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PubMed1984

Molecular abnormality of an inactive aldehyde dehydrogenase variant commonly found in Orientals.

Usual human livers contain two major aldehyde dehydrogenase [(ALDH) aldehyde:NAD+ oxidoreductase] isozymes--i.e., a cytosolic ALDH1 component and a mitochondrial ALDH2 component--whereas approximately equal to 50% of Orientals are "atypical" and have only the ALDH1 isozyme and are missing the ALDH2 isozyme. We previously demonstrated that atypical livers contain an enzymatically inactive but immunologically crossreactive material (CRM) corresponding to the ALDH2 component. The enzymatically active ALDH2 obtained from a usual liver and the CRM obtained from an atypical liver were reduced, S-carboxymethylated, and digested by trypsin. Separation of their digests by high-performance reverse-phase chromatography and by two-dimensional paper chromatography and electrophoresis revealed that ALDH2 contained a peptide sequence of -Glu-Leu-Gly-Glu-Ala-Gly-Leu-Gln-Ala-Asn-Val-Gln-Val-Lys- and that the glutamine adjacent to lysine was substituted by lysine in CRM. All other tryptic peptides, including eight peptides containing S-carboxymethylcysteine, were common in ALDH2 and CRM. It is concluded that a point mutation in the human ALDH2 locus produced the glutamine leads to lysine substitution and enzyme inactivation.

Aldehyde Dehydrogenase↗
PubMed2003

The effect of methylenetetrahydrofolate reductase C677T common variant on hypertensive risk is not solely explained by increased plasma homocysteine values.

The C677T transition of methylenetetrahydrofolate reductase (MTHFR) gene causes a moderate increase in total plasma homocysteine (tHcy). We studied the effect of MTHFR TT homozygosity and mild hyperhomocysteinemia on arterial hypertension. Normotensive controls (n = 223) and hypertensive subjects (n = 235) were matched for age, gender, and history of cardiovascular disease. Homocysteine levels were measured by a polarization immunoassay method. Methylenetetrahydrofolate reductase we determined by polymerase chain reaction and restriction fragment analysis. Hypertensives showed elevated tHcy compared to normotensive group in men (P = 0.039). Homocysteine values higher than 15 micromol/L were associated with increased hypertensive risk in the male population [odds ratios (OR) = 1.63; 95% confidence interval (CI) = 1.06-2.52; P = 0.027]. In multivariate analysis, TT genotype was associated with an increased risk of hypertension in males (OR = 2.27; 95% CI = 1.12-4.60; P = 0.022) An increased hypertensive risk was observed in those TT males with tHcy levels higher than 15 micromol/L (OR = 2.78; 95% CI = 1.05-7.3; P = 0.032) but not in those non-TT males with tHcy levels higher than 15 micromol/L (P = 0.33). Our findings do not support the possibility that mild hyperhomocysteinemia my solely account for the hypertensive risk associated to the TT genotype.

Aged↗
PubMed2003

Variation in a repeat sequence determines whether a common variant of the cystic fibrosis transmembrane conductance regulator gene is pathogenic or benign.

An abbreviated tract of five thymidines (5T) in intron 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is found in approximately 10% of individuals in the general population. When found in trans with a severe CFTR mutation, 5T can result in male infertility, nonclassic cystic fibrosis, or a normal phenotype. To test whether the number of TG repeats adjacent to 5T influences disease penetrance, we determined TG repeat number in 98 patients with male infertility due to congenital absence of the vas deferens, 9 patients with nonclassic CF, and 27 unaffected individuals (fertile men). Each of the individuals in this study had a severe CFTR mutation on one CFTR gene and 5T on the other. Of the unaffected individuals, 78% (21 of 27) had 5T adjacent to 11 TG repeats, compared with 9% (10 of 107) of affected individuals. Conversely, 91% (97 of 107) of affected individuals had 12 or 13 TG repeats, versus only 22% (6 of 27) of unaffected individuals (P<.00001). Those individuals with 5T adjacent to either 12 or 13 TG repeats were substantially more likely to exhibit an abnormal phenotype than those with 5T adjacent to 11 TG repeats (odds ratio 34.0, 95% CI 11.1-103.7, P<.00001). Thus, determination of TG repeat number will allow for more accurate prediction of benign versus pathogenic 5T alleles.

Base Sequence↗
PubMed2004

Common variants in the 5' region of the leptin gene are associated with body mass index in men from the National Heart, Lung, and Blood Institute Family Heart Study.

Linkage of body mass index (BMI) to a broad region of chromosome 7q22-35 has been reported in multiple studies. We previously published a multipoint LOD score of 4.9 at D7S1804 for BMI from the National Heart, Lung, and Blood Institute Family Heart Study. Leptin (LEP), the human homolog of the mouse obesity (ob) gene, is positioned near the linkage peak and is the most prominent candidate gene in this region. Interest in LEP as a susceptibility gene for human obesity has led to numerous linkage and association studies, but the results of these studies are still controversial. In the present study, we employed family-based tests of association with both a quantitative measure of BMI adjusted for age and sex and a dichotomously defined obesity trait. We genotyped 29 single-nucleotide polymorphisms (SNPs) spanning 240 kb around the LEP gene in the 82 extended pedigrees with the strongest evidence for linkage. When the programs TRANSMIT and FBAT were used, a number of SNPs showed association in men but not women, for both the quantitative and qualitative trait definitions (P<.05). Five SNPs (H1328084, H1328083, H1328082, H1328081, and H1328080) positioned 2 kb beyond the previously defined promoter region showed strong association in single-marker and multiple-marker haplotype analysis. This five-marker haplotype (frequency 49% in this sample) is overtransmitted to obese offspring (P=.00005). All five of these SNPs are predicted to modify transcription-factor binding sites. This may indicate new functional variants in an extended promoter region of LEP.

Body Mass Index↗
PubMed2002

The allelic architecture of human disease genes: common disease-common variant...or not?

Linkage disequilibrium (LD) plays a central role in current and proposed methods for mapping complex disease genes. LD-based methods work best when there is a single susceptibility allele at any given disease locus, and generally perform very poorly if there is substantial allelic heterogeneity. The extent of allelic heterogeneity at typical complex disease loci is not yet known, but predictions about allelic heterogeneity have important implications for the design of future mapping studies, including the proposed genome-wide association studies. In this article, we review the available data and models relating to the number and frequencies of susceptibility alleles at complex disease loci-the 'allelic architecture' of human disease genes. We also show that the predicted frequency spectrum of disease variants at a gene depends crucially on the method of ascertainment, for example from prior linkage scans or from surveys of functional candidate loci.

Alleles↗
PubMed2003

The usefulness of different density SNP maps for disease association studies of common variants.

Large-scale discovery and validation of single-nucleotide polymorphisms (SNPs) facilitates indirect association mapping. It has recently been estimated that, in Europeans, 77% of all SNPs with frequency of 10% or more could be ascertained through linkage disequilibrium (LD) by genotyping variants in the database dbSNP. Using a sampling approach from 73 genes with near complete SNP maps, we show here the usefulness of SNP maps at different densities and the large variability of SNP coverage in different genomic regions. While even sparse SNP maps are of some value to genetic mapping, in order to undertake disease association studies providing at least 80% of SNPs in 90% of genes, much denser maps need to be constructed, at more than one SNP per kb in some regions.

Chromosome Mapping↗
PubMed2004

Association of a common variant of the CASP8 gene with reduced risk of breast cancer.

Apoptosis, or programmed cell death, is perturbed in many cancers. We tested the hypothesis that coding polymorphisms of the death receptor 4 (DR4), caspase-8 (CASP8), and caspase-10 (CASP10) genes might act as low-penetrance breast cancer genes. Single-nucleotide polymorphisms (SNPs) of these genes were genotyped in a series of 999 breast cancer case patients and 996 control subjects from Sheffield, U.K., and in a second, independent U.K. population of 2192 case patients and 2262 control subjects from East Anglia. In the Sheffield study, the rare H allele of CASP8, D302H, was associated with a reduced risk of breast cancer in a dose-dependent manner (P(trend) = .007). Furthermore, the CASP8 D302H association, but not that of the other CASP8 SNPs examined (T21914C, G50121A, and G50358A), was replicated in the East Anglian study. The combined adjusted odds ratios for breast cancer were 0.83 (95% confidence interval [CI] = 0.74 to 0.94) for the DH heterozygote and 0.58 (95% CI = 0.39 to 0.88) for the HH homozygote (P(trend) = .0002, adjusted for study). The reproducible, dose-dependent association of CASP8 D302H with breast cancer indicates the potential importance of inherited variation in the apoptosis pathway in breast cancer susceptibility.

Aspartic Acid↗
PubMed1993

Risk of miscarriage and a common variant of the estrogen receptor gene.

An inherited variant of the estrogen receptor gene was previously suggested to be a major determinant of a woman's risk of miscarriage. The authors tested this hypothesis in a case-control study of 29 women who had had two or more miscarriages and 29 women with no miscarriages. All of the women had given birth in North Carolina between 1987 and 1990. Estrogen receptor genotype was determined by direct sequencing of DNA. The gene variant that supposedly produced the risk was found to contain only a silent substitution at codon 87. Furthermore, instead of an odds ratio of 25 (predicted by the previous study), the odds ratio found was 1.8 (95% confidence interval 0.3-11). For a hypothesis which now lacks biologic plausibility, this weak association provides little reason for further investigation.

Abortion, Spontaneous↗
PubMed2004

Molecular and clinicopathologic comparisons of head and neck squamous carcinoma variants: common and distinctive features of biological significance.

To investigate, for the first time, the events associated with the phenotypic and clinical diversities of head and neck squamous carcinomas (HNSC), we performed molecular analyses on 92 primary tumors representing the entire spectrum of the morphologic subtypes using microsatellite markers at chromosome 3p, 4p, 8p, 9p, 11q, 17p, and 18q regions and correlated the results with the clinicopathologic features and patients' survival. Loss of heterozygosity (LOH) at D9S168 and D9S171 markers on chromosome 9p regions was commonly identified in all subtypes. Distinctive alterations in certain subtypes were noted at chromosomes 3p, 4p, 8p, and 11p regions. In general, less aggressive types (verrucous, papillary, and well-differentiated conventional) had a significantly lower LOH incidence than the more aggressive (basaloid, sarcomatoid, and high-grade conventional squamous carcinoma) categories. Significant association between LOH and age, stage, nodal status, and patient outcome was found. Survival analysis revealed that pathologic categorization (less versus more aggressive) and LOH at marker D11S4167 and D3S2432 are independent predictors of patients' survival. Our analysis also defined a set of limited markers that account for most of alterations within and across these tumor subtypes. Our study indicates that 1) certain genetic markers are common to all subtypes of HNSC supporting their early involvement in tumorigenesis, 2) inter- and intratumoral genetic differences evolve subsequently and may underlie their morphologic heterogeneity, 3) high incidence of LOH in certain regions characterizes aggressive tumors, 4) categorical classification and LOH at 11p and 3p regions independently correlated with patient survival, and 5) a limited set of markers identify the majority of genetic alterations in these tumors.

Adult↗
PubMed2005

Pleomorphic pancreatic endocrine neoplasms: a variant commonly confused with adenocarcinoma.

Most pancreatic endocrine neoplasms (PENs) have distinctive endocrine growth patterns and uniform nuclear morphology; they are regarded as relatively low-grade tumors. Significant nuclear pleomorphism is a feature that may raise concerns about aggressive behavior or even obscure the endocrine nature of the neoplasm. Eight PENs exhibiting marked nuclear pleomorphism (>20% of the tumor cells) were identified during a review of 136 PENs (5.9%) from the pathology files of Memorial Sloan-Kettering Cancer Center. The histologic, immunohistochemical, ultrastructural (4 cases), and clinical features were reviewed. There were 6 males and 2 females ranging from 30 to 69 years (mean, 55 years). The tumors averaged 5.8 cm (range, 1.5-14 cm). Six tumors (75%) were initially misdiagnosed in 5 cases as adenocarcinoma and in one as solid-pseudopapillary tumor; in 2 cases, the misdiagnosis was based on fine needle aspiration cytology and in 4 on histologic examination. The architectural features of the tumors resembled those of other PENs, but the nuclei were markedly enlarged, irregularly shaped, and hyperchromatic, with frequent bizarre forms. Cells with pleomorphic nuclei also generally had abundant cytoplasm, sometimes with large perinuclear glassy inclusions. The mitotic rate was not elevated compared with other PENs, averaging 1.9 (range, 0-7) per 50 high power fields. Immunohistochemical findings were (number positive/number stained): chromogranin (8 of 8), synaptophysin (7 of 8), progesterone receptor (4 of 7), CD99 (2 of 5), S-100 protein (3 of 7), and p53 (0 of 6). Scattered cells expressed peptide hormones in a minority of cases. By electron microscopy, abundant dense core granules were identified, in some cases embedded within perinuclear arrays of intermediate filaments. Six patients underwent curative resection; at follow-up, 4 were free of disease at 11, 13, 30, 112 months (mean, 42 months), 1 developed liver metastases at 77 months and was alive with disease at 94 months, and 1 was lost to follow-up. Two patients had unresectable tumors and were alive with disease at 10 and 78 months. Striking nuclear pleomorphism may occur in otherwise typical PENs and commonly causes difficulties in the distinction from adenocarcinoma. There does not appear to be prognostic significance to these nuclear changes, and the morphologic features of pleomorphic PENs otherwise resemble those of their conventional counterparts.

Adenocarcinoma↗
PubMed2004

Preeclampsia and its interaction with common variants in thrombophilia genes.

Recently, it has been proposed that abnormalities in coagulation and fibrinolysis contribute to the development of preeclampsia by increasing the thrombotic tendency. This hypothesis was tested in women who have had preeclampsia (cases) compared with matched controls. Polymorphisms in the thrombophilia genes [plasminogen activator inhibitor type 1 [PAI-1 -675(4G/5G)], thrombin activatable fibrinolysis inhibitor (TAFI -438G/A and 1040C/T), methylenetetrahydrofolate reductase (MTHFR 677C/T), factor V (FV Leiden R/Q506), prothrombin (FII 20210G/A) and factor XIIIA (FXIIIA V/L34)] were determined in 157 women with preeclampsia and 157 women with uncomplicated pregnancy. The associated risk of preeclampsia was analyzed using logistic regression methods. The frequency distributions of the genotypes of these six polymorphisms in thrombophilia genes were similar in the case and control groups. We found no differences in the prevalence of genetic risk factors of thrombosis in women with preeclampsia compared with controls, which makes it unlikely that these polymorphisms are risk factors for preeclampsia.

Adult↗