No evidence for linkage of a novel CA repeat polymorphism for apoptosis antigen 1 (APO-1 or fas) with type I diabetes in a Caucasian population

Abstract DNA typing of four tetrameric repeat loci (HUMVWA, HUMTH0I, D21SII and HPRT) was carried out in a Chinese Han population from Shanghai (East China) and one from Guangzhou (South-East China) using a quadruplex PCR amplification and detection of the fluorescent-labeled alleles on the ALF DNA sequencer. All loci were in accordance with Hardy-Weinberg equilibrium except for D21S11 in the Guangzhou population. A test for population differentiation showed no statistical difference in the allele frequency distribution between the two populations. Comparison of the allele frequency data with other Chinese Han populations from North and South-West China for the STR loci HUMVWA and HUMTH01 revealed heterogeneity between Northern Chinese Han and Southern Chinese Han, which is in accordance with previous studies on the basis of protein markers.     

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.     

Virulent and avirulent Rhodococcus equi infection in T-cell deficient athymic nude mice: pathologic, bacteriologic and immunologic responses

We report a study of polymorphism for seven short tandem repeat (STR) loci in Japanese and Chinese populations. Among 104 to 134 individuals in the both population samples, eight alleles were revealed for locus PLA2, thirteen for D3S1359, eleven for FGA, eight for D8S315 (kw38), ten for D8S1132, five for CYP19, and seven for D3S2459. They correspondingly constituted 10 to 39 genotypes therein. For most of the STRs, there was only a single allele active as the most frequent one among the others, except locus D3S1359 in Chinese samples (two alleles, 206 bp and 210 bp, frequency = 0.273 each). Also, the population genotype configurations were locus specific, varying in the patterns of commonest genotypes on each locus, e.g., one pattern for loci CYP19, D3S1359, and D8S315, one and two for loci PLA2 and D3S2459, two for locus D8S1132, and one and four for locus FGA. The distributions of observed genotypes were in Hardy-Weinberg Equilibrium. Furthermore, the seven STRs were exhibited highly polymorphic and informative for the both populations, and the alleles could be easily separated in electrophoresis and correctly interpreted with side-to-side allelic ladders. Together, the results suggest that the tri- and tetra-meric STRs are useful genetic markers for forensic practice.     

Restriction fragment length polymorphism analysis reveals different allele frequency and a linkage disequilibrium at locus D1S94 in neuroblastoma patients

Deletion of chromosome 1p and MYCN amplification have been reported as frequent abnormalities in human neuroblastoma. We studied loss of heterozygosity (LOH) in 50 (48 informative) Italian neuroblastoma patients by restriction fragment length polymorphisms (RFLPs) analysis using anonymous and hypervariable region (HVR) sequences. Twelve cases (25%) showed LOH at one or more loci. Locus D1S94 was the most frequently involved in LOH events (8/12) of deleted cases (66.6%). MYCN amplification was observed in 20% of patients which showed a significantly lower event-free survival probability (EFSp) (P = 0.004). We also studied the allelic distribution in the constitutional DNA of neuroblastoma patients (n = 44) and a matched group of healthy Italian subjects (n = 79) for loci D1S112 and D1S94. A significantly (P = 0.01) different allele frequency was detected for the two groups at locus D1S94, but not at D1S112. Moreover, the neuroblastoma population did not confirm the Hardy-Weinberg expectations at the former locus. This observation suggests the existence of an allelotype associated with neuroblastoma susceptibility.     

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.     

Scarlet fever in 1996]

A sample population of Rio de Janeiro, Brazil, was tested for D6S132, D7S467, and D17S26 VNTR loci to determine the fixed-bin frequencies of alleles. RFLP analysis was obtained by HaeIII-digested genomic DNA. The three VNTR loci meet Hardy-Weinberg expectations, and there is no evidence for association of alleles between the VNTR loci. The frequency data can be used in forensic analysis, in paternity tests and to estimate the frequency of a DNA profile in the general Brazilian population.     

Swiss population data and forensic efficiency values on 3 tetrameric short tandem repeat loci-HUMTH01, TPOX, and CSF1PO-derived using a STR multiplex system

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci were determined in a Swiss population sample (n = 100) using the GenePrint STR Multiplex System, electrophoresis of the PCR products in DNA sequencing gels and subsequent detection of allelic fragments by silver staining. The loci are HUMTH01, TPOX, and CSF1PO. The observed heterozygosities are 83.0%, 60.0%, and 72.0%, respectively. The discrimination power determined for the individual loci is 0.914, 0.780, and 0.860, respectively, and the combined discrimination power for the triplex is 0.997. All loci meet Hardy-Weinberg expectations and after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence. Moreover, independence of alleles at these STR loci with other PCR-based loci derived from the same Swiss population sample, previously reported, were considered. These loci were DQA1, LDLR, GYPA, HBGG, D7S8, GC and D1S80. Again, after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence among alleles at the 10 different PCR-based loci. Thus, the allelic frequency data can be used in human identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Swiss population.     

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.     

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.     

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.     

Linkage of genetic markers on human chromosomes 20 and 12 to NIDDM in Caucasian sib pairs with a history of diabetic nephropathy

The potential contribution of maturity-onset diabetes of the young (MODY) genes to NIDDM susceptibility in African-American and Caucasian NIDDM-affected sibling pairs with a history of adult-onset diabetic nephropathy has been evaluated. Evidence for linkage to NIDDM was found with polymorphic loci that map to the long arms of human chromosomes 20 and 12 in regions containing the MODY1 and MODY3 genes. Nonparametric analysis of chromosome 20 inheritance data collected with the MODY1-linked marker D20S197 provides evidence for linkage to NIDDM with a P value of 0.005 in Caucasian sib pairs using affected sibpair (ASP) analyses. Non-parametric analysis of chromosome 12 inheritance data collected with the MODY3-linked markers D12S349 and D12S86 provides evidence for linkage to NIDDM with P values of 0.04 and 0.006, respectively, in Caucasian sib pairs using similar analyses. No evidence for linkage of MODY1 and MODY3 markers to NIDDM in African-American sib pairs was observed. In addition, no evidence for linkage to MODY2 (glucokinase-associated MODY) was observed with either study population. Results of multipoint maximum logarithm of odds (LOD) score analysis were consistent with the ASP results. A maximum LOD score of 1.48 was calculated for linkage to MODY1-linked loci and 1.45 to MODY3-linked loci in Caucasian sib pairs. Tabulation of allele sharing in affected sib pairs with D20S197 and D12S349 suggests that affected sibling pairs may inherit susceptibility genes simultaneously from chromosome 20 and chromosome 12. The results suggest that genes contributing to NIDDM in the general Caucasian population are located in the regions containing the MODY1 and MODY3 genes.     

Ultrasound biomicroscopy of the anterior segment of the eyes of infants

Multiplex PCR amplification has been useful for gene mapping with polymorphic short tandem repeat (STR) loci. We have tested the four loci D20S470, D13S325, HumFOLP23 and D10S2325 for the simultaneous typing of more than 100 unrelated Koreans. This analysis allows a single base pair resolution and rapid typing with silver staining. The allele and genotype distributions are in accordance with Hardy - Weinberg expectations. These STR loci have proven useful for forensic analysis and paternity tests in which the variable number of tandem repeat (VNTR) loci have some limitations.     

United States population data on the multiplex short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--and the variable number tandem repeat locus D1S80

Allele frequencies for three tetrameric short tandem repeat (STR) loci HUMTHO1, TPOX, and CSF1PO and a variable number tandem repeat locus D1S80 were determined in United States Caucasian, African American, and Hispanic sample populations. All loci, except the TPOX locus in the Caucasian sample population, meet Hardy-Weinberg expectations. There is no evidence for association of alleles among the four loci. The allelic frequency data are similar to other comparable data within the same major population group.     

Factor V Leiden (G1691A), the prothrombin 3'-untranslated region variant (G20210A) and thermolabile methylenetetrahydrofolate reductase (C677T): a single genetic test genotypes all three loci--determination of frequencies in the S. Wales population of the UK

Simultaneous genetic diagnosis of factor V (FV) Leiden (G1691A), the prothrombin variant (G20210A) and the thermolabile methylenetetrahydrofolate reductase (MTHFR) variant (C677T) has been achieved using multiplex heteroduplex analysis. All three loci are amplified in a single polymerase chain reaction (PCR) containing test DNA and three heteroduplex generators, respectively detecting the three nucleotide substitutions. After PCR, the products are analysed directly without further manipulation and the resulting heteroduplex profiles permit straightforward interpretation of the respective genotypes. The multiplex test has been used to assess the prevalence and allele frequency of each of the three nucleotide substitutions in 300 individuals (150 males and 150 females) from the local (S. Wales) population. A prevalence of 8% and an allele frequency of 0.040 +/- 0.015 (95% confidence interval) was obtained for FV Leiden; the prothrombin variant showed a prevalence of 1% and an allele frequency of 0.007 +/- 0.006 (95% confidence interval); the MTHFR mutation showed a prevalence of 60% and an allele frequency of 0.377 +/- 0.039 (95% confidence interval). This method is applicable to investigation of large cohorts of patients with arterial or venous thrombotic disease.     

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.     

Placental enzyme polymorphisms in Canadian populations. II. Phosphoglucomutase

Phenotype distributions and allele frequencies of phosphoglucomatase loci PGM1, PGM2, and PGM3 were determined for four Canadian populations: SWO-Random, a randomly chosen group from southwestern Ontario; SWO-Caucasian, selected from SWO; Indian and Eskimo from the James and Hudson area. In the two population samples from southwestern Ontario, allele frequencies were similar to those of European populations but there was a marked excess of homozygotes at the PGM1 locus. In Indians the PGM1 1 allele had a frequency of 0.922, that of the PGM1 3 allele was 0.765.The allele frequencies for the Eskimo population were 0.848 for PGM1 1 AND 0.884 FOR PGM1 3. One rare phenotype was found at each of the PGM1 AND PGM2 loci.     

Lumbar epidural perineural injection: a new technique

Molecular variants of individual components of the renin-angiotensin system (RAS) are reported to constitute the inherited predisposition to some cardiovascular diseases in man, e.g. essential hypertension or myocardial infarction. The frequency of these variants depends highly on the race and population. Therefore, we examined the M235T molecular variant of the angiotensinogen gene and the I/D polymorphism of the ACE gene in Slovak healthy population, in patients with diagnosed essential hypertension and in patients who had undergone myocardial infarction. DNA from 241 subjects was tested for the presence of M235T and I/D molecular variants. The frequency of both these polymorphisms in the Slovak population is similar to other Caucasian populations. In the group of hypertensive patients, the frequency of the M235T molecular variant was increased compared to controls, predominantly in males (0.45 vs. 0.28), while in the I/D polymorphism the incidence of the D allele was the same for both controls and hypertensives (0.49 vs. 0.50). A significant increase in the D allele frequency compared to the controls occurred in the group of infarcted patients (0.63). The increased frequency of the M235T allele in hypertensive patients compared to the healthy population confirms that the M235T variants associated with increased blood pressure in the Slovak population. In the Slovak population, I/D polymorphism of the ACE gene is associated with myocardial infarction rather than with hypertension.     

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.     

Concomitant chemoradiotherapy for incompletely resected supratentorial low-grade astrocytoma in children: preliminary report

Interval mapping was used to identify putative quantitative trait loci (QTL) for blood pressure and cardiac mass on Chromosome (Chr) 3 in F1(S x R) x S population of 150 rats raised on an 8% NaCl diet. Two genetic markers 95.7 cM apart, D3Wox3 and D3Mco5 (tightly linked to Edn3), showed "suggestive" linkage to blood pressure (LOD = 2.0 and 1.8 respectively). In addition, D3Wox3 showed "suggestive" linkage to heart weight (LOD = 2.5), and D3Mco5 showed "suggestive" linkage to body weight-adjusted heart weight (LOD = 2.1). Congenic rats (designated S.R-Edn3) were constructed by introgressing the R-rat Edn3 allele (and flanking loci) into the S strain. On a 2% NaCl diet, S.R-Edn3 rats had lower blood pressure (21.4 mm Hg, P = 0. 0005) and heart weight (59 mg, P = 0.0038) compared with S rats, confirming the existence of a blood pressure QTL on Chr 3 near Edn3 even though QTL linkage analysis of blood pressure did not achieve stringent statistical criteria for significance. The results of the congenic experiment and the large distance between the two putative QTL suggest the presence of at least two independent blood pressure/cardiac mass QTL detectable on Chr 3 in the Dahl rat model of genetic hypertension.     

Evaluation of the ALF DNA sequencer for high-speed sizing of short tandem repeat alleles

DNA typing of short tandem repeat (STR) loci with automated real-time analysis of the fluorescent polymerase chain reaction (PCR) products has given forensic DNA analysis a new dimension. In the present work, the ALF DNA sequencer was evaluated for automated size determination of tetra-nucleotide STRs at high speed. Short gel plates, with a well-to-laser distance of 10 cm, allowed for the analysis of four STR loci (HUMvWF, HUMTH01, D21S11 and HPRT) in one gel lane in less than 75 min. Allele size determination was done with two external allelic ladders for each locus. Lane-to-lane variations were overcome by the inclusion in each lane of two fluorescent PCR products of constant size (123 and 375 bp) that migrated below and above the multiplex of the four STR loci. The accuracy of sizing and allele detection within and between different gels was high (99.89%) for all four STR systems investigated and the gels could be reloaded without a decrease in accuracy of the allele size estimation. This way, the throughput of the system was increased, which is of interest for linkage studies, gene mapping, and population diversity studies.