SEARCH · Search PubMed

Results for “clinical variant classification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

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

At least 343 records · Page 19Linked to original sources

PubMed2005

Autopsy case of CD4/CD8 cutaneous T-cell lymphoma presenting disseminated pagetoid reticulosis with aggressive granulomatous invasion to the lungs and pancreas.

Pagetoid reticulosis is a rare cutaneous T-cell lymphoma with striking epidermotropism similar to that present in Paget's disease. There are two forms of pagetoid reticulosis: localized and disseminated. Reported herein is an autopsy case of disseminated pagetoid reticulosis with CD4(-)/CD8(-) phenotype T cells and massive invasion of the lungs and pancreas. The abnormal cells in the epidermis expressed a protein derived from a rearranged T-cell receptor beta gene, and this feature was used to confirm the monoclonality of these cells by polymerase chain reaction. At present, the World Health Organization (WHO) classification system considers pagetoid reticulosis to be an indolent form of primary cutaneous T-cell lymphoma and a variant of mycosis fungoides/Sezary syndrome with prominent epidermotropism. Some differences have been observed between pagetoid reticulosis and mycosis fungoides in terms of clinical course, tumor cell phenotype, and genetic findings; and these differences are highlighted in the present case. The relation between disseminated pagetoid reticulosis, CD4(-)/CD8(-) cutaneous T-cell lymphoma, and gammadelta T-cell lymphoma, including whether pagetoid reticulosis is a variant of mycosis fungoides, remains unclear.

Autopsy↗

PubMed2003

Pathologic classification of focal segmental glomerulosclerosis.

Focal segmental glomerulosclerosis (FSGS) is defined as a clinical-pathologic syndrome manifesting proteinuria and focal and segmental glomerular sclerosis with foot process effacement. The pathologic approach to the classification of FSGS is complicated by the existence of primary (idiopathic) forms and multiple subcategories with etiologic associations, including human immunodeficiency virus (HIV)-associated nephropathy, heroin nephropathy, familial forms, drug toxicities, and a large group of secondary FSGS mediated by structural-functional adaptations to glomerular hyperfiltration. A number of morphologic variants of primary and secondary focal sclerosis are now recognized, including FSGS not otherwise specified (NOS), perihilar, cellular, tip, and collapsing variants. The defining features of these morphologic variants and of the major subcategories of FSGS are discussed with emphasis on distinguishing light microscopic patterns and clinical-pathologic correlations.

Disease Progression↗

PubMed2002

Dorsal bony septum: a split cord malformation variant.

Split cord malformations (SCMs) are rare spinal anomalies and their classification is still a matter of debate. There is no widespread consensus on the embryological basis of this entity. The unified theory, proposed by Pang et al. [Neurosurgery 1992;31:451-480], was an attempt to explain the embryogenetic mechanism as a basic error occurring around the time when the primitive neuroenteric canal closes. We report two unusual cases of SCMs with a dorsally situated bony spur. We analyzed the radiological, clinical and surgical features of the lesions and were not able to classify these cases according to the unified theory. Further embryological studies should be conducted to elucidate the mechanisms of occurrence of these lesions, and the dorsal bony septum variant should be considered in SCM surgery.

Child↗

PubMed2000

Rare variant of the brachial artery: superficial lateral inferior type VII EAB.

This study concerns a variant of the brachial artery with a modified origin and course. The artery was studied in 418 upper limbs removed from cadavers. In one upper limb the left brachial artery bifurcated into: (1) a superficial brachial a. (the variant) crossing superficially to the bicipital aponeurosis in the cubital region and assuming the course, position, and supply area of the radial artery, and (2) the deep brachial a. (another variant). An embryologic interpretation of this anomaly is based on a variant vascular development derived from the eighth intersegmental artery. The variant is termed according to Adachi's classification schedule as arteria brachialis superficialis lateralis inferior Type VII with the addition EAB (epiaponeurosis bicipitalis, i.e., superficial to the bicipital aponeurosis). Accurate information concerning unusual patterns of the arteries in the upper limbs is clinically relevant, especially in the avoidance of accidental intra-arterial injection with reflectory vascular occlusion leading to necrosis.

Aged↗

PubMed2004

Discrepancies between classification systems of childhood obesity.

Despite growing concern about weight-related problems among children, no universally accepted classification system for childhood obesity exists. There is a number of proposed international body mass index (BMI)-based systems in use and national variants also exist in many countries. The absence of a universally accepted standard and confusion concerning which classification system to use on national levels complicate monitoring of the development of the obesity epidemic, stratification for selective interventions in public health, screening in clinical practice and comparisons between studies. Some proposed international classification systems have not only been recommended for global monitoring and comparisons between studies, but also for clinical and national epidemiological use in some countries. Possible discrepancies may thereby lead to inefficiencies in health care delivery and prevention programmes. The problems associated with misclassification of individuals at risk may lead to overconsumption of health care resources by lower-risk individuals and underconsumption by higher-risk individuals, which is costly both in terms of foregone health improvements and in terms of wasteful monetary usage. The aim of this paper was to review the specific problems associated with BMI as a measure of adiposity in childhood, the most commonly used classification systems for childhood obesity based on BMI, and how their performance can be evaluated.

Adipose Tissue↗

PubMed1978

Bilateral acinous cell tumors of the parotid gland.

Acinous cell tumors are uncommon neoplasms which arise either from the secretory cells of the salivary gland acini or from pluripotential duct cells and occur almost exclusively in the parotid gland. Nine previous instances of the bilateral occurrence of this tumor in the parotid gland have been reported. We present a tenth case and illustrate several aspects of the clinical behavior of this unique tumor. The histological pattern of this type of tumor was considered universally to be benign until 1953 when attention was called to a malignant variant. It is difficult to find reference to a benign form after that time. It is, in fact, impossible to forecast the clinical behavior of an individual specimen based upon its histopathology. In order to recognize this unpredictability, the World Health Organization Classification of Epithelial Tumors of Salivary Gland Origin proposed a category, "Acinic Cell Tumors," separate from clearly benign or malignant neoplasms. Later, attention was called to the grammatical designation, "acinous cell tumor." Because acinous cell tumors are uncommon, numerically significant series are gathered from several institutions or over several decades during which treatment methods vary widely. This makes it difficult to accept the validity of conclusions based upon the reported data. There is, however, a clearly documented tendency of the tumor to recur after long symptomless intervals so that extended follow-up is necessary before "cure" is established. Treatment of acinous cell tumors is surgical. The value of radiation therapy in the management of recurrent tumors is not firmly established.

Carcinoma↗

PubMed1991

Superficial oral fungal infections.

Fungal infections in humans are provoked and exacerbated by defects in the cellular immune system. Hence, the emergence of novel clinical variants of oral candidoses and rare mycoses with the pandemic spread of human immunodeficiency virus infection is not surprising. The new clinical entities of oral candidoses that have been described in the past few years have had a significant impact on the classification of these diseases. Classification of oral candidoses is an issue addressed in some detail here. Angular cheilitis is a disease commonly associated with Candida infection. In the West, it is frequently seen in the elderly, but a report from Asia indicates that the disease may be prevalent in the young age groups due to factors such as anemia, despite the similarity of the infective agents. A novel cofactor implicated in infectious states has been the host blood group secretor status, and data from three studies suggest that the latter may play an intriguing role in the pathogenesis of oral candidosis. Finally, a new mouse model has been described as a substitute for the rat model in investigating the host-parasite interactions in oral candidosis, and its pros and cons are reviewed.

Acquired Immunodeficiency Syndrome↗

PubMed1999

Classification of sporadic Creutzfeldt-Jakob disease based on molecular and phenotypic analysis of 300 subjects.

Phenotypic heterogeneity in sporadic Creutzfeldt-Jakob disease (sCJD) is well documented, but there is not yet a systematic classification of the disease variants. In a previous study, we showed that the polymorphic codon 129 of the prion protein gene (PRNP), and two types of protease-resistant prion protein (PrP(Sc)) with distinct physicochemical properties, are major determinants of these variants. To define the full spectrum of variants, we have examined a series of 300 sCJD patients. Clinical features, PRNP genotype, and PrP(Sc) properties were determined in all subjects. In 187, we also studied neuropathological features and immunohistochemical pattern of PrP(Sc) deposition. Seventy percent of subjects showed the classic CJD phenotype, PrP(Sc) type 1, and at least one methionine allele at codon 129; 25% of cases displayed the ataxic and kuru-plaque variants, associated to PrP(Sc) type 2, and valine homozygosity or heterozygosity at codon 129, respectively. Two additional variants, which included a thalamic form of CJD and a phenotype characterized by prominent dementia and cortical pathology, were linked to PrP(Sc) type 2 and methionine homozygosity. Finally, a rare phenotype characterized by progressive dementia was linked to PrP(Sc) type 1 and valine homozygosity. The present data demonstrate the existence of six phenotypic variants of sCJD. The physicochemical properties of PrP(Sc) in conjunction with the PRNP codon 129 genotype largely determine this phenotypic variability, and allow a molecular classification of the disease variants.

Adult↗

PubMed2004

Functional classification of proteins and protein variants.

To help characterize the diversity in biological function of proteins emerging from the analysis of whole genomes, we present an operational definition of biological function that provides an explicit link between the functional classification of proteins and the effects of genetic variation or mutation on protein function. Using phylogenetic information, we establish definite criteria for functional relatedness among proteins and a companion procedure for predicting deleterious alleles or mutations. Applied to the functional classification of sequences similar to 13 human tumor suppressor proteins, our methods predict there are functional properties unique to mammals for three of them, BRCA1, BRCA2, and WT1. We examine protein variants caused by nonsynonymous single-nucleotide polymorphisms in a set of clinically important genes and estimate the magnitude of a disproportionate propensity for disruption of function among the nonsynomous single-nucleotide polymorphisms that are maintained at low frequency in the human population.

Amino Acid Substitution↗

PubMed2003

Recent advances in the diagnosis and management of nonspecific interstitial pneumonia.

Idiopathic interstitial pneumonia is a heterogeneous group of diseases. Recently, the importance of a detailed differentiation of nonspecific interstitial pneumonia from other idiopathic interstitial pneumonias has been demonstrated. Most critical appeared to be a proper classification based on clinical presentation, high-resolution CT findings, bronchoalveolar lavage fluid cell findings, and histopathology. This classification may guide the most appropriate therapeutic approach and has significant implications regarding prognosis. Recent advances in the diagnosis and management of nonspecific interstitial pneumonia, cellular and fibrosing variants, are discussed.

Adrenal Cortex Hormones↗

PubMed2006

Autoimmune neuropsychiatric disorders associated with streptococcal infection: Sydenham chorea, PANDAS, and PANDAS variants.

Streptococcal infection in children is usually benign and self-limited. In a small percentage of children, prominent neurologic and/or psychiatric sequelae can occur. Sydenham chorea is the best defined and best recognized. PANDAS (pediatric autoimmune neuropsychiatric disorders associated with streptococcal infection) is a well-defined syndrome in which tics (motor and/or vocal) and/or obsessive-compulsive disorder consistently exacerbate in temporal correlation to a group A beta-hemolytic streptococcal infection. PANDAS constitutes a subset of children with tics, Tourette syndrome, and obsessive-compulsive disorder. In addition to strictly defined PANDAS, we and others have recognized several PANDAS variants, including adult-onset variant, a dystonic variant, a myoclonic variant, and a "chronic" PANDAS variant. The nosology and classification of these entities are rapidly evolving. The recognition that some pediatric neurobehavioral syndromes have infectious and/or immunologic triggers points to important new avenues of disease treatment. In this review, we summarize this complex and rapidly evolving area of clinical research.

Adolescent↗

PubMed2003

Primary endocrinomas (carcinoids and variant neoplasms) of the gallbladder. A statistical evaluation of 138 reported cases.

This study was carried out to obtain extensive information on carcinoids (the carcinoid group) and related variant endocrinomas (the variant group) of the gallbladder, and to statistically analyze their characteristics from various clinicopathologic aspects. A total of 138 cases were collected from the international sources, 101 belonging to the carcinoid group and 37 to the variant group. The first group consisted of 81 cases of typical and 20 atypical carcinoids. Comparative evaluation was attempted mainly between the carcinoid and variant groups, and occasionally between the typical and atypical carcinoid series when statistical significance was suspected. The carcinoid group showed a statistically significant difference from the variant group by exhibiting a younger average age (61.7 years vs 69.7 years: P<0.01), a higher incidence of associated cholelithiasis (87.3% vs 56.0%: P<0.01), a higher incidence of small tumors 50 mm or less (85.2% vs 52.9%: P<0.01), a smaller average tumor-size (29.6 mm vs 58.7 mm: P<0.01), a lower rate of metastases (40.7% vs 70.6%: P<0.05), a higher immunoreactivity rate of chromogranin (100.0% vs 66.7%: P<0.01), a lower immunoreactivity rate of gastrin (23.8% vs 70.6%: P<0.01), and a higher five-year survival rate (60.4% vs 21.3%: P<0.0005). Significant differences in various clinicopathological aspects confirmed between the carcinoid group and the variant group suggested that endocrine carcinomas of these two groups perform a different clinical pattern, represented most clearly by postoperative outcomes. These groupings are decided on the basis of histologic patterns, namely, well to poorly differentiated endocrine carcinomas (typical to atypical carcinoids) and undifferentiated or anaplastic variants of other endocrine carcinomas. The basic criteria for such classification of these endocrine carcinomas based on international agreements are required.

Age Factors↗

PubMed1980

[Certain features of the morphology of Hodgkin's disease].

Investigation of lymphogranulomatosis process in 42 patients included histological examinations of chains of lymph nodes with varying duration of their involvement. Lymphogranulomatosis was shown to begin with focal involvement of lymph nodes. The specific focus is initially located in the paracortical zone, then the pathological process extends into the medullary zone and finally into the cortical zone. As early and finally into the cortical zone. As early as the focal lesions occur the cell composition already corresponds to one of histological variants of lymphogranulomatosis (by Lukes' classification). No transition from variants with lymphoid prevalence to those with lymphoid exhaustion in groups of removed lymph nodes from the same patient was observed indicating independent development of each histological type and its stability for a given patient. No correlation between the clinical stage and morphological type of lymphogranulomatosis was established.

Adolescent↗

PubMed1991

[Is the new WHO's histological typing clinically useful for the diagnosis of follicular cancer of the thyroid?].

We tried to re-diagnose our 57 cases of thyroid follicular cancer between 1965 and 1988 in accordance with Histological Typing of Thyroid Tumours published by WHO in 1988. 1) The incidence of follicular cancer in differentiated cancers was decreased from 17.9% to 8.3% (26 cases). The number of widely invasive type and minimally invasive type was 13 cases equally. 2) Twenty four cases were diagnosed as papillary cancer. The reason was that 20 cases had a small focus of papillary structure, and other 4 cases had features of follicular variant type of papillary cancer. These 24 cases had good prognosis as our 262 cases of papillary cancer, in contrast to 26 cases of follicular cancer having worse prognosis. 3) The incidence of distant metastasis in follicular carcinoma was increased from 28.1% to 42.3%; 23.9% in minimally invasive type and 61.5% in widely invasive type, respectively. New WHO classification is acceptable according to this clinical study of our cases. We would have to treat more aggressively the patient diagnosed follicular cancer by WHO classification because of high incidence of distant metastasis.

Adenocarcinoma↗

PubMed2026

Reinforcement learning-based dynamic ensemble for missense variant effect prediction and tiered prioritization of VUS.

BACKGROUND: Accurate classification of missense variants remains a challenging task despite major advances in genomics. Numerous computational models have been developed to assist in variant classification, but often require repeated integration and benchmarking efforts. Ensemble methods have been proposed to overcome the limitations of single predictors, but mostly rely on fixed, predefined weights that constrain their ability to capture interactions among predictive signals. METHODS: We present GenixRL, a dynamic ensemble framework that reformulates model fusion as a reinforcement learning optimization problem. GenixRL uses a Q-learning agent to learn a policy that dynamically weights the probabilistic outputs of complementary predictors, including BayesDel (addAF and noAF), ClinPred, and MetaRNN. Replacing static weighting with policy learning allows GenixRL to adaptively identify optimal weightings and substantially improve classification accuracy. RESULTS: In benchmark evaluation against 25 state-of-the-art predictors, GenixRL achieved an AUROC of 0.9644 on an independent ClinVar dataset. On saturation genome editing assays for BRCA1 and BRCA2, GenixRL achieved the best performance and ranked highest on 14 of 17 clinically significant genes in a zero-shot evaluation. Applied to uncertain and conflicting ClinVar variants, GenixRL enabled tiered, evidence-based prioritization of hundreds of thousands of variants as likely pathogenic or pathogenic with high confidence, supported by orthogonal population evidence from gnomAD. CONCLUSION: GenixRL advances pathogenicity prediction for missense variants and provides an adaptive ensemble that sorts variants of uncertain significance into tiered candidates for expert curation and functional validation.

Mutation, Missense↗

PubMed1993

[A resected case of well-differentiated adenocarcinoma simulating fetal lung tubules which is a variant of pulmonary blastoma].

A case of well-differentiated adenocarcinoma simulating fetal lung tubules which is a variant of pulmonary blastoma is reported. A 31-year-old female with an abnormal shadow in the right upper lung field detected by chest X-P during a follow-up for sarcoidosis during pregnancy underwent right upper lobectomy. Post operative histological diagnosis was well-differentiated adenocarcinoma simulating fetal lung tubules. This tumor might be a variant of pulmonary blastoma lacking the sarcomatous features and showing one-sided development of the epithelial component. However, it has been reported by various names, and classifications of pulmonary blastoma differed slightly depending on the reporter. There are also some discrepancies in the clinical course and prognosis of the tumor. Therefore it is considered that further examination of this tumor is necessary.

Adenocarcinoma↗

PubMed2026

XXYLT1 and Mendelian Retinal Dystrophy.

IMPORTANCE: Substantial unexplained heritability remains for pathogenic inherited retinal disease (IRD) variants. Application of genome-wide association studies (GWAS) could help identify causal genes in rare diseases. OBJECTIVE: To leverage a GWAS for the discovery of IRD-associated genes. DESIGN, SETTING, AND PARTICIPANTS: This GWAS analysis was combined with replication of findings in 2 independent IRD cohorts. The study was conducted from January 2024 to December 2025 in a multicenter setting through FinnGen, 100 000 Genomes Project, and the National Health Service Genomic Medicine Service combined with clinical cohort from the Oulu University Hospital. Using IRD criteria from the International Classification of Diseases, 9th and 10th Revisions, 540 individuals with IRD and 473 945 control individuals were identified in the FinnGen study. For validation of FinnGen results, 49 patients were recruited from Oulu University Hospital. Results were further validated in 2 individuals identified from the UK cohort. MAIN OUTCOMES AND MEASURES: The GWAS and proteomics analysis were performed in the FinnGen cohort. Sanger and whole-genome sequencing and RNA approaches were used in a clinical IRD cohort to validate pathogenicity of the identified XXYLT1 variant. RESULTS: This GWAS identified 13 recessive loci reaching genome-wide significance (defined as P < 5 × 10-8). Of these, 4 (near or within XXYLT1, ANKRD10, DYM, and CBLN4) had not been associated with IRD, including the XXYLT1 c.505-1G>C founder variant. This variant was further genotyped in the clinical replication cohort, leading to identification of 5 more homozygous individuals from 4 families. The phenotype was consistent with a cone-rod or macular dystrophy, with visual deterioration, cystoid macular edema and/or schisislike macular abnormalities. The effect of the XXYLT1 c.505-1G>C variant was further investigated using RNA sequencing and complementary DNA amplicon sequencing, demonstrating exon 2 skipping and a loss-of-function effect. These findings were replicated in an independent population identifying 2 patients from the UK harboring a homozygous XXYLT1 c.766G>A, p.(Glu256Lys) missense variant. CONCLUSIONS AND RELEVANCE: This GWAS identified an association between XXYLT1 and IRD. These results affirm that GWAS in a founder population can be used as a potential tool for the discovery of rare mendelian disease genes and that XXYLT1 should be considered in clinical IRD gene panels.

Humans↗

PubMed2000

Human immunodeficiency virus type 2 (HIV-2) in Portugal: clinical spectrum, circulating subtypes, virus isolation, and plasma viral load.

The human immunodeficiency virus type 2 (HIV-2) is responsible for 4. 5% of AIDS cases in Portugal. Six HIV-2 subtypes have been described so far, subtype A being proposed as more pathogenic than the rest. The relationship between the clinical status and levels of both cellular and plasma HIV-2 viraemia is not well known, nor their modifications under antiretroviral therapy. Thirty-two consecutive HIV-2 infected persons (17 men, 15 women) attending two different hospitals in Lisbon in 1997 were enrolled prospectively in the study. All but 4 individuals most likely acquired the infection through heterosexual contact. More than half of the study population was of African origin, mainly from Guinea-Bissau. Eleven (34.4%) patients had developed clinical manifestations included within the B or C groups of the CDC classification system for HIV infection, with the rest being asymptomatic. Half of the population was undergoing antiretroviral treatment at the time of the study. HIV-2 subtypes were investigated using a new Nef-based restriction fragment length polymorphism (RFLP) method that allows differentiation of the main two variants, A and B. Plasma viral load was quantified using a new quantitative competitive reverse transcriptase polymerase chain reaction (QcRT-PCR) procedure as well as the Amp-RT assay. Virus isolation was attempted from peripheral blood mononuclear cells. All but one person carried HIV-2 subtype A. Plasma viraemia examined by QcRT-PCR was measurable in 15 (50%) of 30 subjects, yielding in all instances values below 20,000 HIV-2 RNA copies per ml. Plasma RT activity could be detected in only 10 (33%) of 30 subjects, a rate much lower than that seen in HIV-1 infection. Virus was isolated from 16 (53.3%) of 30 patients. A significant correlation was found between CD4+ counts, clinical status, rate of virus isolation, and plasma viral load by both QcRT-PCR and Amp-RT. In conclusion, HIV-2 subtype A is the predominant variant circulating in Portugal among both natives and immigrants. A lower cellular and plasma viral load with respect to HIV-1 was seen in persons without immunosuppression, from whom the rate of virus recovery was extremely low.

Female↗