Typing of Y chromosome single nucleotide polymorphisms in a Japanese population by a multiplexed single nucleotide primer extension reaction

We have developed a new method for typing single nucleotide polymorphisms (SNPs) on the human Y chromosome based on a multiplexed single nucleotide primer extension. This method has the advantage that several SNPs are typed rapidly and simultaneously. We examined 15 different SNP loci on Y chromosome, M9, M105, M122, M125, M128, M130, SRY465, IMS-JST006241, IMS-JST006841, IMS-JST002611, IMS-JST003305, IMS-JST008425, IMS-JST021354, IMS-JST021355 and IMS-JST055457, in 159 Japanese males. From the typing results of these 15 loci, we found 13 haplotypes. Gene diversity for each locus ranged from 0.025 to 0.486 and the haplotype diversity was estimated to be 0.838. This method could be readily applied for personal identification and paternity testing.     

Comparative analysis of short tandem repeats and single nucleotide polymorphisms on the Y-chromosome in Germans,Chinese and Thais

We have typed genomic DNA samples from 95 individuals from Western Germany, 78 individuals from Bangkok/Thailand and 56 individuals from Chengdu/China for 11 Y-chromosomal diallelic polymorphisms and eight short tandem repeat (STR) systems. For single nucleotide polymorphism (SNP) analysis, a rapid method was applied using the single base extension technology (minisequencing) in combination with capillary electrophoresis. PCR products for SRY-8299, Tat, SRY2627, 92R7, SRY1532, M9, M13, M17/M19 and M20 were pooled and used as templates for the commercially available SNaPshot kit. In addition to these ten SNPs we also tested the Y-chromosomal diallelic Alu repeat insertion DYS287 (YAP) by agarose gel electrophoresis as well as the Y-chromosomal STR systems DYS19, DYS389I+II, DYS390, DYS391, DYS392, DYS393 and DYS385 by fluorescent multiplex fragment analysis. Among the 11 diallelic SNP/Alu systems, only six were found to be polymorphic in the three population samples. From these a total number of seven different haplogroups could be identified in the three populations. Of these, five haplogroups were present in Germans, five in Thais, and only two in Chinese. These haplogroup trees clearly represent population-specific structures. Haplogroup 26 is represented at a high frequency in the Thai and Chinese populations whereas it is absent in Germans. The Y-STR data confirm a haplogroup-specific distribution of Y-STR haplotypes. Only a few cases of identical STR haplotypes in the same SNP haplogroups were detected in each of the three populations studied.     

Y chromosome DNA polymorphisms and their haplotypes in a Japanese population

Allele frequencies of two Y chromosome-specific short tandem repeats, locus DYS385 and DYS19, in addition to the Y Alu polymorphic (YAP) insert (DYS287) were investigated in blood samples obtained from 270 unrelated Japanese in Miyazaki Prefecture (south Japan). A total of 47 genotypes in DYS385 and 6 in DYS19 were detected, and the frequency of the YAP(+) allele was found to be 35.2% (95270). The allele distributions of each locus revealed significant differences compared with those in other populations. One hundred and twelve different haplotypes were observed in the combined 55 alleles of three loci. The gene diversity values range 0.96 for DYS385 and 0.71 for DYS19, and the combination haplotype diversity value is 0.98.     

The polymorphisms of various short tandem repeats on the Y chromosome in Japanese and German populations

In the present study we have analyzed the genotypes at the DYS389-I, DYS389-II, DYS390, DYS391, DYS393 and DYS19 loci on the Y chromosome in Japanese and German populations. The genotypes were determined in the white blood cell DNA of 200 Japanese and 111 German males. The 8-locus haplotype combination of these six loci with our previous data on DYS388 and DYS392 revealed much lower maximum matching probability (0.0053 in Japanese and 0.0092 in Germans), much higher minimum diversity (dw_min) (0.9947 in Japanese and 0.9908 in Germans) and more haplotypes (194 in Japanese and 110 in Germans). These very high abilities for discrimination could provide ideal tools for forensic analysis and population studies. Received: 8 October 1998 / Received in revised form: 7 June 1999 / Accepted: 30 June 1999     

Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography

Mitochondrial DNA control region sequences were determined in 109 unrelated German Caucasoid individuals from north west Germany for both hypervariable regions 1 (HV1) and 2 (HV2) and 100 polymorphic nucleotide positions (nps) were found, 63 in HV1 and 37 in HV2. A total of 100 different mtDNA lineages was revealed, of which 7 were shared by 2 individuals and 1 by 3 individuals. The probability of drawing a HV1 sequence match within the north west Germans or within published sets of south Germans and west Austrians is similar (within a factor of 2) to drawing a sequence match between any two of these three population samples. Furthermore, HV1 sequences of 700 male inhabitants of one village in Lower Saxony were generated and these showed a nearly linear increase of the number of different haplotypes with increasing number of individuals, demonstrating that the commonly used haplotype diversity measure (Nei 1987) for population samples tends to underestimate mtDNA diversity in the actual population. Received: 14 January 1999 / Accepted: 15 February 1999     

The polymorphisms of DYS388 and DYS392 on the Y chromosome in Japanese and German populations

The analysis of a genotype survey in Japanese and German populations at the loci DYS388 and DYS392 located on the Y chromosome is reported. The gene diversities of DYS388 were 0.34 and 0.30 in the Japanese and German males, respectively, and six alleles were found in both groups. The gene diversities of DYS392 were 0.65 and 0.64 and the number of alleles was 8 and 9, respectively in the two populations. The distribution of DYS388 alleles in the Japanese population was different from the German population. The allele distribution of DYS392 showed significant differences among Asian populations. Received: 5 January 1998 / Received in revised form: 27 April 1998     

Phylogenetic classification of Japanese mtDNA assisted by complete mitochondrial DNA sequences

We investigated control and coding region polymorphisms in mitochondrial DNA (mtDNA) in 100 unrelated individuals from a Japanese population and determined the basal phylogenetic haplogroup lineages in all samples under updated information. Many of the basal phylogenetic haplogroup lineages assigned on East Asian mtDNA haplogroups corresponded to those previously established. However, new haplogroup lineages such as M7a2a, M7a2b, M7a2*, M7c1b, M11b2*, G2b*, D4c1b1a, D4g2b, A4*, A9, N9b*, B4d1, B4d2, and F1e were identified and established by complete sequencing. Although sequence comparison of the 1.15-kb control region identified 84 mitochondrial haplotypes, examination of coding region polymorphisms increased the total number of haplotypes to 91. Determination of the basal haplogroup lineages increased the discrimination power of mtDNA polymorphisms for personal identification and their usefulness in determining geographic origin in forensic casework in Japanese and other East Asian populations.     

上海地区汉族健康人群血小板活化因子乙酰水解酶基因7号外显子593位点T/C单核苷酸多态性的研究

目的了解血小板活化因子乙酰水解酶(PAF-AH)基因7号外显子593位点T/C位点单核苷酸多态性(SNP)在中国上海地区汉族健康人群中的分布特征。方法采用聚合酶链反应(PCR)和测序法,对110名上海地区汉族健康者PAF-AH 7号外显子593位点T/C位点的SNP进行检测,计算其基因型和等位基因频率,并结合文献对不同种族该位点的突变情况进行比较。结果对110名上海地区汉族健康者PAF-AH Ile198-Thr(exon7;position 593;T-C)位点多态性进行检测,其PCR扩增产物为240bp。110人中,TT型97人(88.18%),TC型13人(11.82%),未发现CC型。该位点突变的等位基因频率分布也以T(94.09%)最为多见,其次为C(5.91%)。结合文献进行分析发现,上海地区汉族健康人群该位点突变基因型(TC)频率(11.82%)高于德国地区人群(0.95%,P<0.05),但与英国地区人群(7.67%)相比无统计学差异。结论上海地区汉族健康人群PAF-AH第7外显子593位点存在单核苷酸多态性,其T→C位点碱基突变比例较高,该位点突变基因型频率为11.82%,其SNP高于德国地区人群,但与英国地区人群相比无统计学差异。     

Relationship between the 1359 G/A polymorphism of the Central Cannabinoid Receptor 1 (CNR1) gene and susceptibility to cannabis addiction in a Turkish population

In this study, we investigate the existence of a possible genetic association between 1359 G/A polymorphism of the Central Cannabinoid Receptor 1 (CNR1) Gene CNR1 (p.Thr453Thr; rs1049353) single nucleotide polymorphism (SNP) and cannabis addiction. DNA samples used in this work are purified from venous leukocytes of 145 unrelated Turkish cannabis-dependent subjects and 140 Turkish control subjects. No significant difference is observed in genotype or allele frequencies of CNR1 1359 G/A polymorphism between these two groups. We also compared CNR1 1359 G/A polymorphism allele frequency distribution in our healthy Turkish population with other healthy populations. The comparison of healthy Turkish subjects with the healthy subjects from English-Irish, Chinese, European-American, African-American, Italian, German and Japanese populations revealed significant differences in allele frequencies. Data indicate that the 1359 G/A CNR1 polymorphism does not contribute to susceptibility to cannabinoid addiction in Turkish subjects. To the best of our knowledge, this is the first study on 1359 G/A CNR1 polymorphism in the Turkish population.     

Y-chromosomal STR haplotyping in a Japanese population

The Y-specific STR systems including DYS19, DYS385, DYS389I, DYS390, DYS391 and DYS393, were investigated in 117 Japanese males. Analysis of the 6 loci permitted classification of the samples into 90 haplotypes, and the haplotypic diversity was estimated to be 0.984. Distribution of the haplotypes in the Japanese population studied was different from that in European populations.     

Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population

Sequence polymorphisms of the hypervariable mitochondrial DNA (mtDNA) regions HVI and HVII, and coding region polymorphisms were investigated in 211 unrelated individuals from the Japanese population. Sequence comparison of the HVI and HVII regions led to the identification of 169 mitochondrial haplotypes defined by 147 variable positions. Among them 145 types were observed in only 1 individual; the other 24 types were shared by 2 or more individuals. The gene diversity was estimated at 0.9961, and the probability of two randomly selected individuals from the population having identical mtDNA types was 0.86%. We also established phylogenetic haplogroups in the Japanese population based on the coding and control region polymorphisms and compared the haplotypes with those in other Japanese, Korean and Chinese populations. As a result, three new subhaplogroups, G4a, G4b, and N9b, and several haplotypes specific for the Japanese and Korean populations were identified. The present database can be used not only for personal identification but also as an aid for geographic or phenotype (race) estimation in forensic casework in Japan.Electronic Supplementary Material Supplementary material is available for this article if you access the article at     

Expanding X-chromosomal forensic haplotype frequencies database: Italian population data of four linkage groups

Requests for solving complex kinship casework involving at least one female are increasing and in these circumstances the analysis of X-chromosomal STR markers plays a relevant role. Actually, it is well known the superior statistical power of X-STRs compared to autosomal markers in solving relationship when two sisters or half-sisters are involved and none of parents is available, in maternity testing or in cases involving close relatives as alternative putative fathers. In addition, the possibility to amplify more loci simultaneously and the strategy based on the analysis of four linkage groups to obtain the X-haplotype provide a powerful and validated tool. Nevertheless, haplotypes frequency distribution in different populations is still needed for calculation of probabilities in relationship testing. Published haplotype frequencies from German population data are available, but in different caseworks we found unreported X-haplotypes. To enlarge the forensic X-chromosome database, we present haplotype frequencies and other parameter of forensic interest obtained from 200 anonymous DNA samples of unrelated Italian males for the four linkage groups included in the Investigator Argus X-12 kit. From the comparison of the Italian sample haplotype frequencies with other populations, significant genetic distances were found with Asian and African populations, but not with Europeans. Finally, casework examples of complex kinship analysis are presented.     

Mitochondrial DNA sequence analysis of a native Bolivian population

Mitochondrial DNA analysis is very useful for the interpretation of the history of human migration and to estimate the frequency of a haplotype in the forensic context. From a human settlement perspective, La Paz area is greatly interesting since the first planned city of the region is located there. Samples from 110 individuals from La Paz were studied analysing the polymorphisms in the D-loop, hypervariable region I (HVI) and hypervariable region II (HVII) in order to verify the genetic diversity. The aim of this study was to start the creation of a population database in order to obtain the genetic interpopulation variability and classify haplotypes into characteristic haplogroups of South America. A total of 97 different haplotypes were identified, 90 being unique, expressed by 122 polymorphic nucleotide positions. Nucleotide and sequence diversity were estimated to be 0.015 ± 0.0075 and 0.996, respectively. Haplogroup distribution in the samples was 57.27% B4, 19.09% C1, 10.00% A2, 3.64% D1, 2.73% D4h3, 1.82% H, and 0.91% for each of the haplogroups A4, B4c1a, CZ, D4J, M7a and M8/N9b. The rate of length heteroplasmy was 36.36% in HVI and 52.73% in HVII. Phylogenetic analysis reveals proximity to the Korean, Chilean aboriginal, Japanese and Australian populations. The estimated genetic variability of the studied population was high, suggesting an early settlement.     

Haplotype analysis with 14 Y-STR loci using 2 multiplex amplification and typing systems in 2 regional populations in Japan

In this study 14 Y-STR loci (DYS393, DYS19, DYS391, DYS437, DYS435, DYS439, DYS389II, DYS438, DYS436, DYS390, Y-GATA-H4, DYS385, Y-GATA-A7.1 and DYS392) were analysed in 207 Japanese males from Honshu (main island of Japan, Nagoya City) and 87 Japanese males from Okinawa (southernmost islands of Japan) using two multiplex PCR typing systems, a novel 10-plex amplification system and a new commercially available 6-plex typing kit which had two loci in common. The allele frequency distributions were similar at almost all of the 14 loci. Of the haplotypes observed, 244 were unique in both Japanese populations and 17 haplotypes were observed more than once but the 2 populations shared only 7 haplotypes. The haplotype diversities for the 14 loci were 0.9987 and 0.9976 in Honshu and Okinawa Japanese, respectively. The haplotype analysis at 14 Y-STR loci would be useful for personal identification in forensic fields and for population genetics because of the high divergence of these haplotypes.     

Genetic data for 16 Y-chromosomal STR loci in Japanese

Allele frequencies and haplotypes for 16 Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y GATA H4, and DYS385a/b, were determined in 161 unrelated Japanese males using AmpFlSTR Yfiler PCR Amplification Kit. This population was demonstrated 153 haploytpes, of which 146 were unique, six were found in two individuals, and one was found in three individuals. The haplotypes diversity calculated from the 16 Y-STR loci was 0.9994 and the discrimination capacity was 0.9503.     

MATP polymorphisms in Germans and Japanese: the L374F mutation as a population marker for Caucasoids

Inference of the population and ancestry to which an individual belongs is important in forensic individualization and personal identification. In this study, five polymorphisms of the membrane-associated transporter protein (MATP) gene were investigated in German and Japanese populations. The L374F mutation was present at an allele frequency as high as 0.96 in the German population, whereas it was completely absent in the Japanese population. This extreme difference in allele frequency suggests that the L374F mutation is valuable as a population and ancestry informative marker for Caucasoids.     

Forensic and genetic characterization of mtDNA from Pathans of Pakistan

Complete mitochondrial control region data were generated for 230 unrelated Pathans from North West Frontier Province and Federally Administered Tribal Areas of Pakistan. To confirm data quality and to explore the genetic structure of Pathans, mitochondrial DNA haplogroup affiliation was determined by shared haplogroup-specific polymorphisms in the control region and by the analysis of diagnostic coding region single-nucleotide polymorphisms using a multiplex system for the assignment of eight haplogroups: M, N1′5, W, R, R0, T, J, and U. Sequence comparison revealed that 193 haplotypes were defined by 215 variable sites when major insertions were ignored at nucleotide positions 16193, 309, and 573. From a phylogenetic perspective, Pathans have a heterogeneous origin, displaying a high percentage of West Eurasian haplogroups followed by haplogroups native to South Asia and a small fraction from East Asian lineages. In population comparisons, this ethnic group differed significantly from several other ethnic groups from Pakistan and surrounding countries. These results suggest that frequency estimates for mtDNA haplotypes should be determined for endogamous ethnic groups individually instead of pooling data for these subpopulations into a single dataset for the Pakistani population. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pathans of Pakistan.     

Genetic variability of the SNPforID 52-plex identification-SNP panel in Central West Colombia

A set of autosomal single nucleotide polymorphism (SNP) loci was analyzed using the 52-plex assay previously described by Sanchez et al. [J.J. Sanchez, C. Phillips, C. Borsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe-Court, P.M. Schneider, A. Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713–1724] in 140 samples of unrelated individuals born in the Colombian regions of, Risaralda, Caldas, Quindio, Antioquia, Tolima and Valle, and 164 samples of unrelated individuals with declared Native American ancestry from Colombia. Allele frequencies and statistical parameters of forensic interest are presented for the 52 SNPs. All loci were in agreement with Hardy–Weinberg equilibrium while comparisons with population samples of Argentina, Portugal, Spain, Mozambique, and Taiwan revealed significant differences in allele frequency distributions.     

Genetic study of 12 X-STRs in Malay population living in and around Kuala Lumpur using Investigator Argus X-12 kit

We investigated 12 X-chromosomal short tandem repeat (STR) polymorphisms in 283 unrelated Malay individuals (160 males and 123 females) living in and around Kuala Lumpur using the Investigator Argus X-12 kit. Heterozygosity among the present 12 X-STRs showed a distribution of from 55.3 to 93.5 %. The diversity values of the haplotypes constructed using four closely linked groups were all higher than 0.9865. A comparison of allelic frequency in each system and haplotype variation indicated that the nature of these X-STRs in the Malay population differed from that in East Asian, European, or African populations. Several microvariant alleles found in the Malay population were characterized and compared with known sequence data. The present data may be helpful in forensic casework such as personal identification and kinship testing in the Malay population in Malaysia.     

Single nucleotide polymorphisms in the human complement C6 and C7 genes

We analyzed the single nucleotide polymorphisms (SNPs) in the sixth (C6) and the seventh (C7) component genes of the complement system in a sample of the Japanese population, using polymerase chain reaction (PCR)-based methods and PCR direct sequencing. SNPs in the C6 gene studied here are as follows: A413C in exon 3, T1674C in exon 10, T7145A in exon 13, G[357+32]A in intron 2, and G[503-78]A in intron 3. We confirmed that nt413A and nt413C were associated with C6A and C6B, respectively. The result of the nt2145 typing showed that two subtypes exist in the C6B allotype. The SNP of G[357+32]A in intron 2 could be analyzed by using the PCR-RFLP method with HinfI. Allele frequencies in the Japanese population were found to be *G=0.920 and *A=0.080. SNPs in the C7 gene are as follows: T382C in exon 4, G1166C and A1258C in exon 9, and G[+10]A in intron 13. Nt382C and nt1258C would be responsible for C7-5 (=C7-3) and C7-4 allotypes, respectively.