Application of Familial Y-STR Haplotype Mismatch Tolerance in Genealogy Inference / 法医学杂志

OBJECTIVES@#To provide a guideline for genealogy inference and family lineage investigation through a study of the mismatch tolerance distribution of Y-STR loci in Chinese Han male lineage.@*METHODS@#Three Han lineages with clear genetic relationships were selected. YFiler Platinum PCR amplification Kit was used to obtain the typing data of 35 Y-STR loci in male samples. The variation of Y-STR haplotypes in generation inheritance and the mismatch tolerance at 1-7 kinship levels were statistically analyzed.@*RESULTS@#Mutations in Y-STR were family-specific with different mutation loci and numbers of mutation in different lineages. Among all the mutations, 66.03% were observed on rapidly and fast mutating loci. At 1-7 kinship levels, the number of mismatch tolerance ranged from 0 to 5 on all 35 Y-STR loci, with a maximum step size of 6. On medium and slow mutant loci, the number of mismatch tolerance ranged from 0 to 2, with a maximum step size of 3; on rapidly and fast mutant loci, the number of mismatch tolerance ranged from 0 to 3, with a maximum step size of 6.@*CONCLUSIONS@#Combined use of SNP genealogy inference and Y-STR lineage investigation, both 0 and multiple mismatch tolerance need to be considered. Family lineage with 0-3 mismatch tolerance on all 35 Y-STR loci and 0-1 mismatch tolerance on medium and slow loci can be prioritized for screening. When the number of mismatch tolerance is eligible, family lineages with long steps should be carefully excluded. Meanwhile, adding fast mutant loci should also be handled with caution.

Identification Strategy of Biological Half Sibling Relationship / 法医学杂志

OBJECTIVES@#To compare the application value of the likelihood ratio (LR) method and identity by state (IBS) method in the identification involving half sibling relationships, and to provide a reference for the setting of relevant standards for identification of half sibling relationship.@*METHODS@#(1) Based on the same genetic marker combinations, the reliability of computer simulation method was verified by comparing the distributions of cumulated identity by state score (CIBS) and combined full sibling index in actual cases with the distributions in simulated cases. (2) In different numbers of three genetic marker combinations, the simulation of full sibling, half sibling and unrelated individual pairs, each 1 million pairs, was obtained; the CIBS, as well as the corresponding types of cumulative LR parameters, were calculated. (3) The application value of LR method was compared with that of IBS method, by comparing the best system efficiency provided by LR method and IBS method when genetic markers in different amounts and of different types and accuracy were applied to distinguish the above three relational individual pairs. (4) According to the existing simulation data, the minimum number of genetic markers required to distinguish half siblings from the other two relationships using different types of genetic markers was estimated by curve fitting.@*RESULTS@#(1) After the rank sum test, under the premise that the real relationship and the genetic marker combination tested were the same, there was no significant difference between the simulation method and the results obtained in the actual case. (2) In most cases, under the same conditions, the system effectiveness obtained by LR method was greater than that by IBS method. (3) According to the existing data, the number of genetic markers required for full-half siblings and half sibling identification could be obtained by curve fitting when the system effectiveness reached 0.95 or 0.99.@*CONCLUSIONS@#When distinguishing half sibling from full sibling pairs or unrelated pairs, it is recommended to give preference to the LR method, and estimate the required number of markers according to the identification types and the population data, to ensure the identification effect.

Evaluation of Detection Efficiency for Trio Full Sibling Testing / 法医学杂志

OBJECTIVES@#To study the detection efficiency of trio full sibling with another known full sibling reference added under different number of autosomal STR typing systems.@*METHODS@#Based on 43 detection systems consisting of 13 to 55 representative autosomal STR loci, 10 000 true families (full sibling group) and 10 000 false families (unrelated individual group) were randomly simulated. The full sibling index (FSI) was calculated based on the method of family reconstruction. The cumulative sibling relationship index (CFSI) of 0.000 1 and 10 000 were used as the evaluation thresholds, and the detection efficiency parameters were calculated and compared with the identification of the duo full sibling testing.@*RESULTS@#With the increasing number of STR loci, the error rate and inability of judgement rate gradually decreased; the sensitivity, specificity, correct rate of judgment and other parameters gradually increased, and the system efficiency gradually improved. Under the same detection system, trio full sibling testing showed higher sensitivity, specificity, system efficiency and lower inability of judgement rate compared with duo full sibling testing. When the system efficiency was higher than 0.85 and inability of judgement rate was less than 0.01%, at least 20 STRs should be detected for trio full sibling testing, which was less than 29 STRs required by duo full sibling testing.@*CONCLUSIONS@#The detection efficiency of trio full sibling testing is superior to that of duo full sibling testing with the same detection system, which is an effective identification scheme for laboratories with inadequate detection systems or for materials with limited conditions.

Research Progresses of Tri-Allelic Patterns in Autosomal STR in Forensic DNA Analysis / 法医学杂志

Tri-allelic pattern in autosomal STR is a common abnormal typing phenomenon in forensic DNA analysis, which brings difficulties and uncertainties to the evaluation of the evidence weight in actual cases. This paper reviews the types, formation mechanism, occurrence frequency, genetic pattern and quantitative evaluation of evidence of the tri-allelic pattern in autosomal STR in forensic DNA analysis. This paper mainly explains the formation mechanism and genetic patterns based on different types of tri-allelic pattern. This paper also discusses the determination of tri-allelic pattern and the quantitative method of evidence evaluation in paternity testing and individual identification. This paper aims to provide references for scientific and standardized analysis of this abnormal typing phenomenon in forensic DNA analysis.

Short Tandem Repeats in plants: genomic distribution and function prediction

BACKGROUND: Short Tandem repeats (STRs) existed as popular elements in both eukaryotic and prokaryotic genomes. RESULTS: In this study, we analyzed the characteristics, distributions, and motif features of STRs within whole-genomes of 140 plant species. The results showed that STR density was negatively correlated with the genome size. Hexanucleotide repeat was the most abundant type of STRs. The distribution of algae shows a preference different from that of other plants. By analyzing GC contents of STRs and genome, it was concluded that STR motif was influenced by GC contents. Analysis of the long STRs in genome (length 1000 bp) found that dicots have the more long STRs. For STR types, di- and tri-nucleotide accounted for the highest proportion. Analyzing and designing long STRs in CDS (length 500 bp) was to verify the role of long STRs in Gossypium hirsutum TM-1 and Solanum tuberosum. By comparing the long STRs found in Fragaria x ananassa with other species, some evolutionary characteristics of the long STRs were obtained. CONCLUSIONS: We got the characteristics, distribution, and motif features of STRs in the whole genome of 140 plants and obtained some evolutionary characteristics of long STRs. The study provides useful insights into STR preference, characteristics, and distribution in plants.

High genetic diversity of Anaplasma marginale infecting dairy cattle in northeastern Brazil / Alta diversidade genética de Anaplasma marginale em bovinos de leite no nordeste do Brasil

Abstract Anaplasma marginale is an obligate intracellular Gram-negative bacterium found in ruminants' erythrocytes and is the etiological agent of bovine anaplasmosis. The bacterium's genetic diversity has been characterized based on sequences of major surface proteins (MSPs), such as MSP1α. The aim of the present study was to investigate the genetic diversity of A. marginale in cattle in the state of Maranhão, northeastern Brazil. To this end, 343 blood samples were harvested and subjected to iELISA assays using the recombinant surface protein MSP5. Out of 343 blood samples, 235 (68.5%) were randomly chosen and submitted to DNA extraction, qPCR and conventional PCR targeting the msp1α gene to determine amino acid sequences and classify the genotypes. The iELISA results showed 81.34% seropositivity (279/343), whereas qPCR revealed 224 positive samples (95.32%). Among these qPCR-positive samples, 67.4% (151/224) were also positive in the cPCR. Among the 50 obtained sequences, 21 strains had not been previously reported. Regarding the genotypes, H (26/50) and E (18/50) were identified most often, while genotypes F and C were only identified twice each and B and G once each. In conclusion, high prevalence and genetic diversity for A. marginale were observed in dairy cattle herds in the state of Maranhão.

Resumo Anaplasma marginale é uma bactéria Gram-negativa intracelular obrigatória de eritrócitos de ruminantes e responsável pela anaplasmose bovina. A diversidade genética de A. marginale tem sido caracterizada com base nas sequências das principais proteínas de superfície (MSPs), como a MSP1α. O objetivo deste estudo foi investigar a diversidade genética de A. marginale em bovinos no estado do Maranhão, Nordeste do Brasil. Dessa forma, 343 amostras de sangue foram submetidas ao ensaio iELISA, utilizando-se a proteína recombinante MSP5. Das 343 amostras de sangue, 235 (68,5%) foram escolhidas aleatoriamente e submetidas à extração de DNA, qPCR e PCR convencional para gene msp1α, para determinação das sequências de aminoácidos e classificação dos genótipos. Os resultados do iELISA mostraram 81,34% de soropositividade (279/343), enquanto qPCR revelou 224 amostras positivas (95,32%). Dentre estas na qPCR, 67,4% (151/224) mostraram-se positivas no PCR convencional. Das 50 sequências obtidas, 21 cepas não haviam sido relatadas anteriormente. Em relação aos genótipos, H (26/50) e E (18/50) foram os mais frequentes, enquanto os genótipos F e C foram identificados apenas duas vezes cada, e B e G uma vez cada. Em conclusão, alta prevalência e marcante diversidade genética de A. marginale foram observadas em rebanhos leiteiros no estado do Maranhão.

Conservation of gene architecture and domains amidst sequence divergence in the hsrω lncRNA gene across the Drosophila genus: an in silico analysis

The developmentally active and cell-stress responsive hsrx locus in Drosophila melanogaster carries two exons, one omega intron, one short translatable open reading frame (ORFx), long stretch of unique tandem repeats and an overlapping mir-4951 near its 30 end. It produces multiple long noncoding RNAs (lncRNAs) using two transcription start and four termination sites. Earlier cytogenetic studies revealed functional conservation of hsrx in several Drosophila species. However, sequence analysis in three species showed poor conservation for ORFx, tandem repeat and other regions while the 16 nt at 50 and 60 nt at 30 splice junctions of the omega intron, respectively, were found to be ultra-conserved. The present bioinformatic study using the splice-junction landmarks in D. melanogaster hsrx identified orthologues in publicly available 34 Drosophila species genomes. Each orthologue carries a short ORFx, ultra-conserved splice junctions of omega intron, repeat region, conserved 30 -end located at mir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in the repeat sequences. Intriguingly, only the omega intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested in Chironomus and Ceratitis genera. Amidst the high sequence divergence, the conserved organization of exons, ORFx and omega intron in this gene’s proximal part and tandem repeats in distal part across the Drosophila genus is remarkable and possibly reflects functional importance of higher order structure of hsrx lncRNAs and the small omega peptide.

Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis / 中国天然药物

Salvia plebeia has been in use as traditional Chinese medicine (TCM) for more than 500 years. In this study, the complete chloroplast (cp) genome of S. plebeia was sequenced, assembled and compared to those of other five published Salvia cp genomes. It was found that the cp genome structure of S. plebeia was well conserved and had a total size of 151 062 bp. Four parameters were used to display the usage conditions of the codons of the amino acids in Salvia genus. Although the number of protein-coding genes in each species was the same, the total number of codons was different. Except for amino acids Trp and Met whose Relative Synonymous Codon Usage (RSCU) value of one condon was equal to 1, the remaining 19 amino acids had 1-3 preferred codons. The preferred codon names of each amino acid were coincident. The period size for the tandem repeats of six species ranged from 9 to 410 bp. Salvia cp genomes mainly possessed tandem repeats with a copy number less than or equal to 3. The sequence length of tandem repeats of the six species ranged from 25 to 824 bp. Highly viarable regions including four intergenic spacers and six partial genes were discovered as potential specific barcodes for Salvia species through cp genome-wide comparison. Finally, we performed phylogenetic analyses based on the complete cp genome and coding sequences respectively. These results provide information to help construct the cp genome library for Salvia, which may support studies of phylogenetics, DNA barcoding, population and transplastomics.

Influence of uniparental disomy on the conclusion of paternity testing / 中华医学遗传学杂志

Objective@#To explore the influence of uniparental disomy (UPD) on bipartite and tripartite paternity testing.@*Methods@#Two cases of paternity testing were analyzed by multiplex amplification and capillary electrophoresis typing. Suspected UPD was verified by using single nucleotide polymorphism array (SNP array). Parental power index was calculated by using a bipartite or tripartite model.@*Results@#The two cases were found to harbor respectively three short tandem repeats on chromosome 2 and two short tandem repeats on chromosome 15. SNP array verified that both cases were of UPD. Case 1 had a parental power index of 122274987565.23 by a tripartite model, while case 2 had a parental power index of 13500.8463 by a bipartite model. Based on the technical specification, the conclusions supported a biological parent-child relationship in both cases.@*Conclusion@#UPD may lead to misjudgment of paternity testing. The possibility of UPD should be considered when certain loci which do not conform to Mendelian inheritance have aggregated to one chromosome.

Genetic polymorphisms and genetic relationship of 24 autosomal STR loci in Gelao and Miao population of Guizhou / 解放军医学杂志

Objective: To investigate the genetic polymorphisms of 24 autosomal short tandem repeats (STR) loci in Gelao and Miao populations dwelled in Guizhou province, and explore the population genetic relationships and evaluate their application value on forensic medicine. Methods: The DNA samples of 732 unrelated individuals (399 Guizhou Gelao population and 333 Guizhou Miao population) were amplified using SureID® PanGlobal kit, and the PCR products were analyzed by electrophoresis through 3500XL genetic analyzer. The fragment sizes of alleles were subsequently analyzed by GeneMapper ID-X v1.5. Allele frequencies and forensic genetic parameters of 24 STR loci were statistically analyzed and compared with the available data of other populations from different races and regions. Results: For Guizhou Gelao and Miao populations, the individual discrimination power (DP) ranged from 0.7833 to 0.9909 and 0.8010 to 0.9909, respectively; the polymorphic information content (PIC) ranged from 0.5608 to 0.9385 and 0.5677 to 0.9414, respectively; the total discrimination power (TDP) were 1-7.6036 × 10-30 and 1-6.8630 × 10-30, respectively, and the cumulative probability of exclusion (CPE) were 1-1.9608 × 10-11 and 1-1.9738 × 10-14, respectively. Analysis with the matrix of Nei's DA genetic distance indicated that the genetic distance was the smallest (0.0205) between Guizhou Gelao and Hubei Han populations, while was the largest (0.0449) between Guizhou Gelao and Yunnan Miao populations; the genetic distance was minimum (0.0033) between Guizhou Miao and Hunan Han populations, while was maximal (0.0363) between Guizhou Miao and Yunnan Miao. Conclusions: The 24 STR loci are abundant in genetic polymorphism in Guizhou Gelao and Miao populations. It is of great significance to study the genetic diversity of different ethnic groups in order to understand their origin, migration and interrelationship.

Genetic distribution and forensic evaluation of multiplex autosomal short tandem repeats in the Chinese Xinjiang Mongolian group / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

To further enrich the genetic data of the Chinese Xinjiang Mongolian group, the genetic distribution and forensic parameters of 19 autosomal short tandem repeats (STRs) were investigated. Altogether, 249 alleles were observed in these 19 STRs. The mean values of the polymorphism information content (PIC), match probability (MP), discrimination power (DP), and probability of exclusion (PE) for these 19 STRs were 0.7775, 0.0699, 0.9301, and 0.6085, respectively. Additionally, the cumulative DP and PE values obtained in the Mongolian group were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively. Furthermore, population genetic analysis of the Mongolian group and 20 published populations was conducted based on the population data of 15 overlapping STRs. Genetic distances indicated that the Mongolian group had closer genetic similarities with the Uyghur, Xibe, and other Chinese populations rather than the other continental populations. Multidimensional scaling analysis further revealed that the Mongolian group possessed similar genetic distributions as most Chinese populations. To sum it all up, these STRs could be used as an extremely efficient tool for forensic applications in the Xinjiang Mongolian group.

Classification of Common Relationships Based on Short Tandem Repeat Profiles Using Data Mining / 대한법의학회지

We reviewed past studies on the identification of familial relationships using 22 short tandem repeat markers. As a result, we can obtain a high discrimination power and a relatively accurate cut-off value in parent-child and full sibling relationships. However, in the case of pairs of uncle-nephew or cousin, we found a limit of low discrimination power of the likelihood ratio (LR) method. Therefore, we compare the LR ranking method and data mining techniques (e.g., logistic regression, linear discriminant analysis, diagonal linear discriminant analysis, diagonal quadratic discriminant analysis, K-nearest neighbor, classification and regression trees, support vector machines, random forest [RF], and penalized multivariate analysis) that can be applied to identify familial relationships, and provide a guideline for choosing the most appropriate model under a given situation. RF, one of the data mining techniques, was found to be more accurate than other methods. The accuracy of RF is 99.99% for parent-child, 99.44% for full siblings, 90.34% for uncle-nephew, and 79.69% for first cousins.

Association of interleukin 1 receptor antagonist intron 2 variable number of tandem repeats polymorphism with vitiligo susceptibility in Gujarat population

Background: Vitiligo is a multifactorial, polygenic, autoimmune skin disorder caused by selective destruction of melanocytes. Interleukin 1 receptor antagonist intron 2 polymorphism was found to be associated with various autoimmune disorders. Aims: We aimed to investigate the association of interleukin 1 receptor antagonist intron 2 variable number of tandem repeats polymorphism (rs2234663) with vitiligo to assess interleukin 1 receptor antagonist transcript levels and to perform possible genotype–phenotype correlation. Methods: Three hundred and seven vitiligo patients and 316 controls were enrolled in the study, genotyping of interleukin 1 receptor antagonist rs2234663 was performed by polymerase chain reaction, and relative gene expression of interleukin 1 receptor antagonist was carried out in peripheral blood mononuclear cells from patients (n = 36) and controls (n = 36) by real-time-PCR. Results: A significant difference was observed in the frequency of interleukin 1 receptor antagonist *A (1/2) genotype among patients with active and stable vitiligo (P = 0.0172). Interleukin 1 receptor antagonist*A (2/2) genotype and allele frequencies were significantly different between SV patients and controls (P = 0.0246 and P = 0.0046, respectively). Significant difference was also observed for interleukin 1 receptor antagonist*A2 (allele) in active and stable vitiligo patients (P = 0.0060). However, other comparisons did not show any significant difference in genotype and allele frequencies. Moreover, interleukin 1 receptor antagonist*A (3/2) genotype was observed only in patients whereas interleukin 1 receptor antagonist*A (5/2) was observed only in controls. Gene expression analysis showed no significant difference in interleukin 1 receptor antagonist transcript levels in patients compared to controls (P = 0.5962). Interestingly, genotype–phenotype correlation analysis revealed that individuals with IL1RN*A (2/2) exhibited higher interleukin 1 receptor antagonist expression compared to other major genotypes interleukin 1 receptor antagonist*A (1/2) (P = 0.01) and interleukin 1 receptor antagonist*A (1/1) (P = 0.03). Limitations: More case-control studies on interleukin 1 receptor antagonist rs2234663 polymorphism and gene expression from different ethnic populations are required to explore the impact of interleukin 1 receptor antagonist in vitiligo susceptibility. Conclusion: Interleukin 1 receptor antagonist*A2 might be a risk factor for progressive vitiligo.

Genetic polymorphisms of 19 X-STR loci for forensic application in China’s three ethnicities / 基础医学与临床

Objective To investigate the genetic data of the 19 X-STR loci in three ethnicities of China ( Han, Gelao,Miao) and to evaluate the application in forensic science.Methods The DNA samples of unrelated individ-ual in Han (n=308), Gelao (n=398), Miao (n=323) ethnicities were amplified using MicroreaderTM19X ID System kit, and the PCR products were analyzed by electrophoresis through 3500XL genetic analyzer. The fragment sizes of alleles were taken subsequently by GeneMapper? ID-X. Allele frequencies and national genetics parameters of the 19 X-STR were analyzed by statistics. The allele frequencies were compared among the three nationalities and were compared with available data of other Han ethnicities from different regions. Results After the Bonferroni correction at a 95% significance level, no significant departures from the Hardy-Weinberg equilibrium was observed. Linkage disequilibrium test showed no significant allelic association between all 19 X-STR loci after Bonferroni’s correction. The cumulative discrimination power in females and in males were greater than 0.999 999 999 99 and 0.999 999 999 94,respectively. The combined power of exclusion in trios and in duos were greater than 0.999 999 999 36 and 0.999 999 52,respectively. The p values,calculated throuth Arle-quin v3.5 software,there were significantly different as detected at loci of X-STR among the different nationalities. Conclusions This panel of X-STR is highly polymorphic in China’s three ethnicities and can be served as a supple-mentary to the current STR system for individual identification.

Diagnosis and treatment of graft-versus-host-disease after kidney transplantation: A Case Report and Literature Review / 中华器官移植杂志

Objective To investigate the diagnosis and treatment of graft-versus-host-disease (GVHD) after solid organ transplant (SOT) and the possible mechanism.Methods In this study,we retrospectively reported a rare case of GHVD after kidney transplantation and performed a literature review.This 51 year old male patient presented with over 10-day history of sporadic skin rash on postoperative day 50.Skin biopsy examination revealed GVHD.For further clear diagnosis,patient's peripheral blood was collected immediately for short tandem repeats (STR) enriched for CD3+ cells and we also performed immunofluorescent staining for patient's skin with specific HLA-A11 antibody,one of donor specific HLA sites.Meanwhile,the decreased immunosuppression was used for treatment.Results In our report,chimerism analysis by STR revealed no chimerism in patient's peripheral blood.However,immunofluorescent staining of patient's skin demonstrated abundant donor-derived lymphocytic infiltration existed.GVHD was definitely made in this case.After treatment with decreased immunosuppression and a low dose of methylprednisolone (MP),his clinical symptom was quickly alleviated.Now the patient was discharged and the renal function was normal.Conclusion Combined with literature review and our case report,we thought that chimerism analysis by STR and immunofluorescent staining by donor-specific HLA antibody were very useful for diagnosis of GVHD after SOT.Furthermore,GVHD referred to over-immunosuppression and prognosis of GVHD after kidney transplantation is usually satisfactory.

New patient of Hansen's disease in young Korean man / 나학회지

Hansen's disease (leprosy) is a chronic infectious disease caused by Mycobacterium leprae which affect mainly skin and nerve systems. Currently the incidence of leprosy reached the goals set by WHO in the year 2000. In recent 10 years, only 47 new patients were found in Koreans and their average age was over 70. A 21 year-old young man showed multiple erythematous papules, macules and plaque at face, extremities and trunk. In family history, his grandfather was diagnosed with leprosy at young age and leprosy was recurred when the patient was 7 years old. The patient lived with grandfather from birth to 7 years old. Clinico-pathologically he was diagnosed with a lepromatous leprosy. We performed VNTR both at the skin tissue of grandfather and patient to find out the infection pathway of the patient and found some consistent. Herein, we report a new case of young Korean male transmitted from grandfather.

Haplotype and genetic relationship of 27 Y-STR loci in Han population of Chaoshan area of China / 解放军医学杂志

Objective To investigate the genetic polymorphisms of 27 Y-chromosomal short tandem repeats (Y-STR) loci included in Yfiler(R) Plus kit in Han population of Chaoshan area,and explore the population genetic relationships and evaluate its application value on forensic medicine.Methods By detecting 795 unrelated Chaoshan Han males with Yfiler(R) Plus kit,haplotype frequencies and population genetics parameters of the 27 Y-STR loci were statistically analyzed and compared with available data of other populations from different races and regions for analyzing the genetic distance and clustering relation of Chaoshan Han population.Results Seven hundred and eighty-seven different haplotypes were observed in 795 unrelated male individuals,of which 779 haplotypes were unique,and 8 haplotypes occurred twice.The haplotype diversity (HD) was 0.999975 with discriminative capacity (DC) of 98.99％.The gene diversity (GD) at the 27 Y-STR loci ranged from 0.3637(DYS391) to 0.9559(DYS385a/b).Comparing with Asian reference populations,the genetic distance (Rst) between Chaoshan Han and Guangdong Han was the smallest (0.0036),while it was relatively larger between Chaoshan Han and Gansu Tibetan population (0.0935).The multi-dimensional scaling (MDS) plot based on Rst values was similar to the results of clustering analysis.Conclusion Multiplex detection of the 27 Y-STR loci reveals a highly polymorphic genetic distribution in Chaoshan Han population,which demonstrates the important significance of Yfiler(R) Plus kit for establishing a Y-STR database,studying population genetics,and for good practice in forensic medicine.

Genetic polymorphisms of 19 Y-STR loci in in the Han population in Northeast China and the cluster analysis of ethnic groups in northeast Asia region / 重庆医学

Objective To investigate the polymorphisms of the 19 Y-STR loci in the Han population in Northeast China,and analyze the genetic relationships of 15 ethnic groups in northeast Asia region,and to evaluate their forensic value and population genetic value.Methods The 19 Y-STR unrelated Han males in 200 unrelated Han males in Northeast China were amplified with the Y-filer system,and the PCR products were analyzed by the 310 Genetic Analyzer.The AMOVA analysis,cluster analysis and MDS analysis were calculated by Arelquin3.11,Mega4.1 and SPSS17.0.Results The polymorphisms of 19 Y-STR loci in the Han population in Northeast China had generally higher gene diversity value which were ranged from 0.350 9 (DYS391) to 0.971 1 (DYS385a/b),and totally 200 haplotypes were observed.The 19 Y-STR loci displayed high genetic polymorphisms in the Han population in Northeast China,indicating that these 19 loci were useful genetic markers for forensic personal identification and paternity testing.There were distinctions among 15 ethnic groups.The genetic distance between 15 ethnic groups were ranged from 0.000 9 to 0.643 2,and the conclusion of cluster analysis and MDS analysis were similar to the ethnogeny research and ethnic migration history.Conclusion The 19 Y-STR loci displayed high genetic polymorphisms in the Han population in Northeast China,and these 19 loci were useful genetic markers for forensic personal identification and paternity testing.

Comparison of gene frequencies of short tandem repeats loci on Y Chromosome between offenders with initiative-aggressive behavior and impulsive-aggressive behavior / 中华行为医学与脑科学杂志

Objective To explore the distributional differences of the gene frequencies of 22 short tandem repeats loci on Y Chromosome(Y?STRs) between offenders with Initiative?aggressive behavior and impulsive?aggressive behavior,and to probe into the genetic factors of initiative?aggressive behavior and im?pulsive?aggressive behavior. Methods Biological samples of 271 offenders with initiative?aggressive behav?ior and 271 offenders with impulsive?aggressive behavior were collected and PCR compound amplification was carried out with the aid of PowerPlex Y23 System. Then the PCR products were subjected to electrophoresis and gene detection with AB3500xL gene analysis system so as to calculate and compare the alleles and haplo?types of 22 Y?STRs gene frequency in the two groups. Results The distribution of allele frequency were sig?nificantly difference in locus DYS437(P=0.022) between two groups,not in the other 21 Y?STRs loci( all P>0.05) . Univarite analysis showed significant differences at allelle 14 in locus DYS437 between both groups ( initiative?aggressive behavior group:69. 37%;impulsive?aggressive behavior group:58. 67%; P=0. 009 ) . Conclusion Loci DYS437 may be associated with aggressive behavior. In the group of aggressive behavior, allelle 14 on locus DYS437 may be the susceptible factor of initiative?aggressive behavior and the resistant factor of impulsive?aggressive.

Asian Ethnic Group Classification Model Using Data Mining / 대한법의학회지

In addition to identifying genetic differences between target populations, it is also important to determine the impact of genetic differences with regard to the respective target populations. In recent years, there has been an increasing number of cases where this approach is needed, and thus various statistical methods must be considered. In this study, genetic data from populations of Southeast and Southwest Asia were collected, and several statistical approaches were evaluated on the Y-chromosome short tandem repeat data. In order to develop a more accurate and practical classification model, we applied gradient boosting and ensemble techniques. To infer between the Southeast and Southwest Asian populations, the overall performance of the classification models was better than that of the decision trees and regression models used in the past. In conclusion, this study suggests that additional statistical approaches, such as data mining techniques, could provide more useful interpretations for forensic analyses. These trials are expected to be the basis for further studies extending from target regions to the entire continent of Asia as well as the use of additional genes such as mitochondrial genes.