, D10S1248, D12S391 and D22S1045) are part of the European Standard Set (ESS). Five of these loci, D10S1248, D22S1045, D2S441, D1S1656, D12S391, were recommended by the ENFSI and EDNAP groups to be adopted for the analysis of degraded DNA samples, in order to improve the power of national databases and to encourage standardization within Europe [1–5]. Allele frequencies and other forensically relevant statistic data for the STR loci included in the AmpF2STR® NGM™ PCR Amplification Kit, were generated.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

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