OBJECTIVES: To investigate the ethnic origin of Chuanqing people, one of the largest unidentified ethnic groups in Guizhou, China, and analyze its genetic relationships with surrounding populations. METHODS: Based on a self-developed microhaplotype system, we conducted genotyping and analyzed the genetic distribution of microhaplotype loci and their forensic applicability in Chuanqing population in Guizhou Province. Using the microhaplotype data from different intercontinental populations and previously reported data from Han population living in Guizhou Province, we systematically investigated the genetic background of Chuanqing people through population genetic approaches, including genetic distance estimation, principal component analysis, and phylogenetic tree construction. RESULTS: Among the studied population, the number of haplotype per microhaplotype ranged from 6 to 25. The average expected heterozygosity (He), observed heterozygosity (Ho), power of discrimination (PD), and probability of exclusion (PE) were 0.8291, 0.8301, 0.9387, and 0.6593, respectively. The cumulative power of discrimination (CPD) and cumulative probability of exclusion (CPE) for these 33 loci were 1-2.62×10^-41 and 1-7.64×10^-17, respectively. Population genetic analyses revealed that the Chuanqing population had close genetic relationships with the East Asian populations, especially the local Guizhou Han population, Beijing Han population and the Han populations living in southern China. CONCLUSIONS The 33 microhaplotypes exhibit high levels of genetic diversity in the Guizhou Chuanqing population, highlighting their potentials for both forensic identification and parentage testing. The Han populations might have contributed a significant amount of genetic material to the Chuanqing population during the formation and development of the latter.
Humans ; China/ethnology* ; Ethnicity/genetics* ; Forensic Genetics/methods* ; Genetics, Population ; Genotype ; Haplotypes ; Phylogeny ; East Asian People/genetics*

Due to the virtues of no stutter peaks, low rates of mutation, and short amplicon sizes, insertion/deletion (InDel) polymorphism is an indispensable tool for analyzing degraded DNA samples from crime scenes for human identifications (Wang et al., 2021). Herein, a self-developed panel of 43 InDel loci constructed previously by our group was utilized to evaluate the genetic diversities and explore the genetic background of the Han Chinese from Beijing (HCB) including 301 random healthy individuals. The lengths of amplicons at 43 InDel loci in this panel ranged from 87 to 199 bp, which indicated that the panel could be used as an effective tool to utilize highly degraded DNA samples for human identity testing. The loci in this panel were validated and performed well for forensic degraded DNA samples (Jin et al., 2021). The combined discrimination power (PD) and combined probability of exclusion (PE) values in this panel indicated that the 43 InDel loci could be used as the candidate markers in personal identification and parentage testing of HCB. In addition, population genetic relationships between the HCB and 26 reference populations from five continents based on 19 overlapped InDel loci were displayed by constructing a phylogenetic tree, principal component analysis (PCA), and population genetic structure analysis. The results illustrated that the HCB had closer genetic relationships with the Han populations from Chinese different regions.
Beijing ; China ; Forensic Genetics/methods* ; Gene Frequency ; Genetics, Population ; Humans ; INDEL Mutation ; Phylogeny

OBJECTIVES: The previously established 38-plex InDel system was optimized and its performance was validated according to the Scientific Working Group on DNA Analysis Method (SWGDAM) application guidelines. The ancestry inference accuracy of individuals from East Asian, European, African and mixed populations was verified. METHODS: DNA standard sample 9947A was used as the template to establish the optimal amplification conditions by adjusting primer balance, Mg²⁺ final concentration and optimizing PCR thermal cycle parameters and amplification volume. The allelic dropout, nonspecific amplification and whether the origin of the inferred samples matched the known information were compared to evaluate the performance of this system. RESULTS: The optimal dosage of this system was 0.125-2 ng DNA template. The results of InDel typing were accurate, the amplification equilibrium was good, and the species specificity was good. This system showed certain tolerance to DNA samples including the inhibitor such as hemoglobin (≤80 μmol/L), indigo (≤40 mmol/L), calcium ion (≤1.0 mmol/L), and humic acid (≤90 ng/μL). The system enabled the direct amplification of DNA from saliva and blood on filter paper, and the results of ethnic inference were accurate. The system successfully detected the mixed DNA sample from two individuals. The test results of the system for common biological materials in practical cases were accurate. CONCLUSIONS The results of the 38-plex InDel system are accurate and reliable, and the performance of the system meets the requirement of the SWGDAM guidelines. This system can accurately differentiate the ancestry origins of individuals from African, European, East Asian, and Eurasian populations and can be implemented in forensic practice.
Humans ; Polymorphism, Single Nucleotide ; Genotype ; Polymerase Chain Reaction ; DNA/genetics* ; DNA Fingerprinting/methods* ; INDEL Mutation ; Genetics, Population ; Gene Frequency

As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits, a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data, sample quality issues, such as gender mismatch, abnormal inbreeding coefficient, cryptic relatedness, and population outliers, can also have fundamental impact on downstream analysis. However, there is a lack of tools specialized in identifying problematic samples from NGS data, often due to the limitation of sample size and variant counts. We developed SeqSQC, a Bioconductor package, to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access, and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor.org/packages/SeqSQC.
Breast Neoplasms ; genetics ; Cohort Studies ; Continental Population Groups ; genetics ; Female ; Genome, Human ; High-Throughput Nucleotide Sequencing ; methods ; standards ; Humans ; Software ; Whole Exome Sequencing

Genetic markers, such as single nucleotide polymorphism （SNP）, insertion/deletion （InDel）, were discovered and widely used with the development of whole genome sequencing and bioinformatics technology. The origin and genetic structure of the modern population had been gradually revealed from the perspective of genetics. The study on biogeographic ancestry inference in the field of forensic genetics emerged and developed rapidly, providing clues and scientific basis for the determination of investigation direction and for the narrow of the scope of investigation in the process of case investigation. This paper briefly reviews the research progress, inference methods and development trends of DNA ancestry inference technology.
Africa ; Criminals ; DNA/genetics* ; DNA Fingerprinting/methods* ; Forensic Genetics/methods* ; Genetics, Population ; Humans ; Phylogeography ; Polymorphism, Single Nucleotide

Objective To evaluate the effect of 56 ancestry informative single nucleotide polymorphism （aiSNP） genetic markers in the ForenSeq^TM DNA Signature Prep Kit on ancestry inference. Methods A total of 85 samples from five populations including Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population, Xinjiang Uygur autonomous region Uygur population and Nigerian population were collected. The library was constructed with the ForenSeq^TM DNA Signature Prep Kit and sequencing was performed based on the MiSeq FGx Forensic Genomics System. Using universal analysis software （UAS） of ForenSeq^TM, principal component analysis （PCA）, Structure and likelihood ratio method was used on the genotyping data of 56 aiSNP markers, respectively, and the genetic relationships between populations and inference of the origin of ancestors were analyzed. Results Among the five populations tested, the four ethnic populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population and Xinjiang Uygur autonomous region Uygur population） could be significantly distinguished from Nigerian population. Xinjiang Uygur autonomous region Uygur individuals were shown as having mixed origins of ancestors and could be distinguished from the other three Chinese populations. However, the other three populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population and Tibet autonomous region Tibetan population） could not be effectively distinguished by the system. Conclusion The 56 aiSNP markers in the ForenSeq^TM DNA Signature Prep Kit can make accurate ancestry inference from the intercontinental level, but it is not yet able to distinguish between Chinese subpopulations.
Asian People/genetics* ; China ; DNA ; DNA Fingerprinting ; Ethnicity/genetics* ; Forensic Genetics/methods* ; Genetics, Population ; High-Throughput Nucleotide Sequencing/methods* ; Humans ; Polymorphism, Single Nucleotide

OBJECTIVES: To calculate genetic parameters of SNP loci in next generation sequencing kits, and to compare them with STR loci for establishing the conversion ratio between SNP and STR system effectiveness. METHODS: Hardy-Weinberg equilibrium tests were performed in 101 SNP loci of next generation sequencing kits （ForenSeq™ DNA Signature Prep kit and Precision ID Identity Panel kit）. The parameters of system effectiveness of SNP loci in the cases of personal identification, trios, duos, and alleged parents were calculated, which were compared with the genetic parameters of STR loci. RESULTS: Except 2 loci without the data of genotype frequency, other 99 SNP loci conformed to Hardy-Weinberg equilibrium tests （P>0.05）. In ForenSeq™ DNA Signature Prep kit, the CDP of 94 SNP loci was 1-1.152 1×10⁻³⁴, CPE_trio was 1-4.416 9×10⁻⁸, CPE_duo was 1-8.483 7×10⁻⁵, and CPE_AP was 1-1.222 7×10⁻¹². In Precision ID Identity kit, the CDP was 1-2.052 4×10⁻³³, CPE_trio was 1-8.709 3×10⁻⁸, CPE_duo was 1-1.163 8×10⁻⁴, and CPE_AP was 1-3.725 7×10⁻¹². In the cases of personal identification, trios, duos and alleged parents, the system effectiveness of 2.85, 4.51, 4.88 and 4.55 SNP loci was equal to that of 1 STR locus, respectively. CONCLUSIONS With high system effectiveness of SNP loci, the next generation sequencing kits is suitable for personal identification and paternity testing in forensic science.
DNA Fingerprinting ; Forensic Genetics/methods* ; Gene Frequency ; Genetics, Population ; Genotype ; High-Throughput Nucleotide Sequencing/instrumentation* ; Humans ; Microsatellite Repeats ; Paternity ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Reagent Kits, Diagnostic

OBJECTIVETo assess the value of 15 short tandem repeat (STR) loci selected by an AmpFLSTR Identifilersystem for personal identification and paternity testing among ethnic Hans from Xiamen, Fujian.

METHODSFor 400 unrelated individuals, allelic frequencies for the 15 STR loci from the AmpFLSTR Identifilerkit were determined. Population genetics parameters for forensic usage were calculated.

RESULTSNo deviation of the observed allele frequency from Hardy-Weinberg equilibrium expectations was found by Chi-square test (P>0.05). All of the 15 loci were highly polymorphic. Observed heterozygosity has varied between 0.580 and 0.868. Matching probability was between 0.036 and 0.148. Power of discrimination was between 0.798 and 0.967. Polymorphic information content was between 0.560 and 0.850. And power of exclusion was between 0.268 and 0.730.

CONCLUSIONAll of the 15 loci selected by the AmpFLSTR Identifilersystem are highly polymorphic among ethnic Hans from Xiamen. By determining the alleles and allelic frequencies, data for genetic polymorphisms usable for paternity testing and personal identification for local population were obtained.

Alleles ; Asian Continental Ancestry Group ; genetics ; Chi-Square Distribution ; China ; Forensic Genetics ; methods ; Gene Frequency ; Genetics, Population ; methods ; Genotype ; Humans ; Linkage Disequilibrium ; Microsatellite Repeats ; genetics ; Polymorphism, Genetic

OBJECTIVES: To analyse the genetic polymorphisms of 66 biallelic genetic markers on Y chromosome in Eastern Chinese Han population, and evaluate their values in forensic application. METHODS: Genotyping of 66 biallelic genetic markers on Y chromosome was studied in 205 unrelated males of Eastern Chinese Han population by multiplex PCR combined matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-TOF-MS）. The allele frequencies on the loci to be tested were calculated by direct counting method, and the gene diversity （GD） and haplotype diversity （HD） were calculated by corresponding formulas. The haplotypes of this system were tested by software Arlequin v3.5.2.2 and the comparison of population genetics were analyzed. RESULTS: A total of 60 biallelic genetic markers on Y chromosome were polymorphic in males of Eastern Chinese Han population, and the ranges of GD were from 0.038 5 to 0.501 9. Eighty-five different haplotypes were observed and the HD was 0.970 3. The differences of partial SNP loci between the Han population of Eastern China and that of Xinjiang and Guangdong were statistically significance. CONCLUSIONS Sixty biallelic genetic markers and the detection system can complementally provide genetic information in kinship testing and individual identification. The MALDI-TOF-MS technology is able to type biallelic genetic markers.
Asian People/genetics* ; China ; Chromosomes, Human, Y/genetics* ; Gene Frequency ; Genetic Markers/genetics* ; Genetic Variation ; Genetics, Population ; Genotype ; Haplotypes/genetics* ; Humans ; Male ; Multiplex Polymerase Chain Reaction/methods* ; Polymorphism, Single Nucleotide/genetics* ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

OBJECTIVES: To investigate the genetic polymorphism of 23 autosomal STR loci of Huaxia™ Platinum kit in Chinese Han population, and to evaluate the forensic efficiency of Huaxia™ Platinum kit. METHODS: A total of 500 unrelated healthy individuals from Han population were genotyped with Huaxia™ Platinum kit. The frequency distribution and the parameter of population genetics of STR loci were analysed statistically. Huaxia™ Platinum kit was compared with other 7 commercial STR kits commonly seen at home and abroad in the number of STR loci, interior label, fluorescent mark, total number of alleles in Ladder and system effectiveness. RESULTS: All the 23 autosomal STR loci were consistent with Hardy-Weinberg equilibrium （P>0.05）. The discrimination power was 0.791 5-0.986 2. The polymorphism information content （PIC） was 0.559 0-0.914 0. The combined discrimination power （CDP） was 1-4.1×10⁻²⁸, while combined probability of paternity exclusion in trio （CPET） and in duo （CPED） were 1-4.1×10⁻¹⁰ and 1-8.4×10⁻⁷, respectively. Compared with other 7 kits, Huaxia™ Platinum kit contained the most number of alleles within the Ladder. CONCLUSIONS All the 23 autosomal STR loci of Huaxia™ Platinum kit with highly polymorphic in Han population can be used for paternity testing and individual identification. Compared with other 7 kits, it appears that Huaxia™ Platinum kit can provide more genetic information.
Alleles ; Asian People/genetics* ; China ; Forensic Genetics/methods* ; Gene Frequency ; Genetics, Population ; Genotype ; Humans ; Microsatellite Repeats ; Paternity ; Platinum ; Polymorphism, Genetic ; Probability ; Reagent Kits, Diagnostic