Study on the population genetic structure and phylogenetic relationship of the Han population in Dalian / 中国法医学杂志

Objective To study the population genetic structure and phylogenetic relationships by combining Y-STR haplotype genetic information from the Han population in Dalian with 32 domestic and foreign groups.Methods Blood samples of 958 Han male volunteers from Dalian were collected.Genetic typing of 42 genetic loci was completed using Y-STR fluorescent reagent kits and capillary electrophoresis.Related forensic parameters were calculated.Nei's standard genetic distances among 33 populations based on 17 Y-STR loci were computed,in order to create a principal coordinate analysis as well as construct a phylogenetic tree.Results The analysis of genetic polymorphisms at 42 Y-STR loci revealed 30 unconventional alleles at 10 loci.Genetic analysis of the population based on 17 Y-STR loci confirmed that Dalian's Han population had the closest genetic distance to the Anshan's Han population,followed by populations from Henan,Heilongjiang,Jilin,Shandong,and Chongqing.Furthermore,the genetic distances between the Han population in Dalian and the Qiang population in Beichuan or the Miao population in Guizhou were relatively closer than that to the Manchu population living in Liaoning.Conclusion The genetic distance between the Han population in Dalian and other groups is not entirely proportional to ethnicities and geographical proximity.Both population migration and ethnic assimilation or isolation may have influence on it.

The association between the DYS527a/b and DYF387S1a/b multi-allele pattern and Y-SNP haplogroups / 中国法医学杂志

Objective To investigate the association of the DYS527a/b and DYF387S1a/b multi-allele pattern with Y-SNP haplogroups.Methods Samples from 295 unrelated males who carrying the DYS527a/b multi-allele pattern were amplified by the YFilerPlus? kit.The genotypes of their frequency distributions,including three multi-copy loci(DYS527a/b,DYF387S1a/b,DYS385a/b)and other single-copy loci were obtained.The DYS527a/b multi-allele pattern and their haplotypes were examined for the associations with Y-chromosome haplogroups using the AIYSNP42 kit,which contains 42 Y-SNP loci.Based on the above results,the association between the DYS527a/b multi-allele patter and its constituent Y-STR haplotypes and related haplogroups was discussed.Results Among the 295 samples,the DYS527a/b tri-allele pattern and tetra-allele pattern accounted for 97.29%and 2.71%respectively,while the DYF387S1a/b tri-allele pattern and tetra-allele encompassed 54.24%and 4.75%.Null allele was detected in DYS448 in 13.22%of the samples.Here,7 Y-SNPs were deticted such as O-M175 and C-M131 which encompassed 45.76%and 45.08%.The haplogroups of R1-M173,N-M231,D1-M174,J-M304 and F-M89 were less than 13 cases,with frequencies ranging from 4.41%～0.34%.There were Y-STR genotypes differences among haplogroups,as haplogroup O-M175 was represented by 4 genotypes of Y-STR profiles characterized by DYS385a/b(12/12,as well as 12/17,12/18,12/19),DYS392(13),DYS593(16)and DYS393(12),and haplogroup C-M130 was characterized by DYS527a/b(19/20/21),DYS385a/b(11),DYS593(17),DYS390(23),Y_GATA_H4(11),and DYS444(13)and so on.Conclusion The DYS527a/b multi-allele pattern is frequently observed in the Kunming population with haplogroup C-M130.In the samples from haplogroups O,C,R1 and N,the DYS527a/b and DYF387S1a/b haplotypes frequently exhibit the multi-allele pattern.Given the frequencies of different haplogroups and the association between Y-SNP haplogroups and Y-STR loci,it could be helpful to look for more details in the paternal lineage search.

Application of Multiple Genetic Markers in Determination of Full and Half Sibling Relationship： A Case Report / 法医学杂志

Objective To investigate the application of the comprehensive use of multiple genetic markers in full and half sibling relationship testing through the identification of a case of suspected sibling relationship. Methods Genomic DNA were extracted from bloodstain samples from 4 subjects （ZHANG-1, ZHANG-2, male; ZHANG-3, ZHANG-4, female）. Autosomal STR loci, X-STR, Y-STR loci and polymorphisms of mtDNA HV-Ⅰ and Ⅱwere genotyped by EX20 STR kit, X19 kit, Data Y24 STR kit, and Sanger sequencing, respectively. Results According to autosomal STR based IBS scoring results, full sibling relationships were indicated among ZHANG-2, ZHANG-3 and ZHANG-4, but those were not indicated between ZHANG-1 and ZHANG-2 or ZHANG-3 or ZHANG-4. According to autosomal STR based FSI and HSI, with ITO method and discriminant function method, full sibling relationships among ZHANG-2, ZHANG-3 and ZHANG-4 were indicated, and half sibling relationships between ZHANG-1 and ZHANG-2 or ZHANG-3 or ZHANG-4 were also indicated. X-STR and mtDNA sequencing results showed that all the 4 samples came from a same maternal line, and Y-STR results showed that ZHANG-1 and ZHANG-2 did not come from a same paternal line, which supported the half sibling relationship between ZHANG-1 and ZHANG-2 or ZHANG-3 or ZHANG-4, verified by parental genotype reconstruction based on autosomal STR genotyping. Conclusion For the identification of sibling relationships, it is effective to have reliable results with the mutual verification and support of multiple genetic markers （autosomal STR, sex chromosomal STR and mtDNA sequence） and calculations （IBS, ITO, discriminant function method and family reconstruction）.

Assessment on Application of 24 Y-STR Loci in Forensic Science / 法医学杂志

OBJECTIVES@#To select a Y-STR marker system with strong haplotype identification ability, appropriate mutation rate and high compatibility and to assess its forensic application.@*METHODS@#The 24 Y-STR loci were tested by self-built fluorescent multiplex system, and the forensic assessment was conducted by 139 pairs of father-son samples collected in Jinan, Shandong province.@*RESULTS@#Totally 176 alleles were identified among the 24 Y-STR loci in the sample of 139 unrelated individuals labeled with father, and the gene diversity （GD） distributed between 0.083 7 （DYS645）-0.966 9 （DYS385a/b）. According to the 24 Y-STR loci, 139 different haplotypes were detected from 139 unrelated male individuals labeled with father in Han population of Shandong province and with no shared haplotype observed. The overall haplotype diversity （HD） was 1 and the discrimination capacity （DC） was 1. A total of 5 one-step mutations events were observed among the 24 Y-STR loci in 139 pairs of father-son. The average mutation rate was 0.001 5 [95% CI （0.000 5, 0.003 5）].@*CONCLUSIONS@#The system of 24 Y-STR loci shows a strong individual recognition ability and low mutation rate in the population in Jinan, Shandong province, and it has good application value in forensic science.

An analysis of genotypes absence at DYS448 locus / 中国法医学杂志

Objective To provide the basic data for forensic application by analyzing the genotypes absence at DYS448 locus. Method 5487 bloodstain samples from unrelated male individuals of Chinese Han population were obtained. 4479 samples was co-amplified using Y-filerTM and AGCU Y-24 kits. 1008 samples was co-amplified using Yfiler PlusTM and AGCU Y-24 kits .Probability of genotype absence was calculated. Results 35 samples of 35 haplotypes among 5487 non-related individuals were found to have DYS448 genotypes absence ,while 2 individuals displayed additional alleles at else locus. Conclusion The probability of DYS448 genotype absence was 0.637%, forensic scientists should pay more attention in practical cases and YSTR database.

Analysis for genetic polymorphism of OSU49 locus on Y chromosome / 中国法医学杂志

Objective To investigate genetic polymorphism of OSU49 locus on Y chromosome among 300 unrelated males in Henan Han population and to assess its value in forensic science. Methods Under the case of informed consent, the blood samples were collected from 300 male individuals in Henan Han. The primer was labeled with florescent. PCR products were separated from ABI 3130 genetic analyzer. According to the typing test results, the sequence of different alleles was analyzed. Result OSU49 locus contained both pentanucleotide and tetranucleotide core sequence. In the Han population of Henan, the motif of OSU49 locus was showed (CTTTC)pCTT(CCCT)7 T(CTTTC)1(TCTT)5(TCCT)m(TCTT)nTCT(TCCT)4. The number of pentanucleotide repeats varied from12 to 17, and the number of tetranucleotide repeats varied from 20 to 30. Nomenclature for allele was according to the length of the fragment. A total of 34 alleles were detected. The gene diversity was 0.9186 and the discrimination power was 0.9155. Conclusion The complex repeats of locus OSU49 was highly polymorphic in Henan Han population, which can be used in forensic science and human genetics studies.

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 polymorphism study of the Y chromosome in pedigree with the surname Kong and their forensic implications / 中国法医学杂志

Objective Acquiring genetic information of Y-SNPs and Y-STRs genetic makers from samples with the surname of Kong, which is useful for exploring the correlation between surname and Y chromosome in forensic applications studies.Methods Two multiplex genotyping assays and SNaPshot assay were used to analyze 255 unrelated male blood samples who share the same surname Kong and 330 unrelated male blood samples obtained randomly. 17 Y-STRs were typed for the surname Kong population samples. The software Arlequin 3.5.1.2 and the program Network 4.6.1.1 were used for data statistical analysis.Results 13 haplogroups were observed. The highest haplogroup frequency in the two populations were O3a2c1a-M117 (21.57%, 14.85%). 196 haplotypes in Kong population deifned by 17 Y-STRs locus were obtained and the haplotype diversity was 0.9939. 14-12-25-28-19-15-12-19-12-11-12-22-12-11-14-10-19 is the typical haplotype. Median Joining algorithm and Mismatch Distribution were adopted to analyze the Y-STR haplotye under haplogroup O3-M122, and the result shows that there are two “central star” distribution. Conclusion Combined with Y-SNP and Y-STR analysis showed that the Kong population had experienced complicated exchanges and expansion or continued growth, which has more than one surname origin. Hence, its population genetic structure and historical differences have potential applications in forensic science.

Anomalous genotype observation of 4 multi-copy RM Y-STRs / 中国法医学杂志

Objective To observe anomalous genotypes of 4 multi-copy RM Y-STRs in Han population in Hubei province. Methods 252 unrelated male samples were ampliifed using reported and newly designed primers, then detected and analyzed by AB 3130 genetic analyzer. Results A total of 25 anomalous multi-band patterns were observed in 20 samples corresponding to an incident rate of 7.94%. 5 anomalous genotypes were observed in DYF387S1 locus, 15 in DYF399S1, 1 in DYF403S1 and 4 in DYF404S1. Four samples showed extra alleles in more than one locus. Conclusion Anomalous genotype has high incident rates in RM Y-STR markers and requires extensive attention in forensic practice.

Estudo da ancestralidade paterna em amostras de populações do Estado do Rio de Janeiro e do Oeste Africano: “uma dinâmica populacional” / Study of paternal ancestry in samples from Rio de Janeiro and West Africa: “a populational dynamic”

O uso de marcadores do tipo STR e SNP tem se revelado de grande importância na discriminação entre indivíduos de uma mesma população, assim como para estudos evolutivos. A utilização de um conjunto de 17 STRs e 46 SNPs específicos de cromossomo Y permitiu a caracterização de um conjunto de amostras representativas das populações do Rio de Janeiro e do oeste africano, com uma avaliação mais ampla sobre a ancestralidade de origem paterna. Na primeira parte deste estudo foram analisados 605 indivíduos do sexo masculino do estado do Rio de Janeiro. Como resultado, não foram observadas diferenças significativas entre as populações do sudeste e do Rio de Janeiro, que apresentou uma alta diversidade de haplótipos (0,9999 ± 0,0001) e de haplogrupos (0,7589 ± 0,0171). A comparação da população miscigenada do Rio de Janeiro com diferentes grupos étnicos ou populacionais mostrou que a frequência de indivíduos com marcadores tipicamente Europeus é de 77%, africanos é de 14,87% e em ameríndios é de 2,31%. A segunda parte do estudo revelou uma grande diversidade haplotípica (1,0000 ± 0,0018) numa amostra do Oeste africano. Quanto ao valor da diversidade de haplogrupos (0,6895 ± 0,0200), este foi similar aos observados em populações de origem Bantu do oeste e centro africanos, principalmente de Benin, Nigéria e Costa do Marfim. A terceira parte deste estudo mostrou que não existem diferenças significativas entre o componente africano da amostra do Rio de Janeiro e as populações africanas do sudeste, oeste e centro oeste. Por outro lado, observamos diferenças significativas quando comparamos o componente africano do Rio de Janeiro e o oeste africano com populações de Uganda, Quênia e África do Sul. A ampliação de estudos genéticos nas populações da África se fazem necessários para o entendimento da diversidade genética no mundo...

he use of STR and SNP markers has proved to be of great importance to discriminate individuals of the same population as well as for evolutionary studies. The use of a set of 17 STRs and 46 SNPs specific from the Y chromosome allowed the characterization of a group of samples representative of the Rio de Janeiro and the West African populations, with a deep assessment of the paternal ancestry. The first part of this study focused in the analysis of 605 males of the state of Rio de Janeiro. The results showed no significant differences between the Brazilian southeastern populations and Rio de Janeiro, which showed high values of haplotype (0.9999 ± 0.0001) and haplogroup (0.7589 ± 0.0171) diversities. The second part of the study revealed a high haplotype diversity (1.0000 ± 0.0018) in a sample from West Africa. The value of haplogroup diversity (0.6895 ± 0.0200) was similar to those previously seen in the West and Center African Bantu populations, mainly from Benin, Nigeria and Ivory Coast. The third part of this study showed no significant differences between the African component of our sample from Rio de Janeiro and the Southeastern, Western and Midwestern African populations. On the other hand, significant differences were observed when comparing the samples of the African component in Rio de Janeiro and of West Africa with population samples from Uganda, Kenya and South Africa. The increase of genetic studies in African populations is important for a better understanding of world genetic diversity...

DNA Analysis of a Microdeletion Case on Y Chromosome / 대한법의학회지

The Y-chromosome, as with other chromosomes in the cell, is subject to mutations. However, unlike autosomal genes, the Y chromosome does not undergo recombination, and therefore individuals from different geographical regions may have differing distribution patterns with respect to Y-chromosome mutations. More detailed knowledge and information regarding Y-chromosome mutations might therefore provide insights into phylogenetic history and personal identification. Here, we describe a case study involving genotype-phenotype discrepancy in an Indian male individual. We found that the mistyping in sex determination was caused by a deletion in the amelogenin Y (AMEL Y) gene. Furthermore, on examining the short tandem repeat (Y-STR) loci using the PowerPlex(R) Y23 System, we found four more deleted loci on Yp11.2 (DYS576, DYS481, DYS570, and DYS458) in this sample. We performed deletion mapping for this sample, and we propose that the microdeletion on the Yp11.2 locus occurred approximately in the 6.44 Mb to 9.75 Mb region. Previous studies have reported that the AMEL Y deletion is a common mutation in the Indian population. Taking into account regional differences, we also analyzed several area-specific Y-chromosome mutations.

Genetic relationship among twenty-six populations using Y-STR polymorphism information / 解剖学报

Objective To study the genetic relationship of the Y chromosomal short tandem repeat gene loci in Lanzhou Han population and other 25 populations .Methods The frequency of alleles of Y-STRloci was obtained from a sample of 500 unrelated individuals living in Lanzhou City , and other 25 populations in different areas collected from the published data were used to calculate the genetic similarity coefficient and genetic distance .Phylogenetic trees based on the genetic distance were established .Results Populations of Lanzhou , Beijing, Shanxi and Inner Mongolia were in an identical cluster .Compared with minorities , the genetic distance between Lanzhou Han population and Inner Mongolia Mongolian population was dramatically smaller from other subpopulations .The populations in Malays and Indians were far from the other groups .Conclusion The Y-STR gene frequency distribution in 26 populations has identified differentiation in race, clime and evolution, and it is basically identical with the classification of human races which is similar to or according with other molecular anthropology research conclusions .

Forensic Validation of Goldeneye?DNA ID 26Y System / 法医学杂志

Objective To perform the validation and analysis of forensic param eters of G oldeneye?DNA ID 26Y system . Methods B ased on the validation rules of Scientific W orking G roup on DNA A nalysis M ethods (SW G D A M ),the kitwas assessed from several parts, as test of PCR system, reproducibility, ac-curacy, and sensitivity, etc. A nd Y-STR loci of 517 unrelated healthy individuals from E astern C hina were genotypes by this kit. The distribution and frequency of haplotype were calculated and forensic param e-ters of the kit were assessed. Results The com plete profiles can be obtained even when the PC R reac-tion volum e with 6.25μL . A nd correct profile was obtained with DNA down to 125 pg.No reproducible peaks were detected with the DNA of com m on anim als and m icroorganism with the kit. For the m ale-m ale m ixture testing, average 70% of the m inor alleles were obtained when the ratios of 1∶19 and 19∶1. For the m ale-fem ale m ixture testing, results showed that the sensitivity of the kit was no compromised with the addition of fem ale sam ples. Conclusion The validation studies dem onstrated that G oldeneye?DNA ID 26Y system has good sensitivity and specificity, and suitable for m ixture testing. The polym orphism of 26 Y-STR loci included in this kit are good for forensic application.

Haplotype diversity of 17 Y-str loci in an admixed population from the Brazilian Amazon

The allelic and haplotype frequencies of 17 Y-STR loci most commonly used in forensic testing were estimated in a sample of 138 unrelated healthy males from Macapá, in the northern Amazon region of Brazil. The average gene diversity was 0.6554 ± 0.3315. 134 haplotypes of the 17 loci were observed, 130 of them unique and four present in two individuals each. The haplotype diversity index was 0.9996 + 0.0009, with the most frequent haplogroups being R1b (52.2 percent), E1b1b (11.6 percent), J2 (10.1 percent) and Q (7.2 percent). Most haplogroups of this population belonged to European male lineages (89.2 percent), followed by Amerindian (7.2 percent) and African (3.6 percent) lineages.

Development of 19-plex Y STR system and polymorphism studies in Pakistani population / 西安交通大学学报·英文版

For the development of 19-plex Y STR system and polymorphism studies in local ethnic populations sixteen markers of non-recombining regions (NRY) of Y chromosome, which show high power of discrimination among individuals, were selected in this study. Blood samples (600) were collected from the males of three most common castes of Pakistani population (Arain, Awan and Rajput) with different parent lineages. Three markers (DYS385a/b, DYS389I/II and YCAIIa/b) among 16 Y STRs are double-targeted regions of the Y chromosome and thus provide two polymorphic peaks for each respective primer set. These 16 Y-STRs were developed into Megaplex system for simultaneous amplification of all markers within the population. The overall power of discrimination observed in focused populations was 60.5%, 66.5% and 55% in Rajput, Awan and Arain casts respectively. This discrimination power will be helpful in human identification for forensic casework studies including sexual assaults and paternity testing.

Change of Surname?: An application of Y-STR Haplotyping / 대한법의학회지

Y-STR haplotyping is a powerful forensic and anthropological tool for identifying male lineages. We used high-resolution Y-STR haplotyping to evaluate the possibility of an ancestral relationship between two individuals with the different surname. Of the 17 Y-STRs genotyped, 16 had identical alleles in two individuals, except for an unambiguously sporadic mutation (one-step mutation) at DYS385 locus. The common allele 11.1 (U3Ains) at DYS439 locus was also observed in these two individuals. Sequencing analysis of these alleles of two samples demonstrated an A insertion at base 3 upstream from the repeat region's first GATA motif. These findings suggested that two individuals were paternally related, even if male individuals live with different surname.

Development of 19-plex Y STR system and polymorphism studies in Pakistani population / 药物分析学报

For the development of 19-plex Y STR system and polymorphism studies in locl ethnic populations sixteen markers of non-recombining regions (NRY) of Y chromosome, which show high power of discrimination among individuals, were selected in this study. Blood samples (600) were e.ollected from the males of three most common castes of Pakistani population (Arnin, Awan and Rajput) with different parent lineages. Three markers (DYS385a/b, DYS389Ⅰ/Ⅱ and YCAⅡa/b) among 16 Y STRs are double-targeted regions of the Y chromosome and thus provide two polymorphie peaks for each respective primer set. These 16 Y-STRs were developed into Megaplex system for simultaneous amplification of all markers within the population. The overall power of discrimination observed in focused populations was 60.5%, 66.5% and 55% in Rajput, Awan and Arain casts respectively. This discrimination power will be helpful in haman identification for forensic casework studies including sexual assaults and paternity testing.

Population and mutation analysis of Y-STR loci in a sample from the city of São Paulo (Brazil)

The haplotypes of seven Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were determined in a sample of 634 healthy Brazilian males (190 adult individuals and 222 father-son pairs). The 412 adults were unrelated, and the 222 father-son pairs had their biological relationship confirmed using autosomal STRs (LR > 10,000). Among the 412 adults, a total of 264 different 7-loci haplotypes were identified, 210 of which were unique. The most frequent haplotype was detected in 31 instances, occurring with a frequency of 7.52 percent. The haplotype diversity index was calculated as 98.83 percent. Upon transmission of the 1,554 alleles, in 222 father-son pairs, six mutations were observed, with an average overall rate of 3.86 x 10-3 per locus. A haplotype with a duplicated DYS389I locus, and another with duplicated DYS389I, DYS389II, and DYS439 loci were detected in both fathers and their respective sons.

Detection of Y STR markers of male fetal dna in maternal circulation.

BACKGROUND: Circulating fetal cells and cell free DNA in the maternal blood has been shown to help in prenatal diagnosis of genetic disorders without relying on invasive procedures leading to significant risk of pregnancy loss. AIM: The current study was undertaken to detect the male fetal population using Y STR markers DYS 19, DYS 385 and DYS 392 and also to study the extent of persistence of fetal DNA in the mother following delivery. MATERIALS AND METHODS: Blinded study was conducted on 50 mothers delivering male and female babies. Cellular and cell free DNA was extracted from maternal and fetal cord blood and amplified for Y STR markers by PCR. RESULTS: The amplification sensitivity of Y specific STR, DYS19 was 100% (22/22) in the male fetal DNA samples. The incidence of other STRs, i.e., DYS385 and DYS392 were 91% (20/22) each. Analysis of results revealed that thirteen of the twenty six women had detectable male fetal DNA at the time of delivery. However fetal DNA was not detectable twenty four hours after delivery. CONCLUSION: Preliminary results show that the separation of fetal cell-free DNA in the maternal circulation is a good low-cost approach for the future development of novel strategies to provide non-invasive techniques for early prenatal diagnosis.

A Case Related to Identifying Missing Person by the floods in 2006 / 대한법의학회지

The fifteen persons from In-jae, Kang-won do, were missing by floods on July 2006. In relation to the this case, the two unidentified corpses were found nearby So-yang lake on June and September 2007, respectively. In these cases, autosome short tandem repeats (STR) and Y-STR were used for identification. The AmpFlSTR Identifiler kit (amelogenin and 15 STRs) and the AmpFlSTR Yfiler kit (16 Y-STRs) are analysed by multiplex-PCR and automated fluorescent detection using Perkin Elmer Prism 310 DNA sequencer. Finally we could found identify the two missing persons.