Polymorphisms of twelve short tandem repeat loci in a Taiwanese population and their application in parentage testing

With the advancement of techniques in molecular biology, rapid, sensitive, and reliable methods of DNA typing for parentage testing have become available. In this study, we evaluated the usefulness of multiplex polymerase chain reaction (PCR) with 12 unlinked short tandem repeat (STR) loci for paternity testing in Taiwan. The genetic informativeness of this test was then compared with that of conventional human leukocyte antigen (HLA) analysis in 167 parentage studies. The 12 STR loci alone provided a cumulative power of exclusion of up to 0.9998. Paternity was excluded in 59 (35.3%) cases, including 40 of 112 paternity trios and 19 of 55 paternity duos. In the 40 trios in which paternity was excluded, a mean of 6 (range, 3-9) incompatible STR markers were in the 19 duos in which paternity was excluded, a mean of 4 (range, 1-8) incompatible STR markers were noted. In the 72 trios in which the alleged paternity could not be excluded, the mean probabilities of paternity (PP) were 90.6863% with HLA testing alone, 99.9847% with STR analysis alone, and 99.9972% with combined HLA and STR analysis. In the 36 duos in which the alleged paternity could not be excluded, the mean PPs were 81.4768% with HLA testing alone, 99.6124% with STR analysis alone, and 99.9145% with combined HLA and STR analysis. These results suggest that STR analysis is very powerful when used alone for paternity trio testing and when combined with conventional serologic HLA typing for duo parentage testing in the Taiwan population.     

Short tandem repeat polymorphism at the HUMCD4 and HUMF13B loci in a Croatian population

OBJECTIVE: To explore the action mechanism of Qiangji Jianli Capsule (QJJLC) treating myasthenia gravis. METHODS: Internal receptor permeation and degradation test were performed. RESULTS: Volume of receptor permeation in the group with QJJLC at 96 hours was 902.50 +/- 37.48 cpm/mg, while that of control group 738.45 +/- 35.41 cpm/mg. Half-life of receptor degradation in treatment group was 52 hours and that of control 38 hours. Their difference was very significant (P < 0.001). CONCLUSION: QJJLC could accelerate permeation of N-aectylcholine receptor to surface of diaphragm cell membrane and decelerate receptor degradation. It could also increase accumulative amounts of functional receptor in unit time and keep dynamic equilibrium of receptor metabolism in pathologic condition.     

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.     

Allele frequencies of six highly polymorphic DNA loci in the Croatian population

The organization of synthetic oligopeptide trivaline (1) complexes with four types of circular superhelical DNA preparations was studied by electron microscopy. The DNA molecules in the preparations investigated had different sizes ranging from 2.9 kb to 21.0 kb. Two plasmids contained bent DNA sequences from minicircles of kinetoplast DNA of Leishmania gymnodactili and Trypanosoma boissoni. The main structures in all preparations observed were circular compact particles which coincide in their appearance and compaction coefficient (3,5-3,7) with triple rings described earlier. But along with triple rings the new types of compact structures were observed having the shape of a ring with attached rod or the shape of two compact rings attached to each other by a region of compact fiber. The latter structures could be observed in significant quantities in case of DNA preparations longer than 10 kb. The conclusions can be made that due to TVP stimulated compaction of circular DNA molecules compact fibers containing both two or three DNA duplexes arranged side by side can be formed. It is shown that presence of bent DNA sequences stimulates the formation of structures containing more than one triple ring. It demonstrates the possibility of the primary DNA structure influence on the compaction process in case of the circular molecules. The new ways of circular DNA folding described can be of importance for understanding of DNA organization in different cell structures.     

Allelic imbalance and instability of microsatellite loci on chromosome 1p in human non-small-cell lung cancer

The mapping of allelic loss on the short arm of chromosome 1 has been performed in non-small-cell lung cancer. We used a set of 11 microsatellite loci spanning 1p to examine the frequency of allelic imbalance in a panel of 58 tumours. Fifty-one of 58 (87.9%) cases have shown somatic allelic loss at one or more loci tested. The two shortest regions of the overlap (SRO) of the deletions have been identified: SRO 1 at 1p13.1 and SRO 2 at 1p32-pter. Allelic losses at these regions have been compared among adenocarcinoma and squamous cell carcinoma and no difference has been found. In contrast to SRO 1, deletions at SRO 2 significantly correlated with advanced stage of the disease as well as post-operative metastasizing and relapse. These data may suggest that SRO 1 and SRO 2 can harbour tumour-supressor genes (TSGs) involved in different stages of NSCLC development. SRO 2 is still quite large and its refined mapping should help attempts to clone and identify the putative TSG(s). Microsatellite instability (replication errors) affecting only 6 (10.3%) of 58 tumour samples is an infrequent genetic alteration at the loci tested.     

Allelic loss on chromosome 18q as a prognostic marker in stage II colorectal cancer

The aim of the study was to elucidate the vasodilatory mechanism due to Cu2+ by assessing nitric oxide (NO) production as determined by NOx (NO, NO2-, and NO3-) that is released from human pulmonary arterial endothelial cell (HPAEC) monolayers using a NO chemiluminescence analyzer, and also to assess Ca2+ movement using 45Ca and fura 2 in HPAEC. Cu2+ (10(-6)-10(-4) M) significantly increased NO production in a dose-dependent manner when extracellular Ca2+ was present. 45Ca influx into the adherent cells was dose-dependently enhanced by Cu(2+) (10(-6)-10(-4) M), but not by Mn(2+), Zn(2+) or Fe(2+). [Ca2+]i, measured by monitoring the fluorescence changes of fura 2, was significantly elevated in the presence of Cu2+. The increase in [Ca2+]i induced by Cu2+ was inhibited by either diethyldithiocarbamate (DDC) or the depletion of extracellular Ca2+. The dihydropyridine receptor agonist, BayK8644, significantly attenuated the Cu2+-induced increase in [Ca2+]i in a dose dependent manner and nitrendipine or nifedipine, the dihydropyridine receptor antagonists, dose-dependently inhibited a Cu2+-induced increase in [Ca2+]i. These results suggest that Cu2+ activates eNOS through the mechanism of [Ca2+]i elevation due to Ca2+ influx into HPAEC and that the Cu2+-induced [Ca2+]i elevation in HPAEC is likely due to activation of the dihydropyridine-like receptors.     

Analysis of nine short tandem repeat (STR) loci in the Slovenian population

A polymerase chain reaction (PCR)-based short tandem repeat (STR) system consisting of nine loci has recently been introduced in Slovenia for use in routine forensic identity testing. Fluorescently labelled PCR products were analysed using an ABI PRISM 310 Genetic Analyzer. The STR loci analysed exhibit between 6 and 14 observed alleles per locus and have a combined matching probability of 2.3 x 10(-10).     

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.     

Allelic loss on chromosome 22 in oral cancer: possibility of the existence of a tumor suppressor gene on 22q13

PURPOSE: To model the influence of hypoxic radioprotection in fractionated treatments over a range of fraction sizes. To determine whether there is a "therapeutic window" of dose per fraction where hypoxic radioresistance could be reduced, and if so, where it occurs in different cell lines. MATERIALS AND METHODS: A mathematical model has been used to simulate the response of cells to low doses of radiation, in the region of clinical interest. We have used the inducible repair variant of the linear quadratic (LQ) equation, with a hypersensitive region (alphaS) at low doses that gradually transforms to the accepted "resistance" in the shoulder region (alphaR). It contains two new parameters, the ratio alphaS/alphaR, and D(C). We have accepted that the "induction dose" D(C) is modified by anoxia to the same extent as the other parameters. We have initially modeled using theoretical parameters and then checked the conclusions with 14 sets of published experimental data for cell lines investigated for inducible repair. RESULTS: We have computed the clinical hypoxic protection (OER') as a function of dose per fraction in simulations of clinical fractionated schedules. We have identified a therapeutic window in terms of dose per fraction at about 0.5 Gy, where the OER' is minimized, regardless of the precise cell survival curve parameters. The minimum OER' varies from one cell line to another, falling to about 1.0 if alphaS/alphaR = 6-10 and even far below 1.0 if alphaS/alphaR > or = 20. DISCUSSION: Hyperfractionation using 0.5 Gy fractions may therefore be more effective than oxygen mimetic chemical sensitizers, since it could even make some tumor cells more sensitive than oxic normal tissues. The tumor lines that benefit most from this type of sensitization are those with the highest intrinsic oxic radioresistance, i.e. those with high SF2 values.     

Allelic loss on a chromosome 17 in ductal carcinoma in situ of the breast

Multiple tumor suppressor genes are implicated in the oncogenesis and progression of invasive carcinoma of the breast. To investigate the chronology of genetic changes we studied loss of heterozygosity on chromosome 17 in ductal carcinoma in situ, a preinvasive breast cancer. A microdissection technique was used to separate tumor from normal stromal cells prior to DNA extraction and loss of heterozygosity was assayed mainly using simple sequence repeat polymorphism markers and the polymerase chain reaction. Loss of heterozygosity on 17p was observed in 8 of 28 tumors (29%) when compared with normal control DNA, whereas no loss was seen on 17q, suggesting that at least one locus on 17p is involved early in the development of breast cancer.     

Analysis of allele distribution for six short tandem repeat loci in the French Canadian population of Québec

Short tandem repeat (STR) loci represent a rich source of highly polymorphic markers in the human genome which are useful for the purposes of forensic identification and determination of biological relatedness of individuals. Here, as a part of an ongoing extensive study, we report the analysis of a multilocus genotype survey of 642 to 870 chromosomes in the French Canadian Caucasian population of Québec at six STR loci. The loci HUMCSF1PO, HUMTPOX, HUMTH01, HUMF13A01, HUMFESFPS, and HUMvWA were typed using two multiplex polymerase chain reactions (PCR). Amplified DNA samples were subsequently analyzed by polyacrylamide gel electrophoresis followed by silver staining. The heterozygote frequencies of the loci range from 0.614 to 0.820 (0.661 to 0.818 expected) and the number of alleles from 7 to 12 per locus. Although statistically significant deviation from Hardy-Weinberg expectations of genotype frequencies was noted at some loci by one or more tests, in general, the genotype frequencies are well estimated from the product of allele frequencies at all loci. The most frequent six-locus genotype is expected to occur in the French Canadian population with a frequency of 3.50 by 10(-5) and together, these six loci have an average probability of discrimination of 0.9999985. The study presented here indicates that these six STR loci are informative genetic markers for identity testing purposes in the French Canadian Caucasian population of Québec.     

Allelic deletion on chromosome 17p13.3 in early ovarian cancer

Multiple chromosome 17 loci may be involved in ovarian carcinogenesis. Fifty-seven sporadic ovarian epithelial tumors were examined for loss of heterozygosity at 15 loci on chromosomes 17p. Eighty % (39 of 49) of informative tumors had allelic loss in 17p13.3 at D17S30, D17S28, or both loci within this region, including 3 of 7 tumors of low malignant potential and 4 of 5 nonmetastatic carcinomas. The smallest region of overlapping deletions extends from D17S28 to D17S30, a distance of 15 kb. Furthermore, several tumors have breakpoints within the region detected by the D17S30 probe. Chromosome 17p13.3 genes with potential tumor suppressor function include HIC-1, DPH2L (N. J. Phillips et al. Isolation of a human diphthamide biosynthesis gene on chromosome 17p13.3, submitted for publication)/OVCA1, PEDF, and CRK. The HIC-1 coding sequence lies i kb centromeric to the D17S28-S17S30 region of deletion (M. Makos Wales et al., Nat. Med., 1:570-577, 1995) but remains a candidate because 5'-regulatory elements may lie within the critical region. Portions of the DPH2L/OVCA1 coding sequence lie within the D17S28-D17S30 interval. Somatic cell hybrid analysis places PEDF in an interval including D17S28, D17S30, and D17S54, whereas CRK is excluded from this interval. Chromosome 17p13.3 loss precedes TP53 and BRCA1 region deletions because the latter changes are see only in high-stage carcinomas. Microsatellite instability plays only a minor role in sporadic ovarian carcinogenesis because only 1 of 57 tumors showed this finding.     

Allelic deletions on chromosome 11q13 in multiple endocrine neoplasia type 1-associated and sporadic gastrinomas and pancreatic endocrine tumors

Endocrine tumors (ETs) of pancreas and duodenum occur sporadically and as a part of multiple endocrine neoplasia type 1 (MEN1). The MEN1 tumor suppressor gene has been localized to chromosome 11q13 by linkage analysis but has not yet isolated. Previous allelic deletion studies in enteropancreatic ETs suggested MEN1 gene involvement in tumorigenesis of familial pancreatic ETs (nongastrinomas) and sporadic gastrinomas. However, only a few MEN1-associated duodenal gastrinomas and sporadic pancreatic nongastrinomas have been investigated. We used tissue microdissection to analyze 95 archival pancreatic and duodenal ETs and metastases from 50 patients for loss of heterozygosity (LOH) on 11q13 with 10 polymorphic markers spanning the area of the putative MEN1 gene. Chromosome 11q13 LOH was detected in 23 of 27 (85%) MEN1-associated pancreatic ETs (nongastrinomas), 14 of 34 (41%) MEN1-associated gastrinomas, 3 of 16 (19%) sporadic insulinomas, and 8 of 18 (44%) sporadic gastrinomas. Analysis of LOH on 11q13 showed different deletion patterns in ETs from different MEN1 patients and in multiple tumors from individual MEN1 patients. The present results suggest that the MEN1 gene plays a role in all four tumor types. The lower rate of 11q13 LOH in MEN1-associated and sporadic gastrinomas and sporadic insulinomas as compared to MEN1 nongastrinomas may reflect alternative genetic pathways for the development of these tumors or mechanisms of the MEN1 gene inactivation that do not involve large deletions. The isolation of the MEN1 gene is necessary to further define its role in pathogenesis of pancreatic and duodenal ETs.     

Genetic response from marker assisted selection in an outbred population for differing marker bracket sizes and with two identified quantitative trait loci

Effect of flanking quantitative trait loci (QTL)-marker bracket size on genetic response to marker assisted selection in an outbred population was studied by simulation of a nucleus breeding scheme. In addition, genetic response with marker assisted selection (MAS) from two quantitative trait loci on the same and different chromosome(s) was investigated. QTL that explained either 5% or 10% of phenotypic variance were simulated. A polygenic component was simulated in addition to the quantitative trait loci. In total, 35% of the phenotypic variance was due to genetic factors. The trait was measured on females only. Having smaller marker brackets flanking the QTL increased the genetic response from MAS selection. This was due to the greater ability to trace the QTL transmission from one generation to the next with the smaller flanking QTL-marker bracket, which increased the accuracy of estimation of the QTL allelic effects. Greater negative covariance between effects at both QTL was observed when two QTL were located on the same chromosome compared to different chromosomes. Genetic response with MAS was greater when the QTL were on the same chromosome in the early generations and greater when they were on different chromosomes in the later generations of MAS.     

Analysis of the short tandem repeat systems HumVWA and HumF13B in a population sample from northern Thailand

Adenylate kinase activity originating from erythrocytes has been shown to be distinct from muscle adenylate kinase or myokinase activity, until now considered to be identical enzyme activities. The two activities can be differentiated by electrophoretic fractionation, thus making it possible to quantify the erythrocyte adenylate kinase activity present in serum.     

Gene frequencies of human platelet antigens on glycoprotein IIIa in Japanese

BACKGROUND: Polymorphism of glycoprotein IIIa on human platelets is one of the factors in alloimmunization that causes neonatal alloimmune thrombocytopenia and refractoriness to platelet transfusion. STUDY DESIGN AND METHODS: DNA typing methods were originally developed to determine the genotypes of five human platelet antigen (HPA) systems located on glycoprotein IIIa: HPA-1, HPA-4, HPA-6W, HPA-7W and HPA-8W. The gene frequencies of these platelet antigens were determined by DNA typing of 331 unrelated Japanese donors. RESULTS: The gene frequencies of the low-frequency antigens were 0.002, 0.011, and 0.027 for HPA-1b, HPA-4b, and HPA-6W(b), respectively. All 331 Japanese donors tested were HPA-7W(a/a) and HPA-8W(a/a). Moreover, in the present study, none of the donors tested had two or more of these low-frequency antigens. CONCLUSION: The risk of neonatal alloimmune thrombocytopenia and refractoriness to platelet transfusion induced by the antigens of the HPA-1, HPA-7W, and HPA-8W systems was extremely rare in Japanese. However, attention must be paid to the involvement of the HPA-4 and HPA-6W systems in these clinical disorders.     

Regional differentiation of blood group frequencies in the Polish population

The paper presents frequency distributions of alleles of eight blood group systems (ABO, MN, Rh, Hp, Gm(a), AcP, PGM1, EsD) in the Polish population. The blood group determinations concerning 10521 individuals (were carried out during paternity testing in regional serological laboratories throughout the country). Detailed information on the place of residence for all the subjects was also available. Blood group frequencies of subjects living in five regions of Poland were compared with historical date. The analysis has shown an almost complete disappearance of genetic variability in respect of the analysed traits between local populations inhabiting various regions of Poland.     

Human in vivo somatic mutation measured at two loci: individuals with stably elevated background erythrocyte glycophorin A (gpa) variant frequencies exhibit normal T-lymphocyte hprt mutant frequencies

The P3 event-related potential (ERP) component was recorded from 7- to 18-year-old children of alcoholics (COAs, n = 50) and age- and sex-matched control children (n = 50) using a visual oddball paradigm, involving nontarget (76%), target (12%), and novel (12%) stimuli. Topographic maps of P3 and associated scalp current density were obtained to supplement a topographic profile analysis. COAs manifested a smaller amplitude P3 to target stimuli over the centroparietal, parietal, and occipital scalp locations than controls. Also, COAs exhibited a smaller amplitude P3 to novel stimuli over the occipital scalp than controls. There were no significant differences between COAs and controls in the P3 scalp topography, indicating that differences in intracranial source strength rather than in source configuration were responsible for the between-group amplitude differences. Also, no significant group differences were observed in the P3 peak latency or in behavioral performance. These results support the notion that the visual P3 may provide a vulnerability marker of alcoholism.