PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Variant interpretation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,243 records · Page 69Linked to original sources

Mutations of the Walker B motif in the first nucleotide binding domain of multidrug resistance protein MRP1 prevent conformational maturation.

ATP-binding cassette (ABC) transporters couple the binding and hydrolysis of ATP to the translocation of solutes across biological membranes. The so-called "Walker motifs" in each of the nucleotide binding domains (NBDs) of these proteins contribute directly to the binding and the catalytic site for the MgATP substrate. Hence mutagenesis of residues in these motifs may interfere with function. This is the case with the MRP1 multidrug transporter. However, interpretation of the effect of mutation in the Walker B motif of NBD1 (D792L/D793L) was confused by the fact that it prevented biosynthetic maturation of the protein. We have determined now that this latter effect is entirely due to the D792L substitution. This variant is unable to mature conformationally as evidenced by its remaining more sensitive to trypsin digestion in vitro than the mature wild-type protein. In vivo, the core-glycosylated form of that mutant is retained in the endoplasmic reticulum and degraded by the proteasome. A different substitution of the same residue (D792A) had a less severe effect enabling accumulation of approximately equal amounts of mature and immature MRP1 proteins in the membrane vesicles but still resulted in defective nucleotide interaction and organic anion transport, indicating that nucleotide hydrolysis at NBD1 is essential to MRP1 function.

ATP-Binding Cassette Transporters↗

Mutation of regulatory serines of rat tyrosine hydroxylase to glutamate: effects on enzyme stability and activity.

Tyrosine hydroxylase is phosphorylated at four serine residues in its amino-terminus by multiple kinases. Phosphorylation of serine 40 by cAMP-dependent protein kinase results in alleviation of dopamine inhibition [J. Biol. Chem. 267 (1992) 12639]. The other serines are at positions 8, 19, and 31. The effect of phosphorylation at these serines has been investigated using mutated forms of tyrosine hydroxylase containing glutamates at the positions of the serines. The S8E, S19E, and S31E tyrosine hydroxylase variants have similar steady-state kinetic parameters and similar binding affinity for catecholamines to wild-type enzyme. The S8E, S19E, S31E, and S40E variants differ in stability at elevated temperatures. The S40E variant is the least stable, while the others are all more stable than wild-type enzyme. The increased stability of S8E, S19E, and S31E tyrosine hydroxylases may be one of the physiological effects of phosphorylation. It may also have implications for the interpretation of activities of heterogeneous mixtures of tyrosine hydroxylase which have been phosphorylated.

Amino Acid Sequence↗

Cancer causation: the Darwinian downside of past success?

Causal mechanisms in all diseases are diverse and multifactorial, but medical scientists, as pragmatists, inevitably focus on limited or circumscribed components of pathogenetic puzzles. In cancer, epidemiologists have traditionally sought to incriminate exposures; geneticists uncover inherited susceptibility; and molecular biologists deconstruct the proximal mechanisms of cell transformation. Molecular epidemiology promises to deliver new insights in terms of gene-environment interactions. Each of these endeavours has undeniably provided rich dividends and insights into cancer causation, but are these likely to be sufficient as a coherent explanation of our vulnerability to cancer? I suggest that the biological plausibility of causal mechanisms would benefit from a historical, evolutionary perspective. The essential argument is that genes or gene variants and phenotypic traits that were adaptively selected in the past as advantageous now contribute crucially to cancer because of their mismatch with current environmental and social circumstances. The risk attributes of skin pigmentation and some dietary factors in cancer can be plausibly interpreted within this context. A case is made here for a Darwinian perspective on breast and prostate cancers, for which current understanding of causation is limited and contentious.

Causality↗

Analysis of Serpulina hyodysenteriae strain variation and its molecular epidemiology using pulsed-field gel electrophoresis.

Pulsed-field gel electrophoresis (PFGE) was applied as a molecular typing tool for the spirochaete Serpulina hyodysenteriae, the agent of swine dysentery. Analysis of a collection of 40 mainly Australian isolates, previously characterized by other methods, divided these into 23 PFGE types. This confirmed that there are many strains of the spirochaete in Australia. PFGE was more discriminatory for strain typing than both multilocus enzyme electrophoresis and serotyping. It had similar discriminatory power to restriction endonuclease analysis, but the results of PFGE were easier to interpret. When applied to 29 isolates collected from 4 farms over periods of up to 8 years, 2 PFGE patterns were found on 3 farms, and a single pattern on the other. In each case a new strain had apparently emerged as a variant of an original parent strain. PFGE was found to be a powerful technique for investigating the molecular epidemiology of swine dysentery outbreaks.

Animals↗

Locus-specific stratification and prioritization unveil genetic risk mechanism underlying complex diseases.

Although genome-wide association studies have identified thousands of disease-associated loci, the mechanistic understanding and drug target discovery remain challenging, particularly for complex diseases. The multi-signal architecture of complex diseases complicates the interpretation of genetic contributions. To address this challenge, we develop an approach comprising locus-specific stratification (LSS) and gene regulatory prioritization score (GRPS), which uniquely considers multi-signals during fine-mapping and target gene identification. LSS significantly enhances the interpretability of genetic risk associated with complex diseases. For loci associated with serum urate levels, the method identifies candidate causal genes in 34.43% of loci, surpassing the performance of other methods by 5.47% to 25.14%. GRPS considers the regulatory network of LSS-variants comprehensively and successfully nominates under-explored drug targets for hyperuricemia with high confidence such as SLC17A4, which is further validated using epigenetic activation and phenotypic assays. This study introduces an approach to efficiently and comprehensively address the multi-signal challenges in complex diseases.

Humans↗

Contribution to the development of the heart, Part II: Morphogenesis of congenital heart diseases.

A concept for the explanation of the formal genesis of congenital cardiac malformations is introduced, based on the observation that 1. the septa in the outflow-tract of the heart are formed in spatial relation to changes in form of the external cardiac wall and always along the longer sides of the ovally deformed pathway of flow, 2. the muscular septa (ventricular and atrial septa) arise as protrusions due to different directions of ventricular growth. Accordingly, no septa develop when normal deformation fails to occur (e.g. truncus communis); septa are incompletely developed when the deformation is insufficient (e.g. aortico-pulmonary window); septa are formed in wrong positions where the direction of deformation deviates more or less from the normal direction (as in stenosis due to slight deviation, or transposition due to large deviation from the normal). The so-called ventricular inversions and atrio-ventricular discordance are regarded as consequences of dystopic development of the ventricular septum. This concept for the explanation of the formal genesis of cardiac malformations is exemplified by variants of transpositions (anatomically corrected and uncorrected), and by variants of double-outlet-right-ventricle and double-outlet-left-ventricle. Using a common anomaly (tetralogy of Fallot) and 2 rare ones (double-outlet-right-ventricle with complete AV canal, and criss-cross-heart) it is shown that the interpretation of the development of cardiac malformations as a consequence of dystopic development of the septa allows an understanding of the formal genesis of complex malformations without involving hitherto unproven developmental processes.

Animals↗

The demise of follicular carcinoma of the thyroid gland.

Over the past several decades, iodide supplementation to food supplies in many parts of the world has been followed by a corresponding decrease in the incidence of follicular thyroid carcinoma. However, pathologists continue to over-diagnose this tumor. Benign lesions (e.g., partly encapsulated hyperplastic nodules, pseudoinvasion after fine needle aspiration), and malignancies (especially the follicular variant of papillary carcinoma) have been misinterpreted as follicular carcinoma. Since the clinical features and biological behavior of true follicular cancer differ from the entities with which it may be confused, it is essential that appropriate histological criteria be applied to the diagnostic interpretation of thyroid nodules that exhibit follicular architecture. Only in this way will it be possible to define prognosis and to evaluate treatment options.

Adenocarcinoma, Follicular↗

Verocay body--prominent cutaneous schwannoma.

We report on eight cases of a distinct variant of cutaneous schwannoma characterized by prominent Verocay body formation (75-100% of the tumor bulk) that may cause considerable diagnostic difficulties. Like ordinary cutaneous schwannomas, these lesions preferred the head and neck region of young adults without sexual predilection and were clinically interpreted as cyst, basal cell carcinoma, or nevus. Histological examination revealed well-circumscribed nodules. Three of them consisted exclusively of nodular or ribbon-like Verocay bodies. A variable admixture of Antoni A or B type of differentiation (< 25%) was seen in five other cases. The following patterns were seen: fascicular spindle-shaped, onion-like epithelioid, myxoid-hypocellular, and degenerated ("ancient") with prominent fibrosis/hyalinosis and occasional bizarre giant cells. Immunohistochemically, the lesions were positive for S-100 protein (and vimentin) but negative for a broad panel of neurogenic and intermediate filament markers. The capsule showed focal labeling for EMA and--when it was markedly thickened--also for SMA. Labeling with E9, an anti-metallothionein marker indicative of cell activity, was negative, underscoring the slow growth potential of these lesions. No recurrence was seen in the six patients with follow-up information. The differential diagnosis includes other lesions with prominent palisading. (Amianthoid) myofibroblastoma and palisading leiomyoma are consistently positive for SMA and desmin, respectively. Palisading cutaneous fibrous histiocytoma and myofibroblastic dermatofibroma are variably positive for Factor XIIIa, SMA, and E9 and/or NK1C3 (CD57). Palisaded encapsulated neuromas are primarilly differentiated by the presence of nerve fibers with myelin sheaths.

Adolescent↗

Christmas factor: dosage compensation and the production of blood coagulation factor IX.

The amount of factor IX (Christmas factor) for different genotypic classes was determined by means of a variant of the thromboplastin generation test. The mean value for females heterozygous for the Christmas gene was about half the mean values for normal males and for normal homozygous females; means for the latter two groups were about equal. This dosage compensation is interpreted as evidence in support of Lyon's hypothesis, according to which one X chromosome is inactive in mammalian females.

Animals↗

Minisatellites and MVR-PCR for the individual identification of parasite isolates.

In recent years, a wide variety of biochemical and molecular typing systems have been employed in the study of parasite diversity aimed at investigating the level of genetic diversity and delineating the relationships among different species and subspecies. Parasite sequence-specific polymerase chain reaction (PCR)-based genotyping systems are among the most useful tools employed to date, because they can be applied to very small quantities of host-contaminated parasite material and, using repeated loci such as mini- and microsatellites, allow the identification and tracking of individual strains as well as the determination of allele and genotype frequencies in populations. Although minisatellites have been used very successfully to study parasite populations, in particular Trypanosoma brucei populations, there are some technical problems involved in the use of these markers. For example, minisatellite alleles tend to vary in a quasi-continuous fashion, making unambiguous allele identification difficult. The development of minisatellite variant repeat (MVR) mapping by the polymerase chain reaction (MVR-PCR) as a digital approach to DNA typing has overcome many of the drawbacks of minisatellite length analysis. The system assays the dispersion patterns of MVRs within minisatellite alleles, producing an easily interpretable code for each allele. This technique not only allows unequivocal allele identification but also reveals cladistic information that can be used to determine the possible genetic relationships among the different strains and subspecies. The MVR mapping technique has been applied successfully to minisatellites in the parasite Plasmodium falciparum to uniquely identify strains, and more extensively in Trypansoma brucei, where it was used to determine population structure and to examine the relationships among T. brucei subspecies, providing evidence for multiple origins of human infectively. In this chapter, the methods for genotyping of T. brucei parasites using both minisatellite allele length and MVR mapping are described in full and can be easily adapted to apply to mini-satellites in other parasites.

Animals↗

Epileptiform electroencephalographic patterns.

Electroencephalography (EEG) is the most useful test for assessment of patients with epilepsy. It can help establish the diagnosis of epilepsy and determine the type of seizure disorder and its site of origin. Epileptiform abnormalities in the EEG tracing may be focal or generalized. The main types of focal epileptiform discharges arise from the temporal, frontal, occipital, centroparietal, centrotemporal, and midline regions of the brain. Generalized epileptiform discharges consist of the 3-Hz spike-and-wave, slow spike-and-wave, atypical spike-and-wave, paroxysmal fast activity, and hypsarrhythmic patterns. Status epilepticus is manifested by continuous epileptiform discharges or recurrent seizure activity without interim recovery, which can occur in a generalized or focal manner. Benign epileptiform variants unassociated with seizures can also be present in the EEG. Included in this category are the "14 & 6" positive bursts, small sharp spikes, wicket waves, 6-Hz spike-and-wave discharges, and rhythmic temporal theta activity. The EEG findings should be interpreted in the context of the overall clinical picture.

Electroencephalography↗

[Hereditary neuropathies].

BACKGROUND: Hereditary neuropathies constitute a heterogeneous group of diseases that make up a significant proportion of peripheral nerve disease cases. MATERIAL AND METHODS: The paper is based on a review of recent literature, including searches on Medline, and our own clinical and research experience. RESULTS: Charcot-Marie-Tooth disease, itself a heterogeneous disease, is the most common hereditary neuropathy. Several variants of neuropathy are associated with hereditary metabolic disorders. Diagnostic methods include nerve conduction velocity studies and electromyography, quantitative sensory testing, molecular genetic diagnostic testing, and in selected cases processing of nerve biopsies and skin biopsies for determination of epidermal nerve fibre densities. INTERPRETATION: A thorough family history of neuropathic symptoms and signs, and preferably clinical and electrophysiological examination of relatives is essential for the diagnosis of hereditary neuropathy. Molecular genetic analysis is promising for accurate classification of these diseases. Nerve biopsy is only helpful in selected cases.

Charcot-Marie-Tooth Disease↗

Coincidence of paternal 13pYq translocation and maternal increased 13p NOR activity in a child with arthrogryposis and other malformations.

Cytogenetic examination of a boy with congenital multiple arthrogryposis, VSD and dysmorphic facies revealed a probable t(Y; 13)(q?; p1) translocation and three NOR-positive dots on one of the chromosomes 13. The latter variant could be followed in the family of the mother, the 13/Y translocation was found in the relatives of the father. Since all the family members affected by one or the other cytogenetic anomaly were healthy, the abnormal phenotype of the propositus was interpreted as coincidence by chance.

Adult↗

Late paraphrenia: a variant of schizophrenia manifest in late life or an organic clinical syndrome? A review of recent evidence.

A large amount of research has been devoted during the past 15 years to the clinical and neurobiological aspects of the disorder named as 'late paraphrenia' (LP) in 1955. The symptomatology and diagnosis of the disorder, its prognosis, the cognitive functioning of those affected, the structural changes in the brain as revealed by modern techniques of brain imaging and its postmortem neuropathology have all been submitted to investigation. The results have been widely regarded as consistent with the concept of LP as an organic disease of the brain, but increased knowledge of the neurobiology of schizophrenia and of the age-related changes that occur in the brains of elderly people casts doubt on the validity of this interpretation. The findings are consistent with the view that LP is the form in which schizophrenia is manifest in old age. The proposal that LP has a closer kinship with affective disorder than with schizophrenia is part of a general theory of the sex differences in schizophrenia. In LP it becomes entangled with the organicity hypothesis, suggesting that neither of these explanations is adequate, and most of the evidence points to a unitary concept which views LP as a variant of a single disorder, namely schizophrenia, which, however, requires a broad definition. This concept has implications for fresh paths of enquiry.

Aged↗

Kuru in the 21st century--an acquired human prion disease with very long incubation periods.

BACKGROUND: Kuru provides the principal experience of epidemic human prion disease. Its incidence has steadily fallen after the abrupt cessation of its route of transmission (endocannibalism) in Papua New Guinea in the 1950s. The onset of variant Creutzfeldt-Jakob disease (vCJD), and the unknown prevalence of infection after the extensive dietary exposure to bovine spongiform encephalopathy (BSE) prions in the UK, has led to renewed interest in kuru. We investigated possible incubation periods, pathogenesis, and genetic susceptibility factors in kuru patients in Papua New Guinea. METHODS: We strengthened active kuru surveillance in 1996 with an expanded field team to investigate all suspected patients. Detailed histories of residence and exposure to mortuary feasts were obtained together with serial neurological examination, if possible. FINDINGS: We identified 11 patients with kuru from July, 1996, to June, 2004, all living in the South Fore. All patients were born before the cessation of cannibalism in the late 1950s. The minimum estimated incubation periods ranged from 34 to 41 years. However, likely incubation periods in men ranged from 39 to 56 years and could have been up to 7 years longer. PRNP analysis showed that most patients with kuru were heterozygous at polymorphic codon 129, a genotype associated with extended incubation periods and resistance to prion disease. INTERPRETATION: Incubation periods of infection with human prions can exceed 50 years. In human infection with BSE prions, species-barrier effects, which are characteristic of cross-species transmission, would be expected to further increase the mean and range of incubation periods, compared with recycling of prions within species. These data should inform attempts to model variant CJD epidemiology.

Aged↗

Chondroid chordoma--a variant of chordoma. A morphologic and immunohistochemical study.

In 1973, Heffelfinger and coworkers described a variant of chordoma that contained cartilaginous areas indistinguishable from hyaline type chondrosarcoma. They designated these tumors chondroid chordomas and found that they had a better prognosis than classic (nonchondroid) chordomas. Since that time, there has been an ongoing debate over whether chondroid chordoma is best considered a distinct clinicopathologic entity separable from chondrosarcoma or a misdiagnosed chondrosarcoma whose concept developed from the erroneous interpretation of morphology. In an attempt to clarify the issue, the authors used light microscopy and immunohistochemistry to study 12 chondroid chordomas, 38 classic chordomas, and 28 chondrosarcomas that arose in the base of the skull or spine. As a reference, they also analyzed the immunohistochemical profile of fetal notochord, ecchordosis physaliphora, and fetal hyaline cartilage. They found that all chondroid and nonchondroid chordomas were positive for cytokeratin, and the majority were also positive for epithelial membrane antigen (EMA) and carcinoembryonic antigen (CEA). In contrast, none of the chondrosarcomas stained for cytokeratin, EMA or CEA. Vimentin and S-100 were positive in more than 95% of both classic and chondroid chordomas and chondrosarcomas. The immunohistochemical profile of these tumors was similar to the pattern of immunoreactivity of their nonneoplastic counterparts. The authors conclude that chondroid chordomas is a variant of chordoma and should not be confused with chondrosarcoma. Because chondroid chordomas have been reported to have a better prognosis, they felt that this nosologic term should be preserved and that chondroid chordoma should continue to be a focus of clinical and pathologic study.

Adolescent↗

High penetrance of sequencing errors and interpretative shortcomings in mtDNA sequence analysis of LHON patients.

For identifying mutation(s) that are potentially pathogenic it is essential to determine the entire mitochondrial DNA (mtDNA) sequences from patients suffering from a particular mitochondrial disease, such as Leber hereditary optic neuropathy (LHON). However, such sequencing efforts can, in the worst case, be riddled with errors by imposing phantom mutations or misreporting variant nucleotides, and moreover, by inadvertently regarding some mutations as novel and pathogenic, which are actually known to define minor haplogroups. Under such circumstances it remains unclear whether the disease-associated mutations would have been determined adequately. Here, we re-analyse four problematic LHON studies and propose guidelines by which some of the pitfalls could be avoided.

Artifacts↗

Variant pancreatography.

Although variation is the rule with pancreatic duct morphology, certain anomalies occur as a result of altered embryological development. These anomalies can produce obvious clinical symptomatology or may be implicated as a cause of symptoms when noted in the evaluation of patients with gastrointestinal complaints of obscure origin. Gastroenterologists and radiologists should be familiar with these anomalies for more accurate interpretation of pancreatograms and their clinical implications.

Humans↗