Forensic evaluation of the DNATyper™ Y36 system: validation, mutation rates, and discriminative power

RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese

Rapidly mutating Y-STRs (RM Y-STRs) have significant application value in differentiating both related and unrelated males. In this study, 26 RM Y-STRs from 367 father–son pairs revealed a total of 224 repeat mutations across all the markers and pairs. The average mutation rate per marker was 18.2 × 10− 3, ranging from < 2.7 × 10− 3 for DYS1007 and DYS626 to 46.7 × 10− 3 for DYS712. The mutation rates of DYS1007, DYS626, DYF403S1b, DYS518, DYS570, and DYS449 were lower than 10− 2. We integrated previously published RM Y-STR data from both Chinese and international populations. The locus mutation rate ranged from 4.5 × 10− 3 for DYS1007 to 54.5 × 10− 3 for DYF399S1 in the combined Chinese Han population and from 10.0 × 10− 3 for DYF403S1b to 73.6 × 10− 3 for DYF399S1 in the combined international population. Notably, the mutation rates of DYS1007, DYF399S1, DYS570, DYS612, and DYS526b were significantly lower in the combined Chinese Han population than in the combined international population. For male relatives separated by 1 to 4 meioses, the differentiation rates based on these 26 RM Y-STRs were 36.5%, 55.9%, 74.2%, and 79.2%, respectively. Yfiler Plus shows differentiation rates of 16.1%, 26.6%, 45.2%, and 60.4%, respectively. The Y41SE-v1.2 differentiation rates (30 Y-STRs) were 13.4%, 21.3%, 35.5%, and 35.8%, respectively. Overall, the differentiation rates using all 56 Y-STRs were 44.7%, 64.9%, 87.1%, and 92.5%, respectively. For unrelated males, the haplotype discrimination capacity of 26 RM Y-STRs was 100%, the capacity of Yfiler Plus was 99.7%, and the capacity of Y41SE-v1.2 (30 Y-STRs) was 98.6%. Overall, this study provides empirical evidence supporting the ability of 26 RM Y-STRs to differentiate both unrelated males and male relatives in the Chinese Han population.

BackgroundThis study was conducted to examine the differences in the incidence of hypertension and associated risk factors between Mongolian and Han populations in northeast China.MethodsA population-based sample of 4753 Mongolian subjects and 20,247 Han subjects aged ≥35 years and free from hypertension at baseline were followed from 2004–2006 to 2010. Incident hypertension was defined as systolic blood pressure≥140 mmHg, diastolic blood pressure ≥90 mmHg, or current use of antihypertensive medication.ResultsDuring mean 4.3 years follow-up, a total of 8779 individuals developed hypertension. The age-adjusted incidence of hypertension for Mongolian subjects was 12.64 per 100 person-years, for Han subjects was 9.77 per 100 person-years (P<0.05). The incidence of hypertension was positively correlated with age, physical activity, drinking, body mass index (BMI), family of hypertension and prehypertension in the Han population. In the Mongolian population, hypertension was positively correlated with age, physical activity, education level, drinking, BMI, prehypertension and family history of hypertension. The rates of awareness, treatment and control of hypertension for newly developed cases among both Han and Mongolian populations were low. (36.5% vs. 42.3%, 13.1% vs. 18.2%, 0.7% vs. 1.3%, P<0.05, respectively).ConclusionsThe incidence rate of hypertension is higher in the Mongolian populations than that in the Han populations, and hypertension in both ethnic populations was associated with similar risk factors. Our results suggest that most newly-diagnosed cases of hypertension are not adequately treated. Improvements in hypertension prevention and control programs in rural China are urgently needed.

Objective: To understand the distribution characteristics of the relative frequencies of apolipoprotein E (APOE) alleles in Tibetans of Qinghai province, to provide a basis for subsequent research. Method: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to determine the APOE genotypes and analyze the distribution characteristics in 96 indigenous Tibetans randomly selected from the Medical Examination Center of Qinghai Provincial People’s Hospital, and the results of this study were compared with those of other ethnic groups in China. Results: The frequencies of E2, E3, and E4 alleles in the 96 subjects were 1.563%, 89.062%, and 9.375%, respectively, and the genotype frequencies were E2/E2 (0%), E2/E3 (3.125%), E2/E4 (0%), E3/E3 (78.125%), E3/E4 (18.750%), and E4/E4 (0%), respectively. The frequency distribution of the ε2 allele in the Tibetan population was lower than that of the Northern Han, Southern Hakka, Hui, Mongolian, and Dai populations of China. The frequency distribution of the ε4 allele in the Tibetan population was of no significant difference compared with that of the Northern Han, Southern Hakka, Hui, and Mongolian populations, but was higher than that of the Dai population. The frequency distribution of the ε3 allele in the Tibetan population was of no significant difference compared with that of the Northern Han, Mongolian, and Dai populations, but higher than that of the Southern Hakka and Mongolian populations. Conclusion: There are ethnic differences in the frequency distribution of the three common alleles of APOE.

We investigated a possible association between genetic variations in chloride channel Kb (CLCNKB) gene and essential hypertension (EH) in the Mongolian and Han populations in Inner Mongolia. Our study included 414 unrelated Mongolian herdsmen and 524 Han farmers. Two tagSNPs of CLCNKB (rs945393 and rs10803414) were identified from the Chinese HapMap database based on pairwise r2 ≥ 0.5 and minor allele frequency ≥0.05. Genotyping was performed using the PCR/ligase detection reaction assay. There was significant difference in allele frequency of rs10803414 between the EH group (35%) and the control group (26%) in the Mongolian population (P < .05). Significant association was identified between rs10803414 and EH in the Mongolian population (P < .05) and rs945393 and EH in the Han population (P < .01). The frequency of haplotype CC in the EH group (9.4%) was significantly higher than in the control group (4.6%) in the Mongolian population; individuals who possessed the CC haplotype had a significantly higher risk of EH in the Mongolian population. There was no association between haplotype and EH in the Han population. After adjusting for age, sex, and other confounding risk factors, only rs10803414 was the risk factor of hypertension in Mongolians. Our results indicate that rs10803414 in CLCNKB confers a significant risk of EH in the Mongolian population and haplotype CC of CLCNKB is a genetic factor for EH in the Mongolian population. Our study expands the association between CLCNKB and EH to a non-European ancestry population and provides the first evidence of a cross-race susceptibility of EH locus.

Background: Currently, the Han population in China may be comprised of different genetic groups due to geographic, cultural and economic factors. Understanding population structure is very important for forensic purposes. However, knowledge of the genetic substructure within the whole Han population in China is still limited.Aim: This study is designed to ascertain the genetic structure of the Han population in China through genetic data from autosomal short tandem repeats (STRs).Subjects and methods: A set of 41 STR markers were analysed in 8725 unrelated Han Chinese males from the seven geographic regions of Northeast, North, East, Central, South, Southwest and Northwest in mainland China. Allele frequencies and F-statistics were estimated. Principal coordinate analysis (PCoA), phylogenetic analyses, analysis of molecular variance (AMOVA) and discriminant analysis of principal components (DAPC) were performed to explore the population structure.Results: Rare alleles that have not been observed in previous samples were detected. The small overall Fst values (0.0008), AMOVA and DAPC indicated that there is no population structure in Han Chinese. However, the PCoA and phylogenetic tree disclose a genetic differentiation pattern from north to south.Conclusions: There is no apparent population substructure in the Han population in China. However, genetic distances among the Han populations correlate with geographic locations.

Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father–son pairs

Objective To evaluate the discrimination efficiency of the SeqType® P52 Human Ancestry Identification SNP Detection Kit based on a high-throughput sequencing platform in five Chinese ethnic groups. Methods Using the SeqType® P52 Human Ancestry Identification SNP Detection Kit based on a high-throughput sequencing platform, a total of 350 samples from Han, Tibetan, Mongolian, Uygur, and Yi populations in China were detected and population cluster analysis was performed. Results The effective sequencing depth of a single site in a single sample was ≥720×, and the average report rate was 96%. The mean values of allele frequency differences between the Tibetan, Mongolian, Uygur, Yi and Han population were 0.20, 0.05, 0.24 and 0.11, respectively. Using Structure 2.3.4 software under K=5 mode, independent ancestral component in Han, Tibetan and Uygur could be detected, which was consistent with the result observed from the principal component analysis （PCA）. For the Yi population, two thirds of them had relatively independent ancestral component close to the Tibetan population and one third were similar to the Uygur population. The Mongolian population had similar ancestral origin component with Han population. Conclusion The composite detection system with 52 screened ancestry-informative SNP sites has been established in this study, which can effectively analyze the composition and individual genetic components of populations from Han, Tibetan and Uygur. The ability to discriminate among Han, Mongolian and Yi needs to be further improved. The SeqType® P52 Human Ancestry Identification SNP Detection Kit can be used to infer the origin of an individual's ancestors in some forensic DNA cases.

Haplotype study of the CYP4A11 gene and coronary artery disease in Han and Uygur populations in China

To explore associations of CYP2E1 and NAT2 polymorphisms with lung cancer susceptibility among Mongolian and Han populations in the Inner Mongolian region. CYP2E1 and NAT2 polymorphisms were detected by PCR-RFLP in 930 lung cancer patients and 1000 controls. (1) Disequilibrium of the distribution of NAT2 polymorphism was found in lung cancer patients among Han and Mongolian populations (p=0.031). (2) Lung cancer risk was higher in individuals with c1, D allele of CYP2E1 RsaI/PstI, DraI polymorphisms and slow acetylation of NAT2 (c1 compared with c2, OR=1.382, 95%CI: 1.178- 1.587, p=0.003; D compared with C, OR=1.241, 95%CI: 1.053-1.419, P<0.001; slow acetylation compared with rapid acetylation, OR=1.359, 95%CI:1.042-1.768, p=0.056) (3) Compared with c2/c2 and rapid acetylation, c1/c1 together with slow acetylation synergetically increased risk of lung cancer 2.83 fold. (4) Smokers with CYP2E1 c1/c1, DD, and NAT2 slow acetylation have 2.365, 1.916, 1.841 fold lung cancer risk than others with c2/c2, CC and NAT2 rapid acetylation, respectively. (5) Han smokers with NAT2 slow acetylation have 1.974 fold lung cancer risk than others with rapid acetylation. Disequilibrium distribution of NAT2 polymorphism was found in lung cancer patients among Han and Mongolian populations. Besides, Han smokers with NAT2 slow acetylation may have higher lung cancer risk compared with rapid acetylation couterparts. CYP2E1 c1/ c1, DD and NAT2 slow acetylation, especially combined with smoking, contributes to the development of lung cancer. CYP2E1 c1/c1 or DD genotype and NAT2 slow acetylation have strong synergistic action in increasing lung cancer risk.

To discuss the status of epidemiology of stroke in the Mongolian and Han population aged over 45 years and to understand the treatment and prevention of stroke. Data collected on stroke populations aged over 45 years in the six areas in Inner Mongolia were analyzed by using stratified multi-stage cluster sampling. The prevalence rate of stroke in patients aged over 45 years in Inner Mongolia was 4.62%. The stroke prevalence rate increased with age in both males and females, the Han and Mongolian populations, and was higher in males than in females in Inner Mongolia. The prevalence rate of stroke in the Mongolian population was higher than in the Han population. The incidence rate of stroke in patients aged over 45 years in Inner Mongolia was 0.28%, of which the rate of relapsed ischemic stroke was 23.29%. The proportion of ischemic stroke in the stroke patients was higher than hemorrhagic stroke. The prevalence and incidence rates of stroke in patients aged over 45 years in Inner Mongolia were high. The prevalence rate of stroke in both the Han population and the Mongolian population increased with age. Ischemic stroke was the major form of stroke.

This study investigated the current status and distribution of Alzheimer's disease (AD) among Mongolian and Han individuals who were at least 55 years old and living in rural areas of Inner Mongolia. This study sought to provide basic epidemiological data to better understand and treat Alzheimer's disease. Individuals with AD who were at least 55 old and living in one of 27 communities and two settlements in Mongolia, took part in an AD epidemiological survey from June 2008 to June 2009. Stratified, multistage random-cluster sampling was used to analyze data. The first level of random-cluster sampling consisted of data collected from questionnaires and home-visit interviews of individuals living in four Qi (a county level administration region in Mongolia) and in one city in the Xilin Guole League. Data from individuals in four district offices and ten towns from the first level random-cluster formed the second level of random-cluster sampling. The final sample for this epidemiological investigation consisted of 9266 individuals. Analyses revealed that the prevalence rate of AD was 4.79% (SD=4.71%) in the combined Mongolian and Han populations of individuals at least 55 years old and living in rural areas of Inner Mongolia. The individual AD prevalence rates in the Mongolian and Han populations were 4.63% (SD=4.84%) and 4.89% (SD=4.60%), respectively. The AD prevalence rate for women was higher than for men (p<0.05). The AD prevalence rate for individuals aged 65 and older in the two combined populations was 8.06% (SD=8.55%); the rate in the Mongolian population was 7.81% (SD=8.38%) and 8.18% (SD=8.57%) in the Han population. Gender and age were risk factors for the development of AD (p<0.05) in both populations. 1) There was no significant difference in the AD prevalence rate between the Mongolian and Han populations consisting of individuals aged 55 and older, living in rural areas of Inner Mongolia. However, the AD prevalence rates in these populations were higher than the national average. 2) Gender and age were risk factors for the development of AD in the Mongolian and Han populations.

Genetic variants of the RGS5 gene are believed to be risk factors for hypertension and cardiovascular diseases. In this study, we investigated the association between RGS5 gene variants and hypertension in the Mongolian and Han populations. Peripheral blood was obtained from 429 unrelated Mongolian herdsmen and 416 Han farmers [including essential hypertension (EH) patients and controls]. Nine tagSNPs within the RGS5 genes were retrieved from HapMap, and the samples were individually genotyped using the polymerase chain reaction/ligase detection reaction assay. The distribution of the allele frequency of rs12035879 differed significantly between hypertensive subjects and controls in the Han population, while the distribution of the allele and genotype frequencies of rs16849802 differed significantly between hypertensive subjects and controls in the Mongolian population. We observed an association between rs16849802 and EH in the Mongolian population. The frequency of haplotype GAA was significantly higher in the EH group than in controls in the Mongolian population. However, the EH group and controls did not differ significantly in all 6 haplotypes in the Han population. The rs16849802 and haplotype GAA independently increased the risk of EH in Mongolian patients, and may be used as a risk factor for the prediction of high blood pressure.

Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise

Rapidly mutating Y-STRs (RM Y-STRs) harbor great potential to distinguish male relatives and achieve male identification. However, forensic applications were greatly limited by the small number of the initially identified 14 RM Y-STRs. Recently, with the emergence of 12 novel RM Y-STRs, an integrated panel named RMplex was introduced, which contains all 26 RM Y-STRs and four fast mutating Y-STRs (FM Y-STRs). To obtain the first data on the mutation rates and father-son differentiation rates of the 30 newly proposed Y-STRs in Chinese populations, we performed an empirical mutation study on 307 DNA-confirmed Chinese paternal pairs. Previously reported mutation rates for 14 RM Y-STRs in Chinese and European populations were pooled and merged with our data. The highest meiosis number for the two groups reached 4771 and 2687, respectively. Five loci showed significant differences between the populations (DYS570, DYS399S1, DYS547, DYS612, and DYF403S1b). For the new panel covering 30 Y-STR loci, our results show extensive differences in the mutation rates between the two populations, as well. 10 RM Y-STR loci showed relatively low mutation rates (10–3–10–2 per meiosis) and 2 FM Y-STR loci had rapid mutation rates (> 10–2 per meiosis) in the Chinese population. Several-fold differences in mutation rates were found in nine Y-STR loci between the Chinese and reference populations, with two loci having significantly higher mutation rates and one locus with a significantly lower mutation rate in the Chinese population (P < 0.05). Eighteen RM Y-STRs (> 10–2 per meiosis), 8 FM Y-STR loci (5×10–3-10–2 per meiosis), 3 moderately mutating Y-STRs (MM Y-STRs, 10–3-5×10–3 per meiosis), and one locus with no observed mutation events were identified in the Chinese population. 40.06% of the Chinese paternity pairs were discriminated with RMplex while only 20.84% with the initial 14 RM Y-STRs, indicating that RMplex is beneficial for distinguishing paternally related males. Future studies on populations of different genetic backgrounds are necessary to obtain comprehensive estimates of mutation rates at these new loci.