Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel

Forensic biogeographical ancestry inference: recent insights and current trends

BACKGROUND

As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology.

OBJECTIVE

In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed.

METHODS

We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI.

CONCLUSION

While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.

Development of an Okinawa panel for biogeographic inference of Okinawans

BACKGROUND

The Precision ID Ancestry Panel with 165 SNP markers was unable to differentiate between mainland Japanese and Okinawa Japanese or to distinguish either of them from other East Asian populations.

AIM

An Okinawa panel was developed with the aim of further separating Okinawa Japanese individuals from mainland Japanese and other Asian groups. Seventy-five SNPs were selected using the most informative markers from the literature. Further, 22 SNPs were selected to separate Okinawa Japanese at minimum SNPs.

SUBJECTS AND METHODS

Samples were collected from 48 unrelated individuals from mainland Japan and 46 unrelated residents of the Okinawa prefecture. Data were evaluated by STRUCTURE, principal component, and GenoGeographer analyses.

RESULTS

The 22 SNP set had similar levels of differentiation in STRUCTURE and PCA analyses as the 75 SNP set. GenoGeographer analysis showed that, out of the 46 Okinawa Japanese individuals, the 75 SNP and 22 SNP sets correctly assigned the Okinawan population as the most likely population of origin for 32 and 31 individuals, respectively.

CONCLUSION

Neither SNP set could completely differentiate between Okinawa Japanese and other Asian groups, however, these sets should be useful for crime investigation, when the sample, cost and time are limited.

Ancestry resolution of South Brazilians by forensic 165 ancestry-informative SNPs panel

Forensic DNA phenotyping (FDP) includes biogeographic ancestry (BGA) inference and externally visible characteristics (EVCs) prediction directly from an evidential DNA sample as alternatives to provide valuable intelligence when conventional DNA profiling fails to achieve identification. In this context, the application of Massively Parallel Sequencing (MPS) methodologies, which enables simultaneous typing of multiple samples and hundreds of forensic markers, has been gradually implemented in forensic genetic casework. The Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) is a forensic multiplex assay consisting of 165 autosomal SNPs designed to provide biogeographic ancestry information. In this work, a sample of 250 individuals from Rio Grande do Sul (RS) State, southern Brazil, apportioned into four main population groups (African-, European-, Amerindian-, and Admixed-derived Gauchos), was evaluated with this panel, to assess the feasibility of this approach in a highly heterogeneous population. Forensic descriptive parameters estimated for each population group revealed that this panel has enough polymorphic and informative SNPs to be used as a supplementary instrument in forensic individual identification and kinship testing regardless of ethnicity. No statistically significant deviation from Hardy-Weinberg equilibrium was observed after Bonferroni correction. However, seven loci pairs displayed linkage disequilibrium in pairwise LD testing (p < 3.70 × 10^-6). Interpopulation comparisons by F_ST analysis, MDS plot, and STRUCTURE analysis among the four RS population groups apart and along with 89 reference worldwide populations demonstrated that Admixed- and African-derived Gauchos present the highest levels of admixture and population stratification, whereas European- and Amerindian-derived exhibit a more homogeneous genetic conformation.

Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations

The EUROFORGEN NAME panel is a regional ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY system and included 111 SNPs. Here, a custom AmpliSeq EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with a global ancestry panel, the Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied.

Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations

Ancestry informative markers (AIMs), which are distributed throughout the human genome, harbor significant allele frequency differences among diverse ethnic groups. The use of sets of AIMs to reconstruct population history and genetic relationships is attracting interest in the forensic community, because biogeographic ancestry information for a casework sample can potentially be predicted and used to guide the investigative process. However, subpopulation ancestry inference within East Asia remains in its infancy due to a lack of population reference data collection and incomplete validation work on newly developed or commercial AIM sets. In the present study, 316 Chinese persons, including 85 Sinitic-speaking Haikou Han, 120 Qiongzhong Hlai and 111 Daozhen Gelao individuals belonging to Tai-Kadai-speaking populations, were analyzed using the Precision ID Ancestry Panel (165 AISNPs). Combined with our previous 165-AISNP data (375 individuals from 6 populations), the 1000 Genomes Project and forensic literature, comprehensive population genetic comparisons and ancestry inference were further performed via ADMIXTURE, TreeMix, PCA, f-statistics and N-J tree. Although several nonpolymorphic loci were identified in the three southern Chinese populations, the forensic parameters of this ancestry inference panel were better than those for the 23 STR-based Huaxia Platinum System, which is suitable for use as a robust tool in forensic individual identification and parentage testing. The results based on the ancestry assignment and admixture proportion evaluation revealed that this panel could be used successfully to assign individuals at a continental scale but also possessed obvious limitations in discriminatory power in intercontinental individuals, especially for European-Asian admixed Uyghurs or in populations lacking reference databases. Population genetic analyses further revealed five continental population clusters and three East Asian-focused population subgroups, which is consistent with linguistic affiliations. Ancestry composition and multiple phylogenetic analysis further demonstrated that the geographically isolated Qiongzhong Hlai harbored a close phylogenetic relationship with Austronesian speakers and possessed a homogenous Tai-Kadai-dominant ancestry, which could be used as the ancestral source proxy in population history reconstruction of Tai-Kadai-speaking populations and as one of the representatives for forensic database establishment. In summary, more population-specific AIM sets focused on East Asian subpopulations, comprehensive algorithms and high-coverage population reference data should be developed and validated in the next step.

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable "eye-witness" and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay's sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.

Evaluation of a custom GeneRead™ massively parallel sequencing assay with 210 ancestry informative SNPs using the Ion S5™ and MiSeq platforms

A custom GeneRead DNAseq SNP panel with 210 markers was evaluated using the Ion S5 and MiSeq sequencing platforms. Sensitivity, PCR cycle number, and the use of half volume of reagents for target enrichment and library preparation were tested. Furthermore, genotype concordance between results obtained with the different sequencing platforms and with known profiles generated using other sequencing assays was analysed. The GeneRead DNASeq SNP assay gave reproducible results with an input of 200 pg DNA on both platforms. A total of 204 loci were successfully sequenced. Three loci failed completely in the PCR amplification, and three additional loci displayed frequent locus drop-outs due to low read depth or high heterozygote imbalance. Overall, the read depth across the loci was more well-balanced with the MiSeq, while the heterozygote balance was less variable with the Ion S5. Noise levels were low on both platforms (median< 0.2 %). Two simple criteria for genotyping were applied: A minimum threshold of 45 reads and an acceptable heterozygote balance range of 0.3-3.0. Complete concordance between platforms was observed except for three genotypes in one of the poorly performing loci, rs1470637. This locus had relatively low read depths on both platforms, skewed heterozygote balance, and frequent locus drop-outs. There was also full genotype concordance between the results from the GeneRead assay and known profiles generated with the QIAseq and Ion AmpliSeq assays. The few discordant results were either due to locus drop-outs in the poorly performing loci or allele drop-outs in the QIAseq assay. Profiles with a minimum of 179 SNPs were obtained from four challenging case work samples (blood swabs, bone, or blood from a corpse). Overall, the GeneRead DNASeq assay showed considerable potential and could provide a reliable method for SNP genotyping in cases involving identification of individuals, prediction of phenotypic traits, and ancestry inference.

Evaluation of the Precision of Ancestry Inferences in South American Admixed Populations

Ancestry informative markers (AIMs) are used in forensic genetics to infer biogeographical ancestry (BGA) of individuals and may also have a prominent role in future police and identification investigations. In the last few years, many studies have been published reporting new AIM sets. These sets include markers (usually around 100 or less) selected with different purposes and different population resolutions. Regardless of the ability of these sets to separate populations from different continents or regions, the uncertainty associated with the estimates provided by these panels and their capacity to accurately report the different ancestral contributions in individuals of admixed populations has rarely been investigated. This issue is addressed in this study by evaluating different AIM sets. Ancestry inference was carried out in admixed South American populations, both at population and individual levels. The results of ancestry inferences using AIM sets with different numbers of markers among admixed reference populations were compared. To evaluate the performance of the different ancestry panels at the individual level, expected and observed estimates among families and their offspring were compared, considering that (1) the apportionment of ancestry in the offspring should be closer to the average ancestry of the parents, and (2) full siblings should present similar ancestry values. The results obtained illustrate the importance of having a good balance/compromise between not only the number of markers and their ability to differentiate ancestral populations, but also a balanced differentiation among reference groups, to obtain more precise values of genetic ancestry. This work also highlights the importance of estimating errors associated with the use of a limited number of markers. We demonstrate that although these errors have a moderate effect at the population level, they may have an important impact at the individual level. Considering that many AIM-sets are being described for inferences at the individual level and not at the population level, e.g., in association studies or the determination of a suspect's BGA, the results of this work point to the need of a more careful evaluation of the uncertainty associated with the ancestry estimates in admixed populations, when small AIM-sets are used.

Estimation of the number of contributors to mixed samples of DNA by mitochondrial DNA analyses using massively parallel sequencing

We evaluated whether the number of contributors to mixed DNA samples can be estimated by analyzing the D-loop of mitochondrial DNA using massively parallel sequencing. The A- (positions 16,209-16,400) and B- (positions 30-284) amplicons in hypervariable regions 1 and 2, respectively, were sequenced using MiSeq with 2 × 251 cycles. Sequence extraction and trimming were performed using CLC Genomics Workbench 11 and the number of observed haplotypes was counted for each amplicon type using Microsoft Excel. The haplotype ratios were calculated by dividing the number of counted reads of the corresponding haplotype by the total number of sequence reads. Haplotypes that were over the threshold (5%) were defined as positive haplotypes. The number of larger positive haplotypes in either of the two amplicon types was defined as the number of contributors. Samples were collected from seven individuals. Seventeen mixed samples were prepared by mixing DNA from two to five contributors at various ratios. The number of contributors was correctly estimated from almost all of the mixed samples containing equal amounts of DNA from two to five people. In mixed samples of two or three people, the minor components were detected down to a ratio of 20:1 or 8:2:1. However, heteroplasmy, base deletions, and sharing of the same haplotypes caused incorrect estimations of the number of contributors. Although this method still has room for improvement, it may be useful for estimating the number of contributors in a mixed sample, as it does not rely on forensic mathematics.

Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs

The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been studied on a large number of populations and continues to be applied to new population samples. The existing reference database of population samples allows the relationships of new population samples to be inferred on a global level. Analyses show that these autosomal markers constitute one of the better panels of AISNPs. Continuing to build this reference database enhances its value. Because more than half of the 25 ethnic groups recently studied with these AISNPs are from Southwest Asia and the Mediterranean region, we present here various analyses focused on populations from these regions along with selected reference populations from nearby regions where genotype data are available. Many of these ethnic groups have not been previously studied for forensic markers. Data on populations from other world regions have also been added to the database but are not included in these focused analyses. The new population samples added to ALFRED and FROG-kb increase the total to 164 population samples that have been studied for all 55 AISNPs.

Massively parallel sequencing techniques for forensics: A review

DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as biotechnology, virology, and medical diagnostics. Reflected by the growing number of articles published over the last 2-3 years, these techniques have also gained attention in the forensic field. This review contains a brief description of first, second, and third generation sequencing techniques, and focuses on the recent developments in human DNA analysis applicable in the forensic field. Relevance to the forensic analysis is that besides generation of standard STR-profiles, DNA repeats can also be sequenced to look for polymorphisms. Furthermore, additional SNPs can be sequenced to acquire information on ancestry, paternity or phenotype. The current MPS systems are also very helpful in cases where only a limited amount of DNA or highly degraded DNA has been secured from a crime scene. If enough autosomal DNA is not present, mitochondrial DNA can be sequenced for maternal lineage analysis. These developments clearly demonstrate that the use of NGS will grow into an indispensable tool for forensic science.

Implementing a biogeographic ancestry inference service for forensic casework

The Centre of Forensic Sciences has validated the Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry inference service based on the Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, and Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework.

Forensic ancestry analysis in two Chinese minority populations using massively parallel sequencing of 165 ancestry-informative SNPs

Ancestry inference based on SNPs with marked allele frequency differences in diverse populations (called ancestry-informative SNP (AISNP)) is rapidly developed with the technology advancements of massively parallel sequencing. Despite the decade of exploration and broad public interest in the peopling of East-Asians, the genetic landscape of Chinese Silk Road populations based on the AISNPs is still little known. In this work, 206 unrelated individuals from Chinese Uyghur and Hui populations were firstly genotyped by 165 AISNPs (The Precision ID Ancestry Panel) using the Ion Torrent Personal Genome Machine system. The ethnic origin of two investigated populations and population structures and genetic relationships were subsequently investigated. The 165 AISNPs panel not only can differentiate Uyghur and Hui populations but also has potential applications in individual identification. Comprehensive population comparisons and admixture estimates demonstrated a predominantly higher European-related ancestry (36.30%) in Uyghurs than Huis (3.66%). Overall, the Precision ID Ancestry Panel can provide good resolution at the intercontinental level, but has limitations on the genetic homogeneous populations, such as the Hui and Han. Additional population-specific AISNPs remain necessary to get better-scale resolution within geographically proximate populations in East Asia.

Massively parallel sequencing of 165 ancestry informative SNPs in two Chinese Tibetan-Burmese minority ethnicities

The Tibeto-Burman language, one subfamily of the Sino-Tibetan languages, is spoken by over 60 million people all over East Asia. Yet the ethnic origin and genetic architecture of Tibeto-Burman speaking populations remain largely unexplored. In the present study, 169 Chinese individuals from Tibeto-Burman speaking populations (two ethnic groups: Tibetan and Yi) in four different geographic regions in western China were analyzed using the Precision ID Ancestry Panel (165 AISNPs) and the Ion PGM System. The performance and corresponding forensic statistical parameters of this AISNPs panel were investigated. Comprehensive population genetic comparisons (143 populations based on Kidd' SNPs, 92 populations on the basis of Seldin' SNPs and 31 populations based on the Precision ID Ancestry Panel) and ancestry inference were further performed. Sequencing performance demonstrated that the Precision ID Ancestry Panel is effective and robust. Forensic characteristics suggested that this panel not only can be used for ancestry estimation of Tibeto-Burman populations but also for individual identification. Tibetan and Yi shared a common genetic ancestry origin but experienced the complex history of gene flow, local adaptation, and isolation, and constructed the specific genetic landscape of human genetic diversity of Highlander and Lowlander populations. Tibetan-Burman populations and other East Asian populations showed sufficient genetic difference and could be distinguished into three distinct groups. Furthermore, analysis of population structure revealed that significant genetic difference was existed inter-continent populations and strong genetic affinity was observed within-continent populations. Additional population-specific AISNPs and a relatively more comprehensive database with sufficient reference population data remain necessary to get better-scale resolution within a geographically proximate populations in East Asia.