Short tandem repeat (STR) markers are the cornerstone of forensic identity and kinship testing. Markers located on the X and the Y chromosome can complement those found on the autosomes, which are commonly used in laboratories today. The distinctive inheritance pattern of the sex chromosomes affords advantages to the investigation of family pedigrees required by mass disaster victim identification or missing persons cases, as well as mixed samples typically recovered in sexual assault crimes. This review aims to provide an overview of how X and Y STR markers are currently being used in forensic laboratories, including the applications which target their use, the markers and multiplexes facilitating recovery of this genetic information, and the tools available to interpret the resulting data. Emerging research topics are considered as well as issues requiring further study for both marker systems.

Forensic typing of short tandem repeat markers on the X and Y chromosomes

Fifteen autosomal short tandem repeat (STR) loci were genotyped using the AmpFISTR Identifiler PCR Amplification kit from 505 unrelated healthy individuals of Miao ethnic minority living in the Guizhou Province, Southwest China. Also, the genetic distance between Miao and nine related populations was compared.

Population data for 15 autosomal STR loci in the Miao ethnic minority from Guizhou Province, Southwest China

SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for both DNA and RNA-based genotyping. To determine a small set of SNPs with maximally discriminative power, genotype calls were obtained from DNA and blood-derived RNA sequencing data belonging to healthy, geographically dispersed, Dutch individuals. SNPs were selected based on different criteria like genotype call rate, minor allele frequency, Hardy–Weinberg equilibrium and linkage disequilibrium. A panel of 50 SNPs was sufficient to identify an individual uniquely: the probability of identity was 6.9 × 10− 20 when assuming no family relations and 1.2 × 10− 10 when accounting for the presence of full sibs. The ability of the SNP panel to uniquely identify individuals on DNA and RNA level was validated in an independent population dataset. The panel is applicable to individuals from European descent, with slightly lower power in non-Europeans. Whereas most of the genes containing the 50 SNPs are expressed in various tissues, our SNP panel needs optimization for other tissues than blood. This first DNA/RNA SNP panel will be useful to identify sample mix-ups in biomedical research and for assigning DNA and RNA stains in crime scenes to unique individuals.

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A SNP panel for identification of DNA and RNA specimens

The Dong, also called Kam are one of 56 ethnic groups of Chinese population, who have a population of 2,960,293 at the 2000 census and live mostly in eastern Guizhou (54.97%), western Hunan (28.42%), and northern Guangxi (10.23%) Province (Fig. S1). The Dong are thought to be the modern-day descendants of the ancient Liao people who occupied much of southern China. The Dong language belongs to a Tai-kadai (Zhuang-Dong) language, including the codes kmc for the southern dialect and doc for the northern. They speak their own language and sometimes use Chinese characters to represent the sounds of Dong words. Supplementary material related to this article can be found, in the online version, at http://dx.doi.org/10.1016/j.fsigen.2015.02. 005. Bloodstain samples of 600 unrelated healthy individuals were collected from Qiandongnan Miao and Dong Autonomous Prefecture, Guizhou Province, Southwest China after informed consent. DNA was extracted using the Chelex-100 protocol [1]. PCR was amplified using AmpFISTR Identifiler PCR Amplification kit (Thermo Fisher Scientific, MA, USA) on GeneAmp 9700 (Thermo Fisher) according to the manufacturer’s recommendations. Amplification products were separated and detected on an Applied Biosystems 3130xl Genetic Analyzer (Thermo Fisher). Raw data was analyzed using GeneMapper ID v3.2 Software (Thermo Fisher). The experimental procedures were guided in keeping with laboratory internal control standards and kit controls. The control DNA 9947A (Thermo Fisher) was employed as positive control, and the ddH2O was as negative control. The values for power of discrimination (PD), polymorphism information content (PIC), power of exclusion (PE), heterozygosity (He) and Hardy Weinberg equilibrium (HWE) analysis were calculated using the modified PowerStats v1.2 software obtained from Promega [2]. Pairwise Fst and p-value of each locus between populations were calculated using ARLEQUIN Version 3.5 software [3]. Nei’s standard genetic distance between populations was calculated using Phylip 3.69 package [4]. Phylogenetic tree was developed and visualized with the TreeView software [5]. The distribution of allele frequencies, forensic efficiency and statistical parameters are listed in Table S1. The PD ranged from 0.9712 (FGA) to 0.7919 (TPOX) with the value of 0.999 999 999 999 999 991 631 for combined power of discrimination (CPD). The PE ranged from 0.7920 (FGA) to 0.2929 (TPOX) with the value of 0.999 909 585 for combined power of exclusion (CPE). The He ranged from 0.8983 (FGA) to 0.6017 (TPOX). Except for CSF1PO (0.6807), D3S1358 (0.6840), TH01 (0.6419) and TPOX (0.5526), all STR loci presented high polymorphism (PIC > 0.7000) with the highest at FGA (0.8666). There was no statistically significant deviation from HWE after Bonferroni correction (p < 0.0033). Table S2 shows pairwise Fst and p values for differentiation test between the Dong ethnic minority and 8 published populations [6–11], where the statistically significant differences (p < 0.0033) were found with Korean [6] and Japanese [7] at 9 STR loci, Guangxi Maonan [8] and Guangxi Yao [8] at 2 STR loci and Guangxi Han [9] at 1 STR locus. As expected, there was no statistically significant difference at any STR locus within Guizhou Miao [10], Guangxi Zhuang [11] and Guangxi Mulao [8]. Table S3 shows the genetic distances between populations and Fig. S2 indicates the clusters in un-rooted phylogenetic trees. Supplementary material related to this article can be found, in the online version, at http://dx.doi.org/10.1016/j.fsigen.2015.02.005. We have strictly followed ISFG recommendations on the analysis of the DNA polymorphisms and nomenclature [12] and guidelines for publication of population data requested by the journal [13]. Certification of approval by China National Accreditation Service for Conformity Assessment (CNAS) is No. CNAS L3934 (2009-02-27).

Forensic Population Genetics – Letter to the EditorPopulation data for 15 autosomal STR loci in the Dong ethnic minority from Guizhou Province, Southwest China

In the present study, we investigated the genetic characteristics of 25 Y-chromosomal and 15 autosomal short tandem repeat (STR) loci in 305 unrelated Han Chinese male individuals from Liaoning Province using AmpFISTR® Yfiler® Plus and IdentifilerTM PCR amplification kits. Population comparison was performed between Liaoning Han population and different ethnic groups to better understand the genetic background of the Liaoning Han population. For Y-STR loci, the overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. Gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Rst and two multi-dimensional scaling plots showed that minor differences were observed when the Liaoning Han population was compared to the Jilin Han Chinese, Beijing Han Chinese, Liaoning Manchu, Liaoning Mongolian, Liaoning Xibe, Shandong Han Chinese, Jiangsu Han Chinese, Anhui Han Chinese, Guizhou Han Chinese and Liaoning Hui populations; by contrast, major differences were observed when the Shanxi Han Chinese, Yunnan Bai, Jiangxi Han Chinese, Guangdong Han Chinese, Liaoning Korean, Hunan Tujia, Guangxi Zhuang, Gansu Tibetan, Xishuangbanna Dai, South Korean, Japanese and Hunan Miao populations. For autosomal STR loci, DP ranged from 0.9621 (D2S1338) to 0.8177 (TPOX), with PE distributing from 0.7521 (D18S51) to 0.2988 (TH01). A population comparison was performed and no statistically significant differences were detected at any STR loci between Liaoning Han, China Dong, and Shaanxi Han populations. The results showed that the 25 Y-STR and 15 autosomal STR loci in the Liaoning Han population were valuable for forensic applications and human genetics, and Liaoning Han was an independent endogenous ethnicity with a unique subpopulation structure.

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Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China.

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.

A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

Haplotypes and allele frequencies of 17 Y-chromosomal STR loci included in the AmpFlSTR(®) Yfiler(®) system were obtained from a sample of 1021 unrelated individuals living in 6 provinces of South Korea. A total of 938 haplotypes were observed in the 1021 individuals studied, of which 885 were unique. The overall haplotype diversity for the 17 Y-STR loci was 0.9998, and the discrimination capacity was 0.9187. We found 11 atypical alleles (null, duplicated, triplicated, and microvariant alleles), that have not previously been reported in South Korean populations. It seems that these 17 loci are useful genetic markers for forensic personal identification and paternity testing in the South Korean population.

Population genetic polymorphisms of 17 Y-chromosomal STR loci in South Koreans.

Population genetic polymorphisms of 17 Y-chromosomal STR loci in

The genetic pattern of the Y-chromosomal short tandem repeat (Y-STR) haplotypes of 542 unrelated males having the five most common surnames was analyzed to evaluate their usefulness for Korean forensic science and to provide the basic information for Korean genetic genealogy. We identified 439 Y-STR haplotypes, with 385 (87.7%) being found once. Each of the most common Korean surnames examined here showed high haplotype diversity (>0.9949), indicating that Y-STR haplotypes are very heterogeneous within each surname. Population genetic analysis showed that there are little genetic difference among five surnames due to the genetic heterogeneity within each surname and the various kinds of non surname-specific haplotypes (33.6%: 182/542) distributed among five surnames. Surname prediction may not be adequate for narrowing down the suspect list in Korean forensic science, and additional Y-STR haplotype data of thebon-gwans are needed.

Y-STR genetic structure of the most common surnames in Korea

https://www.fsigeneticssup.com/article/S1875-1768(11)00017-5/pdf

Seong Yeon Yoo

Papers

A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

Population genetic polymorphisms of 17 Y-chromosomal STR loci in South Koreans.

Population genetic polymorphisms of 17 Y-chromosomal STR loci in

Y-STR genetic structure of the most common surnames in Korea

Genetic polymorphisms of eight X-STR loci of Mentype Argus X-8 kit in Koreans