Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles

Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age

Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.

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.

Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology

As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.

EASplex: A panel of 308 AISNPs for East Asian ancestry inference using next generation sequencing

Ancestry inference is useful in many scientific fields, such as forensic genetics, medical genetics, and molecular archaeology. Various ancestry inferring methods have been released for major continental populations. However, few reports refer to sub-populations within the East Asian population using hundreds of ancestry informative SNPs (AISNPs). In this study, we developed a 308-AISNP panel (EASplex NGS DNA panel) using multiplex PCR and next generation sequencing (NGS). This panel included 56 SNPs relevant for the continent-level ancestry inference and 252 Japanese-, Korean-, and/or Han Chinese-specific AISNPs to address the ancestry inference of global populations and regional populations among Japanese (JPT), Korean minority (CHK), and Han Chinese (CHH). A total of 87 CHK and 59 CHH samples were used to check the performance of the EASplex NGS DNA panel. By analyzing 146 profiles of samples with JPT and CHH data from Beijing and South China in 1000 genomes project, the following results were obtained: (1) the 146 tested samples were correctly assigned to the East Asian group; (2) the paired population assignment rate was 99.73% for JPT and CHH, 95% for JPT and CHK, and 90.11% for CHK and CHH; and (3) the whole population assignment was 92.14% for the JPT, CHK, and CHH data. Overall, the EASplex NGS DNA panel displayed informativeness for continental ancestry inference and regional ancestry inference among JPT, CHH, and CHK and has the potential for use in forensic and genetic population studies.

Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes

Background

Ancestry informative markers are regarded as useful tools for inferring the ancestral information of an individual, which have been widely used in the criminal investigations and population genetic studies. Previously, a multiplex amplification panel containing 39 AIM-InDel loci was constructed. This study aims to investigate the genetic polymorphisms of these 39 AIM-InDel loci in Yunnan Hani and Miao ethnic groups, and to uncover their genetic affinities with reference populations based on the AIM-InDel markers.

Materials and methods

In this research, 39 AIM-InDel profiles of 203 unrelated Miao individuals and 203 unrelated Hani individuals in Yunnan province of China were acquired. Additionally, we evaluated the genetic polymorphisms of 39 InDel loci in Yunnan Miao and Hani groups. Moreover, the genetic relationships among Yunnan Miao, Hani and reference populations were also clarified based on Nei’s genetic distances, pairwise fixation indexes, principal component analyses, phylogenetic analyses, and STRUCTURE analyses.

Results

Genetic diversity analyses demonstrated that these InDel loci showed varying degrees of genetic polymorphisms, and could be utilized in forensic identifications in Yunnan Miao and Hani groups. The results of principal component analyses, phylogenetic analyses and Structure analyses revealed that Yunnan Miao and Hani groups had closer genetic relationships with East Asian populations, especially with the populations from Southern China. This research enriched the genetic data of Chinese ethnic minority, and provided ancestral information of Yunnan Miao and Hani groups from the perspective of population genetics.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41065-022-00238-9.

The number of SNPs required for distinguishing Japanese from other East Asians

In some cases, it is necessary to estimate the national origin of an unknown subject in forensic medicine. The use of single nucleotide polymorphism (SNP) markers appears to be very effective for this purpose, since genome-wide SNP genotype data of many human populations are publicly available. In this study, we examined the number of SNPs that could objectively and accurately distinguish Japanese subjects (1KG-JPT) from the other East Asians (1KG-CDX, -CHB, -CHS, and -KHV) using the combination of principal component analysis and hierarchical cluster analysis. A computer simulation showed that approximately 3000 randomly selected SNPs were enough for the discrimination. Our results suggest that at least a 0.024% coverage is needed in the next generation sequencing experiment to objectively determine whether an unknown person is Japanese or not if the amount of DNA sample from him/her is insufficient or the quality is low.

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.

A set of novel SNP loci for differentiating continental populations and three Chinese populations

In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.