Genetic analyses in five western Mediterranean populations: variation at five tetrameric short tandem repeat loci.

A population study of the Balearic (Majorca, Minorca, Ibiza, Chueta) and Valencia populations was carried out using the short tandem repeat loci HUMTHO1, D4S243, HUMF13A1, D18S535, and D12S391. All the populations sampled were found to be in Hardy-Weinberg equilibrium for the five markers analyzed. Several statistical analyses showed a clear displacement of the Chueta and Ibiza populations from the other populations sampled. These results are in agreement with those obtained from the analysis of classical markers and mitochondrial DNA restriction fragment length polymorphisms, as well as with the history of these populations. A comparative study performed with other European populations using three of the five markers selected for this study (HUMTHO1, HUMF13A1, and D12S391) revealed a clear differentiation only of the Chueta population. We detected a tendency for a west-east clinal distribution in the frequency of the HUMTH01*6 allele in the European and Mediterranean area. This distribution could reflect some of the migratory events that have happened throughout that area's history. The forensic usefulness of these markers can be judged by their highly combined power of discrimination (0.999997).     

Variation at 4 short tandem repeat loci in 8 population groups of India.

We have determined the nature and extent of variation at 4 STR loci (CSF1P0, TPOX, TH01, VWA) in 8 caste and tribal population groups of eastern and northern India. Large differences in allele frequencies among the groups were found. Average heterozygosities in all populations were high (approximately 80%). The overall extent of gene differentiation among the 8 groups was high (GST = 0.04). The nature of genomic affinities based on these 4 STR loci does not completely agree with our earlier finding based on classical genetic markers that geographic proximity of habitat has a greater influence on genetic similarity between populations than sociocultural proximity does.     

Comparison of five tandem repeat loci between humans and chimpanzees.

Five tandem repeat loci were studied in humans and chimpanzees using VNTR probes derived from human DNA. Shared alleles were found at three loci and were often the modal allele in one species but never in both. There was no difference in the mean number of alleles per locus. However, these species exhibited substantially different levels of gene diversity, with chimpanzees monomorphic at two loci. Evidence of reduced variability in chimpanzees corroborates earlier comparisons using isozymes and plasma proteins. Molecular mechanisms, population dynamics, or both may be responsible for these differences. Equal numbers of alleles per locus may reflect high mutation rates. By one test, chimpanzees were out of equilibrium at one locus, which may reflect a typing error or population substructure. The long divergence time, and the high probability of backward mutations, precludes accurate estimation of genetic distance between these species.     

Genetic variation at nine short tandem repeat loci among islanders of the eastern Adriatic coast of Croatia

We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820) among six populations from Croatia: five distributed in the islands of the eastern Adriatic coast and one from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies; however, the absolute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, namely, heterozygosity, number of alleles, and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast to the two measures of genetic variation, allele size variance and within-locus heterozygosity, the imbalance index (beta) indicates evidence of recent expansion of population sizes in all islands and in the mainland. High mutation rates of the studied loci together with local drift effects are likely explanations for interisland genetic variation and the observed lack of reduced genetic diversity among the island populations.     

北京汉族群体39个短串联重复序列基因座多态性及其遗传关系

本文首次对北京地区汉族人群的13个CODIS(Combined DNA index system)和26个非CODIS系统STR基因座的遗传多态性进行了研究,建立了北京地区汉族人群39个STR基因座的群体遗传多态性数据库并对其法医学应用价值进行了评价。39个STR基因座的基因型分布均符合Hardy-Weinberg平衡且各基因座之间均不存在连锁现象,个体鉴别力(Power of discrimination, DP)在0.7740~0.9818之间,期望杂合度(Expected heterozygosity, He)在0.6000~0.9350之间,多态性信息含量(Polymorphism information content, PIC)在0.5317~0.9047之间,非父排除率(Power of exclusion, PE)在0.2909~0.8673之间,累积个体鉴别力(Cumulative probability of discrimination, CDP)为0.999999999999999999999999999999999999999964971,累积非父排除率(Cumulative probability of exclusion, CPE)为0.999999999973878。另外,结合已公开报道的国内其他11个群体相应基因座的遗传资料,根据等位基因频率计算遗传距离,构建了系统发生树。本研究可为中国法医DNA数据库和群体遗传学数据库提供重要的基础数据,对北京地区汉族人群开展法医学个体识别、亲权鉴定和遗传学研究具有重要的意义。     

DNA typing and genetic mapping with trimeric and tetrameric tandem repeats.

Tandemly reiterated sequences represent a rich source of highly polymorphic markers for genetic linkage, mapping, and personal identification. Human trimeric and tetrameric short tandem repeats (STRs) were studied for informativeness, frequency, distribution, and suitability for DNA typing and genetic mapping. The STRs were highly polymorphic and inherited stably. A STR-based multiplex PCR for personal identification is described. It features fluorescent detection of amplified products on sequencing gels, specific allele identification, simultaneous detection of independent loci, and internal size standards. Variation in allele frequencies were explored for four U.S. populations. The three STR loci (chromosomes 4, 11, and X) used in the fluorescent multiplex PCR have a combined average individualization potential of 1/500 individuals. STR loci appear common, being found every 300-500 kb on the X chromosome. The combined frequency of polymorphic trimeric and tetrameric STRs could be as high as 1 locus/20 kb. The markers should be useful for genetic mapping, as they are sequence based, and can be multiplexed with the PCR. A method enabling rapid localization of STRs and determination of their flanking DNA sequences was developed, thus simplifying the identification of polymorphic STR loci. The ease by which STRs may be identified, as well as their genetic and physical mapping utility, give them the properties of useful sequence tagged sites (STSs) for the human genome initiative.     

Genetic variation of new 21 autosomal short tandem repeat loci in a Chinese Salar ethnic group

In the present study, we reported the allele frequencies for new 21 autosomal short tandem repeat (STR) loci, including D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435 and D5S2500 loci. Forensic statistical parameters were estimated from a sample set of 120 unrelated healthy individuals from the Salar ethnic group in Xunhua Salar Autonomous County of Qinghai province, China. A total of 151 alleles were observed at 21 STR loci in the population, and their allele frequencies were in the range of 0.004–0.554. All STR loci showed a high degree of genetic polymorphisms, and the combined probability of exclusion, combined power of discrimination and combined probability of matching for all 21 STR loci were 0.9999993134, 0.99999999999999999991739 and 8.2607 × 10⁻²⁰, respectively. For all the 21 STR loci in the Salar ethnic group, the observed genotypic data showed no significant deviation from those expected under the Hardy-Weinberg equilibrium. The allele frequency distributions for the 21 autosomal STR loci were compared between the Salar group and its neighboring populations and significant differences were detected among these populations at D1S1677, D2S441, D3S4529, D4S2408, D6S1017, D11S4463, D12ATA63, D14S14343, D18S853, D19S433 and D22S1045 loci.     

Genetic variation at twentythree microsatellite loci in sixteen human populations

We have analysed genetic variation at 23 microsatellite loci in a global sample of 16 ethnically and geographically diverse human populations. On the basis of their ancestral heritage and geographic locations, the studied populations can be divided into five major groups, viz. African, Caucasian, Asian Mongoloid, American Indian and Pacific Islander. With respect to the distribution of alleles at the 23 loci, large variability exists among the examined populations. However, with the exception of the American Indians and the Pacific Islanders, populations within a continental group show a greater degree of similarity. Phylogenetic analyses based on allele frequencies at the examined loci show that the first split of the present-day human populations had occurred between the Africans and all of the non-African populations, lending support to an African origin of modern human populations. Gene diversity analyses show that the coefficient of gene diversity estimated from the 23 loci is, in general, larger for populations that have remained isolated and probably of smaller effective sizes, such as the American Indians and the Pacific Islanders. These analyses also demonstrate that the component of total gene diversity, which is attributed to variation between groups of populations, is significantly larger than that among populations within each group. The empirical data presented in this work and their analyses reaffirm that evolutionary histories and the extent of genetic variation among human populations can be studied using microsatellite loci.     

Genetic polymorphisms of nine X-STR loci in four population groups from Inner Mongolia, China

Nine short tandem repeat （STR） markers on the X chromosome （DXS101, DXS6789, DXS6799, DXS6804, DXST132, DXST133, DXS7423, DXS8378, and HPRTB） were analyzed in four population groups （Mongol, Ewenki, Oroqen, and Daur） from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance betweent Mongol and Han （Xi＇an） populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.     

Survey of the Korean population for 9 short tandem repeat loci

The short tandem repeats with repeat units ranging from two to several nucleotides became a powerful tool in the field of forensic identification and paternity determination as well as for research in human gene mapping. Allele and genotype frequencies for 9 short tandem repeats including HUMCSF1PO, HUMTH01, HUMPLA2A1, HUMF13A01, HUMCYAR04, HUMLIPOL, HUMHPRTB, HUMCD4, and HUMFABP were determined using PCR and subsequent analysis of the PCR products by denaturing polyacrylamide gel electrophoresis followed by silver-staining. DNA samples were obtained from about 100 Korean people and amplified in a thermocycler adopting glass capillaries rather than traditional tubes. We found that the bovine serum albumin was an essential additive for the capillary PCR, presumably to coat the inner surface of the capillary which may adsorb Taq DNA polymerase. The capillary thermocycler was very effective in reducing the cycling time such that most of the amplification reactions could be finished within 30 min albeit the PCR product was less than that for the tube systems. All loci except HUMHPRTB met the Hardy-Weinberg expectations according to the exact test. The cumulative power of discrimination (PD) was 0.9999998 and the power of exclusion (POE) for the paternity test was a little low, being 0.9873989.     

Intrinsic polymorphism of variable number tandem repeat loci in the human genome.

In the human genome, short tandem repetitive (STR) DNA sequences often show restriction fragment length polymorphisms (RFLPs) due to variation in the number of copies of the repeat unit. For a subset of these sequences known as minisatellites or variable number tandem repeat loci (VNTR), it has been proposed that a homologous "core" sequence of 10-12 nucleotides is involved in the mechanism(s) generating the polymorphism. In our present study we have prepared oligonucleotide probes complementary to one or two repeat units of several VNTR loci. Under stringent hybridization and wash conditions these probes hybridize locus specifically thus allowing the evaluation of the intrinsic polymorphism of individual loci. Our results indicate that not all of the loci having STR DNA sequences are polymorphic despite the fact that they share the "core" sequence. This suggests that more than the DNA sequence of the locus is involved in the mechanism(s) generating the polymorphism.     

Germline mutation rates at tandem repeat loci in DNA-repair deficient mice

Mutation rates at two expanded simple tandem repeat (ESTR) loci were studied in the germline of non-exposed and irradiated severe combined immunodeficient (scid) and poly(ADP-ribose) polymerase (PARP-1-/-) deficient male mice. Non-exposed scid and PARP-/- male mice showed considerably elevated ESTR mutation rates, far higher than those in wild-type isogenic mice and other inbred strains. The irradiated scid and PARP-1-/- male mice did not show any detectable increases in their mutation rate, whereas significant ESTR mutation induction was observed in the irradiated wild-type isogenic males. ESTR mutation spectra in the scid and PARP-1-/- strains did not differ from those in the isogenic wild-type strains. Considering these data and the results of previous studies, we propose that a delay in repair of DNA damage in scid and PARP-1-/- mice could result in replication fork pausing which, in turn, may affect ESTR mutation rate in the non-irradiated males. The lack of mutation induction in irradiated scid and PARP-1-/- can be explained by the high cell killing effects of irradiation on the germline of deficient mice.     

Genetic variation at microsatellite loci in Spanish sheep

Genetic variation at 18 microsatellite loci was analysed in six indigenous Spanish sheep: Churra; Latxa; Manchega; Rasa-Aragonesa; Castellana and Merino. Merinos had frequently the highest number of alleles per locus, whereas Latxas showed the lowest one at many loci. Markers ordered decreasingly according to the number of variants differentiated in the whole population were: MAF70; TGLA13; CSSM66; BM143, BM6444; MAF36; MAF64; CSSM6; TGLA53; OarFCB11; MAF33; BM4621; MAF48; MAF65; BM1258; ILSTS002; ADCYC and OarCP34. Parameters of variability such as effective number of alleles and gene diversities corroborated the high level of variation frequently displayed by microsatellite markers. Comparison of allele distributions among populations and loci did not reveal consistent shapes. Distributions were centralised in some cases, whereas in others some kind of skewness was evident. Breed-specific alleles were detected at most loci, being frequent in Merinos and rare in Churras.     

Alleles at four HLA class II loci determined by oligonucleotide hybridization and their associations in five ethnic groups

The use of polymerase chain reaction (PCR) and oligonucleotide hybridization offers a new approach for the definition of HLA class II alleles. It has been possible to determine 43 alleles of DRB1, four of DRB3, two of DRB4, four of DRB5, eight of DQA1, and 14 of DQB1. These alleles are inherited together in members of families and form closely associated groups which are found repeatedly and in characteristics patterns in different populations. We have determined the HLA class II alleles and analyzed their association in 431 healthy unrelated subjects including 161 North American Caucasians, 53 Latin Americans, 61 Blacks, 88 Chinese, and 68 Israeli Jews. For-locus haplotypes (DRB1; DRB3/4/5; DQA1; DQB1) were derived from 79 B cell lines and the analysis of segregation in 34 nuclear families. The B-cell lines yielded 37 and the families showed the same, and 20 other, haplotypic combinations. In addition to these 57 haplotypes, associated alleles were assigned in the unrelated panels following certain rules. The resulting haplotypes were assigned to groups known to share associated alleles. The groups were: (1) DR1, DR2, and DRw10 (13 haplotypes); (2) DR3 and DRw6 (26 haplotypes); (3) DR5 and DRw8 (24 haplotypes); (4) DR4, DR7, and DR9 (24 haplotypes). Their distribution in populations with different ethnic backgrounds was analyzed. The expressed DRB4 allele and its null mutant were determined by PCR and oligonucleotide hybridization. The different DR7 haplotypes resulting from these determinations were analyzed in a panel of 130 North American Caucasoids. This comprehensive analysis of class II HLA haplotypes in human populations should be useful in understanding the role of these genes and in various applications including anthropolgy, disease susceptibility, and transplantation of allogeneic organs and tissues. Address correspondence and offprint requests to: P. Stastny     

Genetic variability and discriminating power of four microsatellite loci in Russian population

Allele and genotype frequencies of 4 STR loci (LPL, vWA, FES/FPS H F 13B), used in forensic medicine, were analyzed in Russian Siberian population. Genetic and molecular diversity of these polymorphic systems were characterized in comparison with US Caucasoid population. High discriminating power (PD = 0.99975) of the system of four studied STR loci was shown. Comparative analysis of genetic diversity in Russian population and Caucasoid US population revealed the significant differences between two populations and demonstrated that STR frequency data for US population should not be used for forensic expertise in Russia. The data obtained in the current investigation may be used as reference data for forensic medicine laboratories in Siberia.     

Improved haplotype analysis of human myelin basic protein short tandem repeat loci

We report an improved haplotype analysis of the human myelin basic protein gene (MBP) short tandem repeat (STR) polymorphism. The polymorphic G-->A transition and 2 conventional STR polymorphisms, MBPA and MBPB, were simultaneously determined by an amplified product length polymorphism technique. After the MBPC fragments containing MBPA and MBPB were amplified, the linkage of these 2 STR loci was determined by a second amplification, using polymerase chain reaction (PCR) technique, of the isolated MBPC fragments. The present haplotype analysis dispensed with family studies for the haplotyping of MBPA and MBPB. Polymorphisms of the MBP loci studied in German and Japanese populations showed a high genomic variation. Haplotype analysis of the MBP loci showed distinct differences between the German and the Japanese populations. Consequently, haplotype analysis of the MBP loci promises to be useful in forensic identification and paternity testing.     

Genetic variation at 9 autosomal microsatellite loci in Asian and Pacific populations.

Genetic variation at 9 autosomal microsatellite loci (CFS1R, TH01, PLA2A, F13A1, CYP19, LPL, D20S481, D20S473, and D20S604) has been characterized in 16 Asian and Oceanic populations, mostly from mainland and insular Southeast Asia. The neighbor-joining tree and the principal coordinates analysis of the genetic relationships of these populations show a clear separation of Papua New Guinea Highlanders and, to a lesser extent, Malayan aborigines (Orang Asli or Semai) from the rest of the populations. Although the number of markers used in this study appears to be inadequate for clarifying the patterns of genetic relationships among the studied populations, in the principal coordinates analysis a geographic trend is observed in the mainland and insular Southeast Asian populations. Furthermore, in an attempt to contrast the extent of variation between autosomal and Y-chromosome-specific microsatellite loci and to reveal potential differences in the patterns of male and female migrations, we have also compared genetic variation at these 9 autosomal loci with variation observed at 5 Y-chromosome-specific microsatellites in a common set of 14 Asian populations.     

Genetic polymorphism study at four minisatellite loci (D1S80, D17S5, D19S20, and APOB) among five Indian population groups

The present study reports the genetic variation observed among five anthropologically distinct population groups of India, using four highly polymorphic minisatellite loci (D1S80, D17S5, D19S20, and APOB 3' VNTR) in order to examine the effect of geographical and linguistic affiliations on the genetic affinities among these groups. Random individuals from five ethnic groups were studied; the sample size ranged from 235 to 364. The population groups belong to two geographically separated regions of India, the state of Maharashtra (western India) and the state of Kerala (southern India). The two Maharashtrian groups (Konkanastha Brahmins and Marathas) speak "Marathi," an Indo-European language, whereas the three Kerala population groups (Nairs, Ezhavas, and Muslims) speak "Malayalam," an Indo-Dravidian language. Genomic DNA was extracted from peripheral blood samples and analyzed using amplified fragment length polymorphism (Amp-FLP) technique. All four loci displayed high heterozygosity with average heterozygosity in the range of 0.82 to 0.84. The Polymorphic Information Content and Power of Discrimination were > or = 0.75 and > or = 0.80, respectively. The coefficient of gene differentiation was found to be low (average G(ST) = 1.2%; range between 0.6% at D1S80 locus to 1.6% at APOB 3' VNTR locus) across the loci, indicating close affinity among the population groups. The neighbor-joining tree revealed two clear clusters, one for the two Maharashtrian population groups and the other for the three Kerala population groups. The results obtained are in conformity with the geographical and linguistic backgrounds of the studied populations.