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PubMed2000

Single-fiber PCR in MELAS(3243) patients: correlations between intratissue distribution and phenotypic expression of the mtDNA(A3243G) genotype.

We performed morphological, biochemical, and genetic studies, including single-fiber PCR (sf PCR), on muscle biopsies obtained from a mother and daughter with MELAS syndrome due to the A3243G transition of mitochondrial DNA (mtDNA). The severity of muscle involvement appeared quite distinct, in spite of the fact that both patients segregated similar mutant mtDNA levels on total muscle DNA. The daughter did not show any clinical muscle involvement: muscle biopsy revealed many ragged red fibers (RRFs) mostly positive for cytochrome-c oxidase (COX) activity. In contrast, her mother had developed a generalized myopathy without progressive external ophthalmoplegia (PEO), morphologically characterized by many COX-negative RRFs. Single-muscle fiber PCR demonstrated in both patients significantly higher percentages of wild-type mtDNA in normal fibers (daughter: 23.25 +/- 15.22; mother: 43.13 +/- 26.11) than in COX-positive RRFs (daughter: 11.25 +/- 5.22, P < 0.005; mother: 9.12 +/- 5.9, P < 0.001) and in COX-negative RRFs (daughter: 8.9 +/- 4.2, P < 0.001 mother: 4.8 +/- 2.8, P < 0.001). Wild-type mtDNA levels resulted higher also in COX-positive vs. COX-negative RRFs (daughter: P < 0.05; mother: P < 0.001). Our data confirm a direct correlation between A3243G levels and impairment of COX function at the single-muscle fiber level. Moreover, the evidence of a clinical myopathy in the patient with higher amounts of COX-negative RRFs bolsters the concept that a differential distribution of mutant mtDNAs at the cellular level may have effects on the clinical involvement of individual tissues. However, the occurrence of a similar morphological and biochemical muscle phenotype also in PEO(3243) patients suggests that other genetic factors involved in the interaction between mitochondrial and nuclear DNA, rather than the stochastic distribution of mtDNA genomes during embryogenesis, are primarily implicated in determining the various clinical expressions of the A3243G of mtDNA.

Adolescent↗
PubMed2006

The CHRNE 470del20 mutation causing congenital myasthenic syndrome in South African Brahman cattle: prevalence, origin, and association with performance traits.

Genotyping of the South African, registered, Brahman cattle population for the 470del20 mutation in the CHRNE gene causing congenital myasthenic syndrome (CMS) was carried out in 1,453 animals. Overall prevalence of carriers was 0.97% (0.50 to 1.68%, 95% confidence interval). Carrier prevalence among breeding bulls in 2004 was 1.22% (0.65 to 2.15%, 95% confidence interval), and had not changed significantly since 2000. Using segregation analysis, CMS genotype probabilities were calculated for all 612,219 animals in the pedigree, leading to the identification of 2 founder animals as the most likely original carriers. Pedigree analysis revealed no ancestors common to all known carriers, but rather that the mutation had been introduced at least twice into the South African Brahman population, probably via animals imported from the United States. The effects of CMS genotype probability on adjusted birth, 200-d, 400-d, and 600-d BW, as well as on EBV for birth, 200-d, 400-d, and 600-d BW, and milk, were estimated, accounting for effects of sire. Heterozygosity for the CHRNE 470del20 mutation was associated with a 13.3-kg increase in adjusted 600-d BW (P = 0.03). Positive effects of CMS carrier status on all BW EBV were found, but no effect was found on milk EBV. We conclude that CMS carriers have a BW advantage at 600 d and possibly also at birth, 200 d, and 400 d. This may confer a selective advantage and tend to increase the frequency of the mutation.

Animals↗
PubMed2005

Influence of genotype-temperature interaction on pollen performance.

Pollen competition and selection have significant evolutionary consequences, but very little is known about how they can be modulated. We have examined in cherry (Prunus avium L.) how pollen performance is affected by the genotype of the pollen and by the environmental conditions under which it grows, namely the pistilar tissue and temperature. The different pollen donor genotypes tested in this work differed in their behaviour both in vitro and in vivo and this behaviour was modulated depending on the female recipient they grew on. Furthermore, there was a significant temperature-genotype interaction that affected the pollen tube population census that succeeded in reaching the base of the style. The combination of these three factors, while enabling a capacity of response to variations in environmental pressures, could maintain variability in pollen performance avoiding the fixation of the genes that control pollen tube growth rate.

Flowers↗
PubMed2004

Hepatitis C genotyping by denaturing high-performance liquid chromatography.

Determination of the hepatitis C virus (HCV) genotype for infected patients increasingly has become accepted as the standard of care. Genotype assignment helps in assessing disease prognosis and assists in establishing the appropriate duration of treatment. The great genetic diversity of HCV, with 11 major genotypes and >70 subtypes, contributes to the technical difficulty of genotype testing. While the "gold standard" for testing is nucleic acid sequencing, a variety of hybridization assays, including the line probe assay, have been developed to provide more rapid and accessible forms of testing. The aim of this study was to determine whether denaturing high-performance liquid chromatography (dHPLC) could be used as a clinical method for distinguishing HCV genotypes 1, 2, 3, and 4. A portion of the 5' untranslated region of the HCV genome was amplified by heminested multiplex reverse transcription PCR. The two amplicons then were analyzed by dHPLC analysis and compared to the genotypes determined by sequence analysis. After 115 specimens were analyzed as standards, 200 masked specimens (specimens whose identity was not known before testing) were analyzed to determine the concordance of the assay. The assay had a concordance of 96% at the genotype level and a concordance of 87% at the subtype level. However, the dHPLC method was not as accurate as other reported methods of HCV genotyping. This is the first time that HCV genotyping has been performed by dHPLC.

5' Untranslated Regions↗
PubMed2006

Systematic evaluation of association between the microsomal glutathione S-transferase 2 common variation and psoriasis vulgaris in Chinese population.

Several recent studies have demonstrated the possible involvement of the microsomal glutathione S-transferase 2 (MGST2) gene in the pathogenesis of psoriasis. The objectives of this work are to determine whether the genetic polymorphisms of the MGST2 gene were associated with an increased risk of psoriasis in Chinese patients. We first characterized the linkage disequilibrium pattern within MGST2 and identified single-nucleotide polymorphisms (SNPs) for tagging common genetic variants. Genotype- and haplotype-based analyses were then performed by genotyping the Tag SNPs in a large-scale sample of cases and controls. We characterized the linkage disequilibrium pattern within MGST2 using 12 densely distributed SNPs and identified 6 SNPs for tagging common genetic variants. We then performed an association analysis by genotyping the six SNPs in 552 cases and 384 controls, but none of the genotype- and haplotype-based analyses revealed significant evidence for association. We also performed family-based association analysis by genotyping the six SNPs in 95 trios; no evidence for association was identified. Our comprehensive genetic analysis of MGST2 common variants in a large Chinese sample of psoriasis did not provide any supporting evidence for MGST2 to be the susceptibility gene within the PSORS9 locus.

Adolescent↗
PubMed1999

Significant associations of HLA-B*5101 and B*5108, and lack of association of class II alleles with Behçet's disease in Italian patients.

Behçet's disease has been known to be strongly associated with human leukocyte antigen (HLA) B51, one of the split antigens of HLA-B5. An increased incidence of HLA-B51 in the patient group has also been reported in an Italian population. Since the B51 antigen has been recently identified to comprise nine alleles, B*5101-B*5109, we performed HLA-B51 allele genotyping by the polymerase chain reaction-sequencing based typing (PCR-SBT) method as well as serological HLA-A and -B typing among 21 Italian patients with Behçet's disease in order to investigate whether there is any correlation of one particular B51-associated allele with Behcet's disease. In addition, HLA class II genotyping was performed by the PCR-restriction fragment length polymorphism (RFLP) method. As a result, only the phenotype frequency of the B51 antigen was found to be significantly increased in the patient group as compared to the ethnically matched control group by the corrected P-value analysis (71.4% in patients vs. 17.9% in controls; chi2 = 14.26, Pc = 0.0042, R.R. = 11.5). In the B51 allele genotyping, 11 out of 15 B51-positive patients were B*5101 and the remaining four were B*5108, whereas all of 5 normal controls were B*5101, showing significant association of each allele with Behçet's disease. No significant difference was observed between the patient and control groups in the HLA class II allelic distribution. This study revealed a strong association of Behçet's disease in Italian with B*5108 as well as B*5101, providing important insight into the molecular mechanism underlying an HLA association with Behçet's disease.

Alleles↗
PubMed2005

Neurological soft signs are associated with APOE genotype, age and cognitive performance.

Neurodegeneration is associated with increased frequency of neurological soft signs (NSS). We designed the present study to investigate the association between NSS and subjective memory complaints, cognitive function and apolipoprotein E genotype in a community-dwelling sample of volunteers participating in an ongoing longitudinal program investigating predictors of cognitive decline. NSS were found to be associated with apolipoprotein E (APOE) epsilon4 genotype (p = 0.015), age (p = 0.012) and poor cognitive performance, as assessed by the Mini Mental State Examination (p = 0.053). There was no significant difference between subjects with and without memory complaints in relation to the frequency of NSS (p = 0.130). The association with age and the APOE epsilon4 genotype suggests that the systematic investigation of NSS may contribute to identify subjects at risk of clinically significant cognitive decline in later life.

Adult↗
PubMed2005

Frequency of bovine Nramp1 (Slc11a1) alleles in Holstein and Zebu breeds.

Natural resistance against brucellosis in cattle is linked to the Nramp1 gene, which encodes a divalent cation transporter that localizes in the phagolysosome membrane in macrophages. Nramp1 gene in mouse plays a critical role in innate immunity favoring bacterial killing by macrophages in addition to its influence on adaptative immunity. Polymorphisms at the bovine Nramp1 3' untranslated region (3'UTR), detectable by Single Strand Conformational Analysis (SSCA), are associated with natural resistance against brucellosis. Such polymorphisms are associated with variation in the number of GT repeats. This study compared the frequency of Nramp1 3'UTR polymorphisms between Zebu and European bovine breeds. Eighty-one Holsteins (Bos taurus taurus) and 167 Zebu (Bos taurus indicus), including the following breeds: Nelore (n=95), Guzerá (n=37), and Gir (n=35), totaling 248 pure breed cattle studied. DNA extraction was performed using the guanidium protocol and genotyping was performed by SSCA. DNA from cattle considered genotypically resistant to brucellosis resulted in a single band (homozygous) with 175bp, corresponding to the 3'UTR with 13 GT pairs (GT13), whereas DNA from genotypically susceptible cattle generated one single band with 177bp (homozygous GT14) or double bands with both 175 and 177bp, or 175 and 179bp (heterozygous GT13/GT14 or GT13/GT15, respectively). A marked difference in the frequency of alleles was detected between the Zebu and Holstein cattle. Holsteins had an extremely homogeneous genotype, with 100% of the individuals with a GT13 genotype. In sharp contrast the Nelore breed had the most heterogeneous genotype with four allelic combinations, namely, homozygous GT13, homozygous GT14, heterozygous GT13/GT14, and heterozygous GT13/GT15. When the Zebu breeds were compared to each other, the only significant difference observed was the frequencies of the genotypes GT13 and GT14 between the Nelore and Guzerá breeds. The knowledge of allelic frequencies in different breeds of cattle may prove to be very useful in the future for planning breeding strategies for selection of resistant cattle.

3' Untranslated Regions↗
PubMed2003

Clinical applications of denaturing high-performance liquid chromatography-based genotyping.

AIM: To develop and evaluate heteroduplex forming templates (HFTs) as a common set of molecular standards for genotyping by denaturing high-performance liquid chromatography (DHPLC) using hypervariable regions of human mitochondrial DNA (mtDNA) as a model system. METHODS: Hypervariable regions 1 and 2 from the mtDNA D-loop of 22 maternally related and unrelated human volunteers were amplified by polymerase chain reaction (PCR) and individually mixed with each of three HFTs. Following denaturation and reannealing of the mixture, the resulting hetero- and homoduplicies were separated by DHPLC using temperature-modulated heteroduplex analysis. RESULTS: Each of three HFTs, when cross-hybridized with a target mtDNA amplicon, induced the formation of an assemblage hetero- and homoduplex peaks, which were uniquely characteristic of a given mtDNA sequence variant. The mtDNA DHPLC profiles obtained in the current study were identical between maternal relatives and different between unrelated individuals--consistent with uniparental maternal inheritance of mtDNA in humans. CONCLUSION: DHPLC in combination with a common set of HFTs targeted to a locus of interest can be used as a reliable means of genotyping. DHPLC profiles can be readily stored as a bit-coded string of hetero- and homoduplex peak retention times to form a searchable database. This approach to DHPLC genotyping will have immediate utility in extended pedigree analyses, where it will allow rapid sorting and/or confirmation of maternal lineages. Additional applications of DHPLC profiling include the discovery and scoring of clinically relevant nuclear and mitochondrial loci.

Chromatography, High Pressure Liquid↗
PubMed2006

Association study between C-reactive protein genes and ischemic stroke in Japanese subjects.

BACKGROUND: C-reactive protein (CRP) is reported to be involved in the development of atherosclerosis. Elevated CRP levels are considered to be a predictor of ischemic stroke (IS) in elderly individuals. Some single-nucleotide polymorphisms (SNP) are reportedly associated with elevated CRP levels. The aims of this study were to genotype some of the SNP in the human CRP gene and to assess the association between the CRP gene and IS. METHODS: Japanese patients with IS (72.4 +/- 8.2 years of age, n = 152) and elderly Japanese subjects without IS (78.0 +/- 4.2 years of age, n = 304) were genotyped for four SNP of the human CRP gene: rs1341665, rs1800947, rs1130864, and rs1205. Each genotyping was performed using the TaqMan SNP genotyping assay. The haplotype-based association study was assessed with a permutation test. RESULTS: The genotype rs1800947 was statistically significant between patients with IS and control subjects (CC+GC versus GG variant, P = .016 by multiple logistic regression analysis). This analysis revealed that the CC+GC variant of rs1800947 was an independent risk factor of IS. All four SNP were located in one haplotype block. The haplotype was constructed using rs1341665, rs1800947, and rs1130864, in that order. There was a significant association between IS and the C-C-C haplotype (P = .015). CONCLUSIONS: The rs1800947 SNP and the C-C-C haplotype in the CRP gene appear to be prognostic markers of ischemic stroke and this polymorphism could be a useful genetic marker.

Aged↗
PubMed2006

Host cytokine genotype is related to adverse prognosis and systemic inflammation in gastro-oesophageal cancer.

BACKGROUND: Systemic inflammation has been linked with reduced survival in cancer, however, the role of the host cytokine genotype versus tumour phenotype in the generation of this response is not clearly established. This study examined the relationship between cytokine polymorphisms (IL-1beta 511, IL-6 174, IL-10 1082, TNFalpha 308 and LTalpha +252) and serum cytokine concentrations, serum CRP concentration and survival duration in patients with gastro-oesophageal malignancy. METHODS: Two hundred and three newly diagnosed patients with gastric or oesophageal cancer had serum CRP and cytokine concentrations determined by ELISA. SNP genotyping was performed by Taqman allelic discrimination genotyping and compared with the genotype observed in 266 healthy volunteers. Clinico-pathological information was collected prospectively and survival duration was recorded. RESULTS: Distribution of the cytokine genotypes was similar between patients and controls. The IL-6 174 CC and IL-10 1082 GG genotypes were associated with elevated serum CRP (P = .03, P = .01, respectively; Mann-Whitney U test) and sTNF-R (P = .015, P = .02) concentrations. These genotypes were also associated with reduced survival duration (P = .01, P = .047; log-rank test). TNFalpha AA genotype was also associated with reduced survival duration on univariate (P = .032) and multivariate analysis (P = .006, multivariate model), but not with inflammatory markers. No other cytokine polymorphisms were associated with systemic inflammatory markers or prognosis. CONCLUSIONS: There is a pro-inflammatory cytokine haplotype (IL-6 CC, IL-10 GG, TNFalpha AA) that is associated with adverse prognosis that may act, at least in part, through an inflammatory mediated mechanism. Determining patients' cytokine haplotype may improve prognostication and allow stratification for intervention studies.

Adolescent↗
PubMed2005

Model for assessment of proficiency of human immunodeficiency virus type 1 sequencing-based genotypic antiretroviral assays.

Use of sequencing-based genotyping as a diagnostic assay for human immunodeficiency virus (HIV) antiretroviral resistance is increasing. Periodic evaluation of the proficiency of laboratories performing this assay should be established. It is important to identify components of the assay that influence the generation of reliable sequencing data and that should and can be monitored. A model was developed to determine what parameters were reasonable and feasible for assessing the performance of genotyping assays. Ten laboratories using the genotyping platform, HIV-1 Genotyping System (HGS) v. 1 and software versions 1.1 or 2.0, participated in two rounds of testing. For each round, each group was sent a panel consisting of three clinical samples to sequence in real time. Six months later, seven laboratories using the TRUGENE HIV-1 Genotyping Kit participated in a separate round, working with both panels at the same time. Analysis of the data showed that one main indicator of genotyping proficiency was achievement of > or =98% sequence homology of a sample tested to a group consensus sequence for that sample. A second was concordant identification of codons at sites identified with resistance mutations in the sample, although scoring of these criteria is still undetermined from this study. These criteria are applicable to all sequence-based genotyping platforms and have been used as a baseline for assessing the performance of genotyping for the determination of antiretroviral resistance in our ongoing proficiency program.

Anti-HIV Agents↗
PubMed2003

A large kindred with familial cold autoinflammatory syndrome.

BACKGROUND: Familial cold autoinflammatory syndrome (FCAS), formerly known as familial cold urticaria, is a rare condition characterized by fever, rash, and arthralgias elicited by exposure to cold. Recently, mutations responsible for FCAS were identified in a novel gene (CIAS1), making it possible to confirm the diagnosis in most patients. OBJECTIVE: We present a summary of clinical data from a large family with FCAS to further define the characteristics of the disorder and to validate previously proposed clinical criteria. METHODS: A total of 73 participants were evaluated by interview and questionnaire, including 36 affected individuals. Responses from the questionnaire were analyzed and comparisons of proportions were made using the Z test. DNA was isolated and genotyping was performed on all subjects. Affected haplotypes (genotype patterns) were identified and used to confirm the diagnosis. Sequencing of the CIAS1 gene was performed in selected patients to confirm the mutation. RESULTS: The prevalence of rash, fever/chills, joint complaints, nausea, headache, and thirst were not significantly different from previously reported proportions. There was statistically significant differences in conjunctivitis, sweating, and drowsiness with alpha = 0.01. The mean temperature required to produce symptoms was 22 degrees C, and the average earliest onset of symptoms after exposure was 1.5 hours. CONCLUSIONS: Applying the proposed clinical criteria, 41% of affected subjects met all six criteria, 90% met five criteria, and 100% met four criteria for FCAS. None of the unaffected subjects met more than two criteria. Using a threshold of 4 of 6 clinical criteria, the data support the diagnostic validity of the proposed clinical criteria.

Adolescent↗
PubMed2004

Effect of low-density lipoprotein receptor mutation on lipoproteins and cardiovascular disease risk: a parent-offspring study.

Studies on the clinical consequences of different low-density lipoprotein (LDL) receptor genotypes in adult patients have yielded conflicting results. We hypothesized that children with familial hypercholesterolemia (FH) provide a better model to perform genotype-phenotype analyses than adults. We tested this hypothesis and assessed the effect of LDL receptor genotypes on lipoprotein levels and on parental risk of cardiovascular disease (CVD) in a pediatric FH cohort. We identified 75 different LDL receptor mutations in 645 children with heterozygous FH; in these children, null alleles were clearly associated with more elevated LDL cholesterol levels compared to receptor-defective mutations. Familial factors explained 50.4% of the variation in LDL cholesterol levels of this pediatric cohort compared to only 9.5% in adults. Parental CVD risk was not significantly different between carriers of null alleles and receptor-defective mutations (RR, 1.22; 95% CI, 0.76-1.95; p=0.4). The N543H/2393del9 mutation was associated with a less deteriorated lipid profile and the parents had less often CVD relative to parents with other mutations (RR, 0.39; 95% CI, 0.20-0.78; p=0.008). We could confirm that children with FH provide a better model to perform genotype-phenotype analyses. In particular, children with null alleles had significantly more elevated LDL cholesterol levels than carriers of other alleles but this was not associated with higher risk of CVD in the parents. Nonetheless, a specific LDL receptor mutation was associated with less deteriorated lipoprotein levels and a milder CVD risk.

Adolescent↗
PubMed1990

Multilobated lymphoma of B cell type: a multiparameter investigation.

Multilobated lymphomas were originally described as T-cell neoplasms, but many of B-cell type have subsequently been reported. A case of B-cell origin is reported in which both immunophenotypic and genotypic studies performed on a cell suspension of the lymphoma gave inconclusive and potentially misleading information, while paraffin and frozen section immunohistologic studies, as well as genotypic studies performed on DNA obtained from snap-frozen tissue, were definitive. Thus, this case illustrates some of the problems that may be encountered using cell suspensions as a source for immunophenotypic, and even the much more sensitive genotypic, studies.

Antigens, CD↗
PubMed2006

Detection of mutations using microarrays of poly(C)10-poly(T)10 modified DNA probes immobilized on agarose films.

Allele-specific hybridization to a DNA microarray can be a useful method for genotyping patient DNA. In this article, we demonstrate that 13- to 17-base oligonucleotides tagged with a poly(T)10-poly(C)10 tail (TC tag), but otherwise unmodified, can be crosslinked by UV light irradiation to an agarose film grafted onto unmodified glass. Microarrays of TC-tagged probes immobilized on the agarose film can be used to diagnose mutations in the human beta-globin gene, which encodes the beta-chains in hemoglobin. Although the probes differed widely regarding melting point temperature ( approximately 20 degrees C), a single stringency wash still gave sufficiently high discrimination signals between perfect match and mismatch probes to allow robust mutation detection. In all, 270 genotypings were performed on patient materials, and no genotype was incorrectly classified. Quality control experiments conducted using a target DNA specific for the TC tag of the immobilized probes showed that the spotting and hybridization procedure had a variance of 20%, indicating that signal differences as low as twofold could be detected between perfect match and mismatch. Together, our results show that the use of microarrays of TC-tagged probes that have been immobilized on agarose films grafted onto glass is a robust and inexpensive genotyping method.

Alleles↗
PubMed2006

Common variants of Cholesteryl ester transfer protein gene and their association with lipid parameters in healthy volunteers of Tamilian population.

BACKGROUND: Cholesteryl ester transfer protein (CETP) is involved in a key pathway of reverse cholesterol transport implicated in atherosclerosis and coronary heart disease. CETP gene is known to have many single nucleotide polymorphisms which have been associated with CETP activity and plasma high density lipoprotein cholesterol (HDL-C) concentrations. No data on the prevalence of these polymorphisms and their phenotypic association is available in South Indian population. METHODS: Three CETP polymorphisms: TaqIB, -629C/A and I405V were studied in 171 healthy volunteers from Tamilnadu, a major population of South India. Subjects were clinically examined and lipid profile was estimated. Genotyping was performed by PCR-RFLP and genotype frequencies estimated. RESULTS: The allele frequencies of TaqIB: B1 allele was 0.51; -629C/A: C allele was 0.36; and that of I405V: I allele was 0.47. Study of association between these three polymorphisms and plasma lipid concentrations revealed no significant differences in lipid parameters between genotypes. A gender based subgroup analysis revealed a significant increase in HDL-C in men with B2B2 genotype and decrease in TG in B1B2 genotype. Analysis of the combined effect of multiple mutant genotypes revealed that as the number of mutant genotypes increased, the concentrations of low density lipoprotein-cholesterol (LDL-C), HDL-C and total cholesterol (TC) increased whereas that of triglyceride (TG) decreased in the group of three mutant genotypes significantly. CONCLUSION: The frequency of B2 and A alleles of TaqIB and -629C/A polymorphisms were highest in Tamilian population when compared to other major ethnic groups while that of V allele of I405V polymorphism is between Caucasians and African Americans. Taq1B polymorphism was associated with HDL-C and TG concentrations only in men. Combination of these three polymorphisms was significantly associated with lipid profile than the individual polymorphisms.

Cholesterol Ester Transfer Proteins↗