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Results for “Genotype-phenotype”

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PubMed1997

Phenotypic consequences of mutations in the Fanconi anemia FAC gene: an International Fanconi Anemia Registry study.

Fanconi anemia (FA) is a genetically and phenotypically heterogeneous disorder defined by cellular hypersensitivity to DNA cross-linking agents; mutations in the gene defective in FA complementation group C, FAC, are responsible for the syndrome in a subset of patients. We have performed an analysis of the clinical effects of specific mutations in the FAC gene. Using the amplification refractory mutation system assays that we developed to rapidly detect FAC mutations, at least one mutated copy of the FAC gene was identified in 59 FA patients from the International Fanconi Anemia Registry (IFAR). This represents 15% of the 397 FA patients tested. FA-C patients were divided into three subgroups based on results of a genotype-phenotype analysis using the Cox proportional hazards model: (1) patients with the IVS4 mutation (n = 26); (2) patients with at least one exon 14 mutation (R548X or L554P) (n = 16); and (3) patients with at least one exon 1 mutation (322delG or Q13X) and no known exon 14 mutation (n = 17). Kaplan-Meier analysis shows that IVS4 or exon 14 mutations define poor risk subgroups, as they are associated with significantly earlier onset of hematologic abnormalities and poorer survival compared to exon 1 patients and to the non-FA-C IFAR population. There was no direct correlation between the degree of cellular hypersensitivity to the clastogenic effect of diepoxybutane and severity of clinical phenotype. Sixteen of the 59 FA-C patients (27%) have developed acute myelogenous leukemia. Thirteen of these patients have died; AML was the cause of death in 46% of the expired FA-C patients. This study enables us to define this clinically heterogeneous disorder genotypically to better predict clinical outcome and aid decision-making regarding major therapeutic modalities for a subset of FA patients.

Alleles↗

PubMed1997

[Genetic testing for cancer susceptibility: the present situation in Japan].

Genetic diagnosis of hereditary tumors has progressed extensively and contributed to the presymptomatic testing for mutation carriers. This evolution of genetic testing for cancer susceptibility leads to improved prevention and early detection of cancers. However, the benefits and limits of testing, and the range of prevention and treatment are different in each hereditary tumor. The American Society of Clinical Oncology (ASCO) made the statement on genetic testing for cancer susceptibility and showed three categories for consideration of cancer predisposition testing. They recommend that genetic testing should be offered only for the categories including well-defined tumors. We described the characteristics of hereditary tumors in the three categories and discussed the significance of genetic testing for each tumor. In conclusion, genetic testing for cancer susceptibility should be applied only for subsets of hereditary syndromes, and it is important to continue the analysis of the significance (frequency or penetrance) of mutations of cancer predisposition genes and to make clear the genotype-phenotype and other correlations.

Breast Neoplasms↗

PubMed1997

[Hereditary cardiac arrhythmia].

Progress in molecular biology has advanced our medical knowledge. The identification of genetic abnormalities has been transformed into the new approach of "inverse genetic s" which is based on close collaboration between clinicians, geneticians, molecular biologists and physiologists. In monogenic affections of unknown mechanism, the scientific method of determining the culprit gene is based essentially on precise phenotypic identification of all members of a large family and on DNA studies. The following steps consist in localising the gene with polymorphic genetic probes and then demonstrate the causal mutations and, finally, reexpress the normal and abnormal genes to study their function and thereby confirm the mutation. This approach has recently been applied to cardiac arrhythmias. Genes responsible for atrioventricular conduction defects, Wolff-Parkinson-White syndromes associated with hypertrophic cardiomyopathy and arrhythmogenic right ventricular dysplasia have been localised in the human genome showing that these syndromes are often very variable. The greatest progress has been achieved in the congenital long QT syndrome. Four genes have been localised on chromosomes 3, 1, 7 and 11, and three have already been identified which has allowed study of their function and genotype-phenotype analysis.

Arrhythmias, Cardiac↗

PubMed1997

Dystrophies and heart disease.

The muscular dystrophies are a clinically and genetically heterogeneous group of skeletal muscle-wasting diseases that differ widely in their frequency and pattern of cardiac involvement. Myocardial disease manifesting predominantly as cardiomyopathy and congestive heart failure is characteristic of Duchenne and Becker muscular dystrophies and X-linked dilated cardiomyopathy, whereas conduction system abnormalities that cause heart block, arrhythmias, and sudden death are more commonly seen in limb-girdle type 1B, myotonic, and Emery-Dreifuss muscular dystrophies. Primary defects in the mechanical stabilization of the plasma membrane and signal transduction may underlie these two groups of muscular dystrophies. The identification of several new disease genes has yielded additional insights into the pathophysiology of muscular dystrophy. Molecular genetic and biochemical analyses of patient samples now permit accurate diagnosis and genotype-phenotype correlations. Ultimately, this knowledge will provide the foundation for etiology-specific gene therapy.

Cardiomyopathies↗

PubMedDate not supplied

Relationship between mutation genotype and biochemical phenotype in a heterogeneous Spanish phenylketonuria population.

Genotyping of the phenylalanine hydroxylase (PAH) gene offers a new tool for characterizing patients with phenylketonuria (PKU), refining the diagnosis and aiding in the prediction of the clinical outcome and in the implementation of a more adequate treatment. The primary goal of this work was the detailed study of the different allele combinations and the metabolic phenotypes in Spanish PKU patients in order to understand better the clinical heterogeneity of PAH deficiency in our population. The results show that the disease phenotype is a consequence of a combination of mutations at the PAH locus and this observation is valid throughout the spectrum of clinical and biochemical varieties found in Spanish PKU patients. A stronger correlation was found between the predicted residual activity, when known from previous in vitro studies of the mutant proteins, and the Phe tolerance than between the predicted residual activity and the inverse of Phe levels at diagnosis. The observed genotype-phenotype correlations and the available data on the in vitro residual activity of the mutant proteins has enabled the estimation of the severity of most of the mutations found in Spain. This study includes relevant data for clinicians and pediatricians adding to the present knowledge which relates allelic PAH genotypes to biological phenotypes.

Genetic Heterogeneity↗

PubMed1997

Association analysis of a regulatory variation of the serotonin transporter gene with severe alcohol dependence.

The present study tested the hypothesis that the short, low activity variant of a biallelic polymorphism in the 5' regulatory region of the human serotonin transporter (5-HTT) gene confers susceptibility to severe alcohol dependence marked by severe withdrawal symptoms. Applying a phenotype-genotype strategy, our population-based association analysis included 216 German controls and an extreme sample of 103 severely affected alcoholics who were selected from 315 German alcohol-dependent subjects by a history of alcohol withdrawal seizure or delirium. The frequency of the short allele (S) was significantly increased in the severely affected alcoholics, compared with that in the controls (X2 = 3.87, df = 1, nominal p = 0.049). The post-hoc exploration indicated that this allelic association resulted exclusively from a significant excess of the S/S genotype in the severely affected alcoholics (p = 0.035), suggesting a recessively acting effect. Consistently, we found a weak but significant correlation (p = 0.013) between the frequency of the S/S genotype and severity of withdrawal symptoms (WDS): no WDS [18.3%, odds ratio (OR) = 1.16], vegetative WDS only (21.8%, OR = 1.44), and severe WDS with either withdrawal seizure only or delirium only (25.0%, OR = 1.69), and both withdrawal seizure and delirium (30.8%, OR = 2.30). Further studies are required to test whether the tentative genotype-phenotype relationship occurred by chance or reflects a real genotypic association between a recessively modifying effect of the short variant of the functional 5-HTT promoter polymorphism and alcohol withdrawal vulnerability.

Adult↗

PubMed1997

[Identification of the gene associated with type 1 multiple endocrine neoplasia (NEM 1) susceptibility: a new pathway in the pathogenesis of neuro-endocrine tumors].

Multiple endocrine neoplasia type 1 (MEN 1) is an autosomal dominant inherited disorder characterized by tumors of the parathyroids, endocrine pancreas, anterior pituitary, thymic, bronchic and digestive neuro-endocrine tissues and adrenal glands. The MEN1 gene has been recently cloned by two independent groups. The function of the protein encoded by the MEN1 gene is unknown until now. Germline mutations associated to the diseases in MEN1 families are distributed throughout all the open reading frame, suggesting the absence of founder effect. No consistent genotype-phenotype correlations have been yet recognized. Further studies on the functional domains of the MEN1 encoded protein could be useful to relate clinical expression of the disease with each type of mutation.

Chromosomes, Human, Pair 11↗

PubMed1997

[Familial hyperkalemic periodic paralysis: a brief review of the adult human skeletal muscle sodium channel and the application of LA-PCR to the SCN4A gene analysis].

Recent work has revealed that familial hyperkalemic periodic paralysis, paramyotonia congenita and other non-dystrophic myotonias result from point mutations in the gene encoding the alpha-subunit of the adult human skeletal muscle sodium channel (SCN4A). Sodium channel myotonias are a diverse group of skeletal muscle disorders that share a common pathophysiological mechanism: all are caused by impaired rapid inactivation of skeletal muscle sodium channel. Clinical studies, pharmacology, electrophysiology and molecular genetics have contributed to an elucidation of the genotype-phenotype correlation within these disorders. This article briefly reviews recent advances in our understanding of skeletal muscle sodium channel and sodium channel myotonias. The application of LA-PCR to the SCN4A gene analysis is also referred.

Adult↗

PubMedDate not supplied

Autosomal dominant polycystic kidney disease: clinical and genetic aspects.

Autosomal dominant polycystic kidney disease (ADPKD) is an inherited systemic disease caused by at least three different genes. The renal and extrarenal clinical manifestations, and the systemic complications due to cystic and non-cystic abnormalities in ADPKD patients have been widely investigated. Cellular and molecular aspects of cystogenetic mechanisms concern epithelial tubular cell proliferation, remodelling of extracellular matrix, fluid secretion and accumulation, and relations between cell proliferation and apoptosis. In vitro studies on cystogenesis suggest a key role of cell-to-cell or cell-to-matrix interactions. Surface proteins mediating cell-to-cell contact, such as E-cadherin (polycystin?), integrin interactions, growth factors, receptor expression, are involved in the process of differentiation of the cellular condition and of the extracellular matrix. Blocking any one of these complex mechanisms should influence the orientation and polarization of epithelial tubular cells and should mediate the inversion of fluid secretion which ends in renal cystogenesis. ADPKD comprises at least three phenotypically indistinguishable but genetically distinct entities, caused by mutations in three autosomal genes: PKD1 (chromosome 16p13.3) is present in about 85% of patients; PKD2 (chromosome 4q13q23) in 10%; PKD3 (unknown chromosome) in a few families. PCR-based mutation detection methods, automated DNA sequencing, and other "functional" methods are used to screen and analyse ADPKD patients. It is not yet known whether the mutations identified so far in PKD1 and PKD2 inactivate the genes or generate an aberrant product. The products of PKD1 and PKD2 genes have been called polycystin 1 and 2. Polycystins are members of a family of interactive proteins involved in complex adhesive cell-cell, cell-matrix, protein-protein, and protein-carbohydrate interactions in the extracellular compartment, and are involved in the same pathway (ion channel regulator? ion channel? pore?) where mutations in only one of the simple genes (PKD3 too?) may cause the ADPKD phenotype. Genotype-phenotype correlations, in terms of disease severity and/or progression to end-stage renal disease, probably depend on other factors, both genetic and environmental (for instance: DD genotype of the ACE gene in ADPKD hypertensive patients), that might influence the clinical course and progression of ADPKD. The hypothesis of the "two hits" has been proposed to explain at the molecular level the focal nature of cyst formation.

Genetic Counseling↗

PubMed1998

Monozygotic twins concordant for Cayler syndrome.

Deletions within chromosome band 22q11.2 are associated with a variety of conditions, although a simple genotype-phenotype correlation has not been established so far. Environmental factors, chance events, or a second hit theory were supported by two observations of monozygotic twins with 22q11.2 deletions and discordant phenotypes [Goodship et al., J Med Genet 1995;32:746-748; Fryer, J Med Genet 1996;33:173]. We present monozygotic twins concordant for 22q11.2 deletion and Cayler syndrome, favoring the view that there exists a predominant genetic determination of the del 22q11.2 phenotype. As these twins are diamniotic and dichorionic, they may offer a more reliable insight in genetic phenotype determination than the other published, probably monochorionic, twins who may have a discordant malformation by twinning itself.

Chromosomes, Human, Pair 22↗

PubMed1997

A new case of Pfeiffer syndrome with mutation in FGFR2.

We report on a sporadic case of Pfeiffer syndrome in a male newborn with complex craniosynostosis, broad thumbs and great toes and early demise. SSCP and direct sequencing revealed a missense mutation at position 1037 of the exon B (or IIIc) of the FGFR2 gene (codon 342) resulting in a cysteine to serine modification (TGC-TCC). Genotype-phenotype correlations between the FGFRs mutations and the different craniosynostotic syndromes are discussed.

Acrocephalosyndactylia↗

PubMed1998

Novel recurrent nonsense mutation causing neurofibromatosis type 1 (NF1) in a family segregating both NF1 and Noonan syndrome.

Neurofibromatosis type 1 (NF1), a genetic disorder with neuroectodermal involvement, demonstrates phenotypic overlap in some patients with Noonan syndrome (NS), ultimately resulting in the so-called neurofibromatosis-Noonan syndrome (NF-NS). A strong association of the two phenotypic traits was recently illustrated by a four-generation family, although NF1 and NS were eventually demonstrated to segregate independently on the basis of polymorphic DNA markers [Bahuau et al., 1996: Am J Med Genet 66:347-355]. Identification of the causal NF1 mutation seemed a prerequisite to further dissecting this singular familial association. Using the protein truncation assay, a nonsense mutation (C2446T-->R816X) of the neurofibromin gene was evidenced. This mutation occurred on a CpG dinucleotide within exon 16 and 5' to the GAP domain-specifying region of the gene. R816X creates a recognition site for endonuclease HphI, absent in 2 individuals with NS only. Screening 184 unrelated NF1 patients, three novel occurrences of the mutation were found in individuals diagnosed with classical NF1. Based on the assumption of genotype-phenotype correlation in these individuals, clinical and molecular analyses of this four-generation family demonstrated that the NF-NS phenotype was additive, being the result of both classical NF1 and NS. This particular observation also suggests the presence of an NS locus on 17q, which might be of interest for further linkage studies.

DNA Mutational Analysis↗

PubMed1998

[Molecular diagnosis of mitochondrial disorders].

Mitochondrial disorders are caused by either nuclear or mitochondrial DNA abnormalities. The latter but not the former can be examined as a means of diagnosis at present. The peculiarities and problems of the mtDNA test depend strongly on the characteristics of mtDNA itself, such as the multiplicity in number, vulnerability to mutation, and maternal transmission. The mtDNA abnormalities observed in patients with mitochondrial disorders indicate heteroplasmy, tissue/cell specificity, and threshold effects. It should be stressed that the presence of mutant mtDNA in an individual does not mean that he or she is ill. The problems of the mtDNA test could be solved if the genotype-phenotype relationship is farther elucidated in the future study.

DNA, Mitochondrial↗

PubMed1998

Rapid capillary zone electrophoresis in isoelectric histidine buffer: high resolution of the poly-T tract allelic variants in intron 8 of the CFTR gene.

The poly-T tract in intron 8 of the cystic fibrosis conductance transmembrane regulator (CFTR) gene exists in three variants, 5T, 7T, and 9T. The 7T and 9T variants generate a predominantly normal transcript, whereas the 5T variant engenders an anomalous product. The analysis of the poly-T tract is assuming increasing relevance, both to assess the implication of the CFTR gene in congenital bilateral absence of the vas deferens and to evaluate genotype-phenotype correlation in cystic fibrosis. Mapping of the poly-T tract has been performed by cumbersome and time-consuming methodologies. Capillary zone electrophoresis, combined with laser-induced fluorescence detection, was introduced for a rapid separation of the poly-T tract amplified products. As separation buffer, we adopted 200 mmol/L histidine (pH = pI = 7.6), and the capillary was filled with 10% polyacrylamide, allowing separations in less than 10 min. Capillary zone electrophoresis results were in perfect agreement with dot-blot analysis.

Alleles↗

PubMed1998

Phenotypic variability associated with 14 splice-site mutations in the NF2 gene.

Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder caused by mutations in the NF2 gene. Patients carrying NF2 mutations are predisposed to cerebral and spinal tumors with bilateral vestibular schwannomas as the hallmark. Using single strand conformation polymorphism and temperature gradient gel electrophoresis analysis, we have screened 87 unrelated NF2 patients for mutations in the NF2 gene. In this study, we report phenotypes associated with 14 splice-site mutations carried by 14 propositi and 11 relatives. The mutations were distributed in exons 2, 3, 5, 7, 8, 14, and 15. These splice-site mutations were associated with various phenotypes, from severe to asymptomatic. Phenotypic variation was also observed within families. Mutations downstream from exon 8 resulted more often in mild phenotypes. No meningiomas were found in any of 13 affected or mutation bearing individuals from three families with splice-site mutations of exons 14 and 15. These data suggest that splice-site alteration is a relatively common cause of NF2, and that unlike other mutations the clinical outcomes of splice-site mutations in the NF2 gene are variable. These results add to the growing body of information on genotype-phenotype correlation in NF2.

Adolescent↗

PubMed1998

Fatal familial insomnia around the world. Introduction.

Despite decades of research, much intensified in recent years, transmissible spongiform encephalopathies (TSEs) or prion diseases have remained enigmatic in many aspects. Among these, the intricate connection between infectivity and genetics, genotype-phenotype correlation, and pathogenesis of brain damage are major problems in need of clarification. Fatal familial insomnia (FFI) appears as an ideal model situation for answering some of these problems: it has been understood to have a distinctive clinicopathological phenotype based on a specific genotype as well as transmissibility. However, as always with good science, new data prompts more questions than it is able to answer. The following survey of FFI cases in Europe and around the world is no exception from this rule.

Brain↗

PubMed1993

Correlation between genotype and phenotype in patients with cystic fibrosis.

BACKGROUND: Cystic fibrosis is the most common lethal autosomal recessive disorder among whites. Seventy-two percent of patients with this disease are homozygotes or compound heterozygotes for eight mutations of the cystic fibrosis transmembrane conductance regulator gene on chromosome 7: delta F508, G542X, R553X, W1282X, N1303K, 621 + 1G-->T, 1717-1G-->A, and R117H. We studied the relation between genotype and phenotype in patients from 14 countries. METHODS: Each of 399 patients who were compound heterozygotes for delta F508 and one other mutation was matched with the delta F508 homozygote of the same sex who was the closest in age from the same center. A paired analysis was performed of the following outcome variables: age at diagnosis, sweat chloride concentration, growth percentiles, pulmonary-function values, chest-film score, pseudomonas colonization, nasal polyps, pancreatic sufficiency, pancreatitis, diabetes mellitus, meconium ileus, distal intestinal obstruction syndrome, rectal prolapse, cirrhosis, and gallbladder disease. RESULTS: The compound heterozygotes having the genotype R117H/delta F508 clearly differed from the age- and sex-matched delta F508 homozygotes: they more often had pancreatic sufficiency (87 percent vs. 4 percent, P < 0.001), were older when the diagnosis was first made (mean [+/- SD] age, 10.2 +/- 10.5 vs. 2.5 +/- 4.3 years; P = 0.002), and had lower sweat chloride concentrations (80 +/- 18 vs. 108 +/- 14 mmol per liter, P < 0.001). There were no statistically significant differences between delta F508 homozygotes and other compound heterozygotes with regard to any variable tested. CONCLUSIONS: Prenatal and prognostic counseling for patients with the R117H/delta F508 genotype should include the likelihood that they will have long-term pancreatic sufficiency. Patients with the other genotypes should expect the early onset of pancreatic insufficiency. For none of the genotypes studied can predictions be made about the occurrence of common complications or the severity or course of pulmonary disease.

Adolescent↗

PubMed2026

Genome-based predictions of metabolic preferences and substrate phenotypes in psychrotrophic bacteria from permafrost environments.

Genomes reveal vast functional potential, but harbor genomic noise that obscures prediction of metabolic and environmental preferences. Genomic databases are skewed towards clinically relevant and easily cultivated bacteria, limiting predictions for diverse and underrepresented environmental taxa. Psychrotrophic bacteria, which can survive and grow in cold, nutrient-limited, dry, and saline environments, are especially underrepresented despite their relevance for understanding microbial responses to changing cold environments and potential biotechnological value given growth at low temperatures. Assembling complete genomes of 48 isolates from Alaskan permafrost, seasonally frozen active layer soils, and terrestrial ice, we used Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog annotations to evaluate the predictability of metabolic resource-use traits observed using phenotypic tests. Genome-predicted values for glycolytic versus gluconeogenic catabolic preference index, or sugar-acid preference (SAP), explained over 50% of the variance in empirically observed SAP. SAP was inversely correlated to genomic GC content, which follows phylum-level trends, indicating that coarse metabolic preference covaries with phylogeny. Regularized elastic net models offered a more granular view, linking KEGG genes to specific substrate utilization and sensitivity phenotypes and yielding moderate but reproducible accuracy (AUC 0.70-0.79) for 11 substrates, demonstrating that specific substrate responses may be predictable from relatively small subsets of KO genes. These results extend recent advances, such as the SAP metric, and highlight associations among genomic GC content, phylum, and broad metabolic strategy. Linking genomic content to phenotype using isolates is a necessary step toward predictive models of microbial function in environmental communities, and this work can be used for hypothesis generation, with applications towards more expansive data sets.IMPORTANCECold region soils and ice host psychrotrophic bacteria with metabolic traits and adaptations that enable persistence in harsh, resource-limited environments. However, these taxa are underrepresented in genomic reference databases dominated by well-studied, mesophilic organisms. This gap limits inference of ecological strategies and our ability to predict how these microbes may influence the large, thaw-vulnerable carbon reservoirs in permafrost. Here, we show that genomic GC content is associated with the sugar-versus-acid catabolic preference (SAP) of isolates across major phyla, suggesting that broad genomic features may provide a coarse signal of metabolic strategy. We demonstrate that a modified SAP metric, using binary (positive/negative) substrate utilization rather than detailed growth rate measurements, is moderately predictive, thus extending its application to slow-growing or difficult-to-culture taxa. Together, these advances broaden the toolkit for linking genome content to resource-use traits (phenotype) in poorly characterized, cold-adapted bacteria and offer a tractable entry point to broad prediction and hypothesis generation.

Genome, Bacterial↗