Allele frequency distributions at several variable number of tandem repeat (VNTR) and short tandem repeat (STR) loci in a restricted Caucasian population from south Italy and their evaluation for paternity and forensic use

Allele frequencies at six VNTR loci, 11 STR loci, and at the HLA-DQA1 locus were evaluated in a well-defined population from Campania (South Italy). The allele frequencies of three VNTR loci, 11 STR loci, and the HLA-DQA1 locus were compared with data obtained from a general Caucasian reference population in the USA. The aim of this study was to determine the power of each single locus and group of loci for forensic and paternity testing purposes. Significant differences between the allele frequencies of the two populations were found in two VNTR loci, four STR loci and in the HLA-DQA1 locus. The two populations were in Hardy-Weinberg equilibrium for the STR loci, but as expected, not for some VNTR loci. It was also found that: (i) the discriminatory power of two STR systems (nine and 11 loci, respectively) is similar in the two populations analysed; and (ii) that the allele frequencies for the STR systems of a large reference population can always be applied to subjects of a small subpopulation. In conclusion, for forensic purposes and for paternity testing, most of the 11 STR loci examined can be analysed using allele frequencies from a general Caucasian reference population without typing subpopulations, whereas the VNTR loci must be subtyped.     

Genetic polymorphisms and ethnic admixture in African-derived black communities of northeastern Brazil

Unrelated individuals from 3 relatively isolated African-derived communities in the state of Piauí, northeastern Brazil, and blood donors from Teresina (admixed population), the capital city of Piauí, were analyzed for the ESD, CA2, GC, HP, GLO1, PGM1, HB, ACP1 protein loci and for the VWF1 and VWF2 short tandem repeat (STR) loci. As expected, high frequencies of alleles considered characteristics of African populations were detected. The VWF1 allele distribution was bi-modal, whereas the VWF2 distribution was unimodal, suggesting differential action of mutation and selection factors in the 2 STRs despite their close location on the same gene. The genetic distances between the Brazilian isolates coincide with their geographic distances. The ethnic admixture estimated by a maximum-likelihood method showed African, European, and Amerindian components of 61%, 17%, and 22% for Mimbó, 72%, 12%, and 16% for Sítio Velho, and 31%, 21%, and 48% for Teresina, respectively.     

Genetic relationships among Japanese, northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian, and Italian populations based on allelic frequencies at four VNTR (D1S80, D4S43, COL2A1, D17S5) and one STR (ACTBP2) loci

The genetic polymorphism at four variable number of tandem repeats (D1S80, D4S43, COL2A1, D17S5) and one short tandem repeat (ACTBP2) loci was assessed by polymerase chain reaction analysis of genomic DNA obtained from blood samples of eight human populations (Japanese, Northern Han, Hui, Uygur, Kazakh, Saudi Arabian, Greek, Italian). Allele frequencies at all loci were in the Hardy-Weinberg equilibrium for each population. With the exception of ACTBP2, the allelic distribution patterns for these loci revealed a marked genetic divergence among the eight populations. A dendrogram constructed by the neighbor-joining method based on the allele frequencies of the five loci suggested that the five Asian populations (Japanese, Northern Han, Hui, Uygur, and Kazakh) formed one cluster, whereas the two European populations and one West Asian population (Italian, Greek, and Saudi Arabian) formed another. The genetic relationship among these populations may have been greatly influenced by admixture as a result of the migration of individuals along the Silk Road throughout history.     

Genetic typing of HLA class II genes in Swedish populations: application to forensic analysis

In an attempt to determine the value of DNA based typing of HLA class II loci to forensic analysis, allele and genotype frequencies at DQA1, DQB1, DPB1, and DRB1 were determined in samples from two Swedish populations using hybridization with sequence specific oligonucleotides to PCR amplified DNA. Significant allele frequency differences were observed at the DQB1 and DRB1 loci between the two populations, as well as between one of the Swedish and a Norwegian population. The average heterozygosity varies between 0.74 to 0.91 and the power of discrimination between 0.90 to 0.98, with the highest values obtained for the DRB1 locus. The probability of genotype identity by chance differs on average 2% between the populations. When applied to a paternity case with one parent deceased and a criminal case, typing of class II loci proved in both cases informative. Analyses of DR and DQ genes does not increase the power of discrimination, due to strong linkage, but offers through the reconstruction of putative haplotypes an internal control for the consistency of the typing results at several loci. Typing of the DRB1 and DPB1 loci was found to result in an approximate combined average probability of genotype identity by chance of one in a thousand.     

Subtyping of the HLA-DQA1 locus and independence testing with PM and STR/VNTR loci

Allele and genotype frequencies for six loci (HLA-DQA1 and PM loci) were determined in African Americans, United States Caucasians, and Southwestern Hispanics. The data include allele frequencies of the HLA-DQA1 4 subtypes. The HLA-DQA1 4 allele subtyping affords greater power of discrimination in African Americans and Southwestern Hispanics than in Caucasians, due to the relatively lower 4.2/4.3 allele frequency in Caucasians. Based on the exact test, all loci, except the GYPA locus in the African American sample (p = 0.011), meet Hardy-Weinberg expectations. There were two examples of significant departures from expectations of independence between alleles of the HLA-DQA1 and PM loci (HBGG/Gc in African Americans, p = 0.30; LDLR/DQA1 in Caucasians, p = 0.023). The HLA-DQA1 and PM loci also were tested for associations with three STR loci and the DIS80 locus. There were four examples of significant departures from expectations of independence (TPOX/D7S8 and THO1/HBGG in African Americans, p = 0.035 and 0.028, respectively; THO1/LDLR in Caucasians, p = 0.028; and GYPA/D1S80 in Hispanics, p = 0.046). The HLA-DQA1 and PM allele frequency data were compared with previously reported data on other sample populations of the same population categories from our laboratory; the allele frequencies at all loci, except the D7S8 locus in Hispanics (p = 0.028), were statistically similar. The frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a multiple locus DNA profile in various general United States populations.     

PM and D1S80 loci gene frequencies in the Zaragoza population of northern Spain

LDLR, GYPA, HBGG, D7S8, GC (PM loci) and D1S80 are widely used in forensic casework analyses and population data are required to estimate the frequency of a DNA profile. This paper presents the results of a survey aimed at investigating the allele and genotype frequency distribution of these loci in an important Spanish population (Zaragoza, North Spain). Statistical analysis to determine whether allele frequencies were in Hardy-Weinberg equilibrium was carried out as well as to obtain some parameters of medicolegal interest. There was no evidence of association between the alleles of the loci. The Zaragoza sample does not differ substantially from other Caucasian populations.     

The male-sterility polymorphism of Silene vulgaris: analysis of genetic dat from two populations and comparison with Thymus vulgaris

Results are given of genetic studies of male sterility using plants from two natural populations from Sussex, England. Both populations have substantial frequencies of females, approximately 0.25 in population 1 and 0.60 in population 3. As in the few other gynodioecious populations studied in detail, many genetic factors are present. In population 1, there are at least two, and more likely three, different cytoplasmic types, one of which appears to produce male sterility in progeny from any hermaphrodite pollen donor; in other words restorer alleles for this cytoplasm are rare or absent from the population. The other two populations can be carried in hermaphrodites that have the dominant restorers. In population 1, there are also probably three restorer loci with complementary recessive male-sterility alleles, as well as a locus with duplicate action, which cannot produce male sterility unless the plant is also homozygous for the recessive allele at another locus. The results from population 3 are quite similar, though there was no evidence in this population for an unrestored sterility cytoplasm. A similar joint nucleocytoplasmic model with multiple restorers fits data from Thymus vulgaris.     

Genetic diversity at six short tandem repeat loci within the state of Victoria, Australia

A new multiplex PCR system, developed by the Forensic Science Service (FSS) in the United Kingdom, permits the coamplification and typing of six short tandem repeat (STR) loci: HUMFGA, D8S1179, HUMTHO1, HUMvWA, D18S51, D21S11 and the sex determining marker Amelogenin. Data are presented on these six STRs for two populations in the state of Victoria, Australia: Caucasian and Asian. Whilst several worldwide databases are already available for the STR loci HUMTHO1 and HUMvWA, only relatively few databases exist for D8S1179, D18S51, D21S11 and HUMFGA. Allele frequencies at each locus displayed some fluctuations between the two populations. This is particularly so for HUMTHO1. Generally, however, the most common allele at each locus was the same in all populations, at all loci. A novel D8S1179 allele was found in Asians, provisionally identified as allele 19. Results for the six loci were compared with similar data from three UK resident populations: Caucasian, Afro-Caribbean and Asian (Indian/Pakistani) populations. These indicated that ethnically similar populations display similar allele frequencies, while the Australian Asian and UK Afro-Caribbean were found to be distinct.     

Isolated limb infusion with cytotoxic agents: a simple alternative to isolated limb perfusion

We use population genetics theory and computer simulations to demonstrate that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci. Bottlenecks cause alleles at low frequency (< 0.1) to become less abundant than alleles in one or more intermediate allele frequency class (e.g., 0.1-0.2). This distortion is transient and likely to be detectable for only a few dozen generations. Consequently only recent bottlenecks are likely to be detected by tests for distortions in distributions of allele frequencies. We illustrate and evaluate a qualitative graphical method for detecting a bottleneck-induced distortion of allele frequency distributions. The simple novel method requires no information on historical population sizes or levels of genetic variation; it requires only samples of 5 to 20 polymorphic loci and approximately 30 individuals. The graphical method often differentiates between empirical datasets from bottlenecked and nonbottlenecked natural populations. Computer simulations show that the graphical method is likely (P > .80) to detect an allele frequency distortion after a bottleneck of < or = 20 breeding individuals when 8 to 10 polymorphic microsatellite loci are analyzed.     

Breeding structure of screwworm fly populations (Diptera: Calliphoridae) in Colima, Mexico

Starch gel electrophoresis was used to resolve gene frequencies among populations of screwworm, Cochliomyia hominivorax (Coquerel). The loci examined coded for alpha-glycerophosphate dehydrogenase, octanol dehydrogenase, and phosphoglucomutase. Flies were sampled by traps widely distributed in Colima Province, southwestern Mexico. Gene frequencies at Odh differed significantly among the 11 populations. Alleles segregating at Pgm and alpha-Gpdh were homogeneous among populations. There were significant departures from random mating within populations, but no genetic differentiation among populations was detected. The data suggest unrestricted gene flow among populations. Departures from random mating within populations were explained by the pooling of samples from separate breeding units.     

Images in pediatric neurosurgery. Neuroimaging quiz

OBJECTIVE: To understand the distribution of allele frequencies of inter-alpha-trypsin inhibitor(ITI) in Chinese populations. METHODS: The polymorphism of this protein in six Chinese populations was investigated using isoelectric focusing followed by immunoblotting technique. RESULTS: Three common alleles, ITI*1, ITI*2, and ITI*3 were observed in four populations, namely Han living in Jilin, Mongol in Hailaer, Tibetan in Lasa, and Bai in Dali respectively. In other two populations, Zhuang in Guangxi and Han in Guangdong, only ITI*1 and ITI*2 were observed. For these populations, the frequency of ITI*1 ranges from 0.5500 to 0.7525; that of ITI*2 from 0.2475 to 0.4322; and that of ITI*3 from 0.0034 to 0.0729. CONCLUSION: This study reveals that there is no parallel relationship between variation of allele frequencies and geographic differences.     

Study of 15 protein polymorphisms in a sample of the Turkish population

Anatolia, because of its geographic position and its use as an area of settlement, was also a land of transit that accommodated a succession of populations. The last important invasion occurred in the Middle Ages with the arrival of the Turks, an Altaic-speaking nomadic population descended from the Oguz tribes and originating in Mongolia. Although the Turks imposed their culture, their genetic contribution seems to have been modest. To validate this hypothesis, we studied the genetic structure of the Turkish population by examining 15 genetic markers in a sample of 93 subjects. The allele frequencies observed were HP*1 = 0.240; GLO1*1 = 0.344, ESD*2 = 0.134, GC*1S = 0.613, GC*1F = 0.129, PGM1*2S = 0.322, PGM1*2F = 0.041, PGM1*1F = 0.027, F13B*1 = 0.762, F13B*2 = 0.101, ORM1*S = 0.327, AHSG*2 = 0.181, C6*B = 0.239, C7*1 = 0.983, APOC2*1 = 1.0, APOE*3 = 0.868, APOE*2 = 0.063, BF*F = 0.258, BF*S07 = 0.017, BF*SQ0 = 0.011, C4A*Q0 = 0.145, C4A*2 = 0.070, C4A*5 = 0.012, C4A*6 = 0.023, C4B*Q0 = 0.101, C4B*2 = 0.048, C4B*3 = 0.005, and C4B*11 = 0.005. The present Turkish population was compared to other European, Middle Eastern, and North African populations by means of correspondence analysis. Turks cluster with Turkomans, who share the ancient Turks' derivation from the Oguz tribe. Moreover, Turks clearly belong to European groups and resemble the populations of neighboring countries. Therefore the present data support the hypothesis that the ancient Turkish tribes, who started to enter Anatolia 1000 years ago, contributed little to the gene pool of the preexisting Anatolian populations. Alternatively, if the genetic structure of the invading Turks resembled that of the ancient Anatolians, it will be impossible to find traces of their admixture with the autochthonous inhabitants of Anatolia. However, further analysis of other samples from Turkey and from populations living in the homelands of the Turkish tribes, namely, the eastern area of the Caspian Sea and Mongolia, is needed.     

Allele distribution at nine STR loci--D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820--in the Japanese population by multiplex PCR and capillary electrophoresis

Nine tetranucleotide short tandem repeat (STR) loci, D3S1358, vWA, FGA TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820, were analyzed in the Japanese population with a newly released kit for personal identification using multiplex PCR with fluorescent-labeled primers following capillary electrophoresis. The observed heterozygosities were 0.67, 0.77, 0.82, 0.61, 0.62, 0.73, 0.78, 0.81 and 0.74, respectively, and the combined discrimination power of the nineplex was 0.9999999991. None of the nine loci deviated from Hardy-Weinberg equilibrium expectations using the chi-square test, homozygosity test, likelihood ratio test and exact test after the grouping of the alleles. The nine STR loci allele frequencies were significantly different from those of other ethnic populations.     

Different molecular events result in low protein levels of mannan-binding lectin in populations from southeast Africa and South America

Previous studies have shown that three point mutations in exon 1 and a particular promoter haplotype of the mannan-binding lectin (MBL) gene lead to a dramatic decrease in the serum concentration of MBL. In this study, MBL genotypes and serum concentrations were determined in unrelated individuals in a population from Mozambique (n = 154) and in two native Indian tribes from Argentina (i.e., the Chiriguanos (n = 43) and the Mapuches (n = 25)). In both populations, the MBL concentrations were low compared with those found in Eskimo, Asian, and European populations. In Africans, the low serum concentrations were due to a high allele frequency (0.24) of the codon 57 (C) variant, which resulted in a high frequency of individuals with MBL deficiency (0.06), and were also due to the effect of a relatively high frequency (0.13) of low-producing promoter haplotypes. The low concentrations in the South American populations were primarily due to an extremely high allele frequency of the codon 54 (B) variant in both the Chiriguanos (0.42) and the Mapuches (0.46), resulting in high frequencies of individuals with MBL deficiency (0.14 and 0.16, respectively). In the search for additional genetic variants, we found five new promoter mutations that might help to elucidate the evolution of the MBL gene. Taken together, the results of this study show that different molecular mechanisms are the basis for low MBL levels on the two continents.     

Distribution of allelic forms of erythrocyte H1 histones in Japanese quail populations divergently selected for amount of weight loss after transient starvation

Three polymorphic subtypes of erythrocyte histone H1 (H1.a, H1.b, and H1.z) were analyzed using a sodium dodecyl sulfate polyacrylamide gel in quail populations divergently selected for a high (line 1) or low (line 2) reduction in body mass following temporary food withdrawal. Both H1.b and H1.z histone alleles were found to be differently distributed in these populations during the selection period. The frequency of b1 in line 2 was approximately 1.9-2.8 times lower than in line 1 and approached the values in line 1 when the selection was suspended. Similarly, the frequency of allele z2 at locus H1.z increased significantly (about 1.6-2.3 times) in line 2 during selection and returned to the initial values when selection was stopped. On the other hand, allele a0 at locus H1.a was kept at relatively low levels (usually below 0.05) in both lines during selection. At that time its level was approximately three to four times lower than in a random mating control population. When selection was suspended, the frequency of a0 in line 1 increased significantly, approaching the values in the control line, and remained essentially unchanged in line 2. Thus, all three polymorphic histone H1 loci in quail responded through changes in allele frequencies to the breeding selection, which was directed at the amount of body weight loss upon transient starvation. It seems that either H1 histone locus could be linked to loci controlling the rate of body weight reduction following starvation or weight loss during fasting might be influenced by a panel of H1 histone alleles that can contribute to functional differences in avian chromatin.     

Jejunal and ileal absorption in patients with chronic renal disease. Effect of 1alpha-hydroxycholecalciferol

Gene conversion causes deviations from the 2:2 segregation of allele pairs in meiosis. Thus, gene conversion is a potential cause for changes of allele frequencies in populations. Equations are derived for the effects of conversion in a large random-mating population. The influence of gene conversion on allele frequencies is compared with that of spontaneous mutation and meiotic drive.     

Population genetics and structure of Buryats from the Lake Baikal Region of Siberia

Genetic polymorphisms of blood groups, serum proteins, red cell enzymes, PTC tasting, and cerumen types are reported for five Mongoloid populations of Buryats from the Lake Baikal region of Siberia (Russia). These groups are characterized by relatively high frequencies of alleles ABO*B, RH*D, cerumen D, GC*1F, ACP1*B, ESD*2, and PGD*C. Significant genetic heterogeneity between populations was demonstrated for the loci RH, MN, cerumen, PGD, ABO, GC, GLO, TF, and PGM1. Genetic distance analyses using five loci revealed a lower level of genetic microdifferentiation within the Buryat populations compared with other native Siberian groups. The distribution of gene markers in Buryats is similar to that found in neighboring Central Asian groups, such as the Yakuts and the Mongols. Intrapopulational analyses of the five Buryat subdivisions, based on R matrix and rii, indicate that one of the subdivisions is reproductively more isolated than the others and that two of the communities have received considerable gene flow. A nonlinear relationship was demonstrated between geographic and genetic distances of Buryat population subdivisions.     

Does the biocompatibility of the hemodialysis membrane influence the prognosis of acute renal insufficiency?

OBJECTIVE: This study was aimed at the use of old blood stains for investigating the distribution of three STR loci in Jingpo ethnic group. METHODS: DNA extraction from old blood stains (106 in number) and multiplex amplification of CSF1PO, TPOX and TH 01 were carried out. Using denaturing polyacrylamide gel electrophoresis and silver stain, the authors investigated the distribution of allele frequencies of CSF1PO, TPOX and TH01 loci in a Jingpo ethnic group in the southwestern part of Yunnan province. RESULTS: 7 alleles and 26 genotypes of CSF1PO locus,7 alleles and 19 genotypes of TPOX locus, and 6 alleles and 18 genotypes of TH01 locus were observed. CONCLUSION: The satisfactory results demonstrate that multiplex amplification of CSF1PO, TPOX and TH01 is sensitive and the old stain of a drop of blood is sufficient for such amplification.     

Spanish population data on 7 tetrameric short tandem repeat loci

Allele and genotype frequencies for 7 tetrameric short tandem repeat loci were determined in a Spanish population sample (N = 186-244) using PCR and subsequent analysis of the PCR products by denaturing polyacrylamide gel electrophoresis followed by silver staining. The loci were HUMFES/FPS, HUMVWA, HUMTHO1, HUMF13B, HUMCSF1PO, HUMF13A1 and HUMTPOX and all loci met Hardy-Weinberg expectations. In addition, little evidence was found for association of alleles among the 7 loci. Thus the allele frequency data can be used in identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Spanish population.