Search PubMedSearch

SEARCH · Search PubMed

Results for “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.

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

At least 271 records · Page 15Linked to original sources

Prognostic implications of blast cell morphology in childhood acute lymphoblastic leukemia: a report from the Childrens Cancer Study Group.

The Childrens Cancer Study Group (CCSG) has evaluated French-American-British (FAB) morphology in newly diagnosed children with acute lymphoblastic leukemia (ALL) since 1975. A modification of the FAB system was used in which individual lymphoblast cells were scored and designated as either L1 or L2 on the basis of distinctive morphologic characteristics. L1 ALL was defined as less than 10% L2 cells and greater than 90% L1 cells; L2 ALL was defined as greater than or equal to 10% L2 cells and less than 90% L1 cells. FAB morphology was an independent predictor of overall survival (P = 0.02) in CCSG-141 and a highly significant predictor of successful induction of complete remission and event-free survival in the CCSG-160 series (P = 0.00001). These studies involved nearly 3900 patients. Two concordance studies have been performed. In the first (1981) study, overall concordance between the FAB reference laboratory and member institutions was 76% using a two-category system (L1, non-L1), 86% for L1 cases, and 47% for non-L1 cases. In the second (1984) concordance study, the use of more stringent, semiquantitative definitions of L1 and L2 lymphoblasts did not improve overall (75%), L1 (89%), or non-L1 (46%) concordance. The results of reference laboratory classification more powerfully predicted event-free survival than did member institutions (P = 0.016 vs P = 0.125). Quality control factors (slide preparation, cellularity, staining quality, and discipline of the reviewer) did not influence concordance. These results justify the continued assignment of patients to protocols of the CCSG-100 series on the basis of the modified FAB classification. The biological significance of the FAB morphologic variants remains to be determined.

Child

[Clinico-morphological characteristics and working classification of kidney diseases in patients with systemic scleroderma].

Based on a study of 110 patients with systemic scleroderma (SSD) (74 had involved and 36 uninvolved kidneys) the authors provide the clinico-functional and morphological characteristics of renal lesions and the working classification of sclerodermic nephropathy (SN). The two basic variants of SN were recognized: acute and chronic. The latter one was subdivided into clinical, moderate and pronounced SN. A correlation was revealed between the functional (glomerular filtration lowering) and ultrastructural (reticulation of endotheliocytes and thickening of the basal membrane of the glomerular capillaries) signs evidencing derangement of the microcirculatory bed. Morphological examination of the kidneys disclosed alterations that mirror the complex pathogenesis of SSD: derangement of the microcirculatory bed, immunopathological disorders, activation of connective tissue components.

Adolescent

[Carcinoma of the major duodenal papilla].

The analysis of 134 postmortem cases and 65 clinical observations of carcinoma of the major duodenal papilla (MDP) has revealed different variants of development of carcinoma of MDP. The classification by the TNM system is made. In 34% of cases carcinoma was found to spread beyond the duodenum limit. Papillectomy should not be considered radical intervention. Average survival time after papillectomy was 17 months, after pancreatoduodenal resection it was 34 months. Fibroduodenoscopy, laparoscopic cholecystocholangiography in combination with relaxation duodenography was used for early diagnosis of carcinoma of MDP. Laparoscopic investigation was always accomplished by laparoscopic cholecystostomy which permitted avoiding hepatic insufficiency in the postoperative period.

Adult

[Classification of the types of blood supply of the muscles from the standpoint of plastic surgery].

Based on an experience with 120 composite flaps including the muscle and with special account of literature data the author describes a new classification of types of blood supply of muscles. The author proposes 6 types of blood supply of muscles and substantiates a direct relationship between the anatomy of muscle vessels and variants of its use for plasty. A comparison of the new classification and other classifications was made.

Blood Vessels

[Effects of immunologic markers on prognosis in acute lymphoblastic leukemia in young children].

Altogether 77 children aged up to 3 years with acute lymphoblastic leukemia (ALL) were examined for the immunological phenotype of blast cells. L1, L1/L2, L2/L1, L2 variants of ALL and the undifferentiated one were established in accordance with criteria of the FAB classification. T1, zero and Ia immunosubvariants were recorded most frequently. Mature cell T2 and pre-B variants (3 and 2 cases, respectively) were rare; B-cellular acute lymphoblastic leukemia was lacking; the "common" subvariant was revealed in 28 patients. The patients' age produced the highest effect on the prognosis: the significantly least disease standing and remissions were noted in a group of children under 2 years as compared to those aged 2 to 3 years. As for immunological markers, expression of Thy1-antigen exerted an unfavourable effect on the prognosis and duration of the first remission.

Antibodies, Monoclonal

Classification and survival rate of patients with serous cystadenocarcinoma of the ovaries.

The comparative evaluation of two stage classifications including USSR Ministry of Health stage classification and TNM system was performed on the base of studies of the end results of 419 patients with serous cystadenocarcinoma of the ovaries. It has been established that TNM system is of a greater importance in establishing more accurate prognosis than the stage classification of the Ministry of Health. In TNM system four variants of the degree of extension correspond to each stage that allows to evaluate not only the extent of the primary tumor that also of the metastatic spread. The achieved results point to the superiority of the TNM system and serve as a base for transition to the TNM system in the classification of ovarian carcinoma.

Cystadenocarcinoma

Hürthle cell (oxyphilic) papillary thyroid carcinoma: a variant with more aggressive biologic behavior.

The latest World Health Organization International Classification defines papillary thyroid carcinoma by its "follicular cell differentiation...as well as characteristic nuclear changes". However the oxyphilic (Hürthle cell) papillary carcinoma have nuclei which generally resemble the nuclei seen in oxyphilic follicular carcinomas, and such oxyphilic papillary tumors may behave more aggressively than typical papillary cancers. To further characterize these rare tumors, we identified during a 32-year period 22 patients with oxyphilic papillary cancer and compared them with 1,084 patients with typical papillary cancers and 57 patients with oxyphilic follicular cancers treated by the Mayo surgical group during the same time period. Although typical papillary and oxyphilic papillary cancers were comparable with regards to patient age, tumor size and extent, TNM stage, and prognostic score (AGES), there were significant differences. Compared to typical papillary tumors, oxyphilic papillary cancers had fewer neck nodal metastases at primary diagnosis (5% vs 40%, p less than 0.0001), were more often DNA non-diploid (71% vs 21%, p less than 0.001), and after 10 postoperative years had higher rates of both tumor recurrence (28% vs 11%, p less than 0.0001) and cause-specific mortality (1.7% vs 4%, p less than 0.0005). In these four important respects the oxyphilic papillary cancers more resembled the oxyphilic follicular cancers. For oxyphilic follicular cancers, the frequency of initial neck nodal metastases was 7% (cf 5%); 83% of the oxyphilic follicular tumors were non-diploid (cf 71%), and at 10 years postoperatively the tumor recurrence and cause-specific mortality rates were 28% and 18%, insignificantly different from 28% and 17% seen with the oxyphilic papillary cancers.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent

Uveal Melanoma and the Lynch Syndrome Tumor Spectrum.

IMPORTANCE: To date, no environmental factors and few therapeutic options are known for uveal melanoma (UM), the most common malignant intraocular primary tumor in adults. Identification of new predisposition factors could lead to better monitoring and possibly improved treatments of patients with UM. OBJECTIVE: To identify new genetic alterations predisposing for UM. DESIGN, SETTING, AND PARTICIPANTS: This was a prospective cohort study conducted at Institut Curie in Paris, France, among 381 consecutive patients diagnosed with UM between July 2021 and February 2023. UM was diagnosed clinically by ophthalmologists, and a senior pathologist confirmed the diagnosis when tumor or biopsy was available. All participants received genetic counseling and consented to extended genetic testing. A panel of 122 genes predisposing to cancer were analyzed by targeted sequencing on germline DNA from these patients. MAIN OUTCOMES AND MEASURES: Frequency of pathogenic variants (PVs) in genes from a targeted panel, with classification of germline PVs done according to the American College of Medical Genetics and Genomics guidelines and the French Unicancer Genetics Group. RESULTS: A total of 79 PVs were identified in 70 participants (41 female and 29 male; mean [SD] age, 60.6 [15.3] years). Among them, 21 were found in clinically relevant genes, with an enrichment in the mismatch repair (MMR) genes, involved in Lynch syndrome, a frequent predisposition to colon and endometrial cancers. This finding suggested MMR germline PVs could also predispose to UM. One tumor was available from a participant carrying a MLH1 germline PV. The tumor exhibited a monosomy 3 with loss of the wild-type allele of MLH1, located on chromosome 3. Loss of expression of MLH1 was observed by immunohistochemistry, and MMR variant signatures SBS6, ID1, and ID2 were identified from the whole-genome sequencing of this tumor, supporting the possibility that MLH1 contributes to the oncogenesis of this UM. CONCLUSIONS AND RELEVANCE: This prospective germline study on patients with UM provided evidence supporting the notion that MMR germline alterations are enriched among patients with UM and may contribute to oncogenesis of UM, and that UM may therefore be a rare tumor manifestation of Lynch syndrome.

Humans

Multilobated non-Hodgkin's lymphoma. A clinicopathologic entity.

Multilobated non-Hodgkin's lymphomas (NHL) have recently been recognized as an NHL variant. During a period of 10 years we observed 30 individuals with NHL in which more than 30% of the malignant cells had a characteristic multilobation. The immunologic phenotype was determined in 14 of these cases. One was of T-cell lineage, and the others exhibited B-lymphoid markers. Sixty-eight percent of the patients presented with extranodal localizations. In the clinical follow-up a complete remission was observed in 78% of patients with a mean duration of 37 months (range, 5 to 120 months). The actuarial survival after 5 years was 45%. From these data we conclude that multilobated NHL are comparable to diffuse, large cleaved-cell NHL of an intermediate grade malignancy according to the Working Formulation or are comparable to the diffuse centrocytic-centroblastic NHL according to the Kiel classification. The neoplastic cells are to be considered as variants of follicle center cells, but the clinicopathologic correlation indicates that multilobated NHL represent a distinct nosologic entity.

Adolescent

[The genetics of rheumatic diseases: genetic basis of the classification of multifactorial diseases].

Examination of the pattern of hereditary predisposition allows a more precise determination of pathogenetic relationships between individual clinical forms and variants of multifactorial diseases (MFD), as well as assessment of the possibilities and approaches to a genetic classification to be made. The construction of genetic classifications is based on the identification of differences in the type of inheritance, the study of the progeny in families where both parents have the same or different forms of the disease, the results of the marker adhesion test, and the genetic correlation coefficients. The study has made use of some clinical forms of rheumatic diseases, whose relationships are a subject of controversy among the clinicians, as splitting phenotypes. Segregation analysis of the selected clinical forms of rheumatic diseases and genetic correlation coefficients obtained within the framework of a quasi-continuous model provide no indication that these forms can be isolated as independent nosologic entities. Possible phenotype splitting into individual subtypes and the potentialities of a marker approach to the construction of genetic MFD classifications are demonstrated, with rheumatoid arthritis associated with HLA antigen Dr 4 taken as an example.

Classification

Withdrawal akathisia: case reports and a proposed classification of chronic akathisia.

Two patients with akathisia developing only after neuroleptic dosage reduction or withdrawal are described. The literature dealing with tardive or chronic akathisia is reviewed with an emphasis on the existence of variants including the occurrence of symptoms upon withdrawal of the causative drug. A classification of tardive or chronic akathisia syndrome is proposed.

Adolescent

Exploring the Melanoma and Pancreatic Cancer Phenotype of a Potential CDKN2A Founder Variant, I49T (c.146T>C; p.Ile49Thr), in Individuals of Predominantly Mexican Ancestry.

PURPOSE: Pathogenic/likely pathogenic variants (P/LPVs) in the CDKN2A gene cause an increased risk of melanoma (MEL) and pancreatic cancer (PANC). The CDKN2A variant I49T (c.146T>C), reported to be recurrent in Hispanics, has conflicting pathogenicity classifications at laboratories, affecting clinical care. Multiple genetics clinics collaborated to explore cancers associated with I49T. METHODS: Institutional clinical databases were queried for the CDKN2A variants, I49T, known P/LPVs, and c.-2G>A (a benign variant [BV]), and history of PANC and MEL was abstracted. A combination of statistical tests was used to investigate cancer history associations. RESULTS: Data on 203 individuals, with qualifying CDKN2A variants detected on multigene testing between 2012 and 2023, were analyzed (I49T, n = 101; known CDKN2A P/LPVs, n = 57; BV, n = 45). Those with I49T were 91% less likely to have MEL than known CDKN2A P/LPVs (odd ratio [OR] = 0.089 [95% CI, 0.031 to 0.025]; P < .001) and were also less likely to have PANC (OR = 0.45 [95% CI, 0.14 to 1.41]; P = .17). However, mean age at PANC diagnosis for I49T was 56.0 years, significantly younger than known CDKN2A P/LPVs (&#x3bc; = 71.0 years; P = .026). CONCLUSION: In the largest I49T study to date to our knowledge, MEL was significantly less frequent compared with known CDKN2A P/LPVs. Although a nonsignificant trend was observed for less PANC in I49T than known P/LPVs, individuals with I49T presented with PANC at a significantly younger age than those with known CDKN2A P/LPVs. The presence of I49T in Hispanics of mostly Mexican ancestry supports that it is a founder variant, relevant to understanding cancer risk in a large proportion of Hispanics in the United States.

Humans

Autosomal dominant Emery-Dreifuss syndrome: evidence of a neurogenic variant of the disease.

The first German family with autosomal dominant Emery-Dreifuss syndrome (EDS) is described, with electrophysiologic and myopathologic results providing evidence of a primary neurogenic disease. According to classification of the scapulo peroneal syndrome without cardiomyopathy, we conclude that there are two variants of EDS: one myopathic, the other neurogenic in origin. Therefore, the term Emery-Dreifuss muscular dystrophy should be avoided. Instead, each case of EDS should be classified as myopathic or neurogenic with X chromosome recessive or autosomal dominant inheritance.

Adolescent

Ovarian neoplasms resembling sex cord tumors with annular tubules.

A clinicopathologic analysis of 6 patients with ovarian neoplasms resembling sex cord tumors with annular tubules (SCTAT) was performed. The patients' ages ranged from 20 to 43 years. Most had signs and symptoms of estrogenic hormonal imbalance; none had evidence of the Peutz-Jeghers syndrome. The tumors were unilateral in all cases and, except for one lesion of microscopic size, were from 3 to 18 cm in greatest dimension. One tumor was combined with a germinoma. Surgery alone was the primary mode of therapy in all cases. Lymph nodal metastases developed in 2 patients 7.5 and 10.5 years postoperatively. They are the first documented examples of malignant behavior recorded. At the time of last known contact, all patients were alive without demonstrable tumor for intervals from 1.5 to 16.3 years (mean, 7.8 years) after initial treatment. While the annular patterns of growth have often been attributed to Sertoli cell differentiation, histologic and cytologic features of granulosa cell tumor were observed in areas of the primary tumors and in metastatic lesions. True lumen formation was never observed in the so-called tubules. We propose classification of SCTAT as a distinctive annular and membranous variant of granulosa cell tumor in view of the morphologic similarities and comparable clinical behavior of these two neoplasms.

Adult

A new von Willebrand factor (vWF) defect in a patient with factor VIII (FVIII) deficiency but with normal levels and multimeric patterns of both plasma and platelet vWF. Characterization of abnormal vWF/FVIII interaction.

The patients with inherited bleeding diathesis related to quantitative, structural, and/or functional abnormalities of von Willebrand factor (vWF) are said to have von Willebrand's disease (vWD). We report here the clinical and laboratory features of a 50-year-old woman with a life-long history of excessive bleeding. Her particular laboratory data are factor VIII (FVIII) deficiency, subnormal bleeding time, and the presence of all plasma and platelet vWF multimers in normal amounts. Infused with FVIII/vWF concentrate, she showed a persistent increase in FVIII that led us to discard hemophilia A carrier or "acquired hemophilia" diagnoses. vWF devoid of FVIII purified from normal and patient's plasma by immunoaffinity on anti-vWF monoclonal antibody (MoAb) was immobilized onto polystyrene tubes that were further incubated with purified normal FVIII. The bound FVIII was evidenced using radiolabeled anti-FVIII MoAb. The data showed that the patient's vWF, in contrast to vWF purified from normal plasma, was unable to bind FVIII. Furthermore, no inhibitor of FVIII/vWF interaction was evidenced in incubating purified normal vWF with the patient's plasma before the addition of FVIII and anti-FVIII MoAb. These results support the concept that the bleeding diathesis of this patient appears to be due mainly to her abnormal vWF preventing FVIII/vWF interaction. This abnormality, which is not yet described in present classification of vWD, could be considered as a new variant of vWD.

Factor VIII

Von Willebrand factor and von Willebrand's disease: a complex protein and a complex disease.

Von Willebrand factor is a complex protein which is important in several ways for normal hemostasis. Von Willebrand's disease results when there is either a quantitative or qualitative disorder of von Willebrand factor. In this review, the structure and function of von Willebrand factor are discussed. Additionally, the current laboratory and clinical classification of von Willebrand's disease and closely related variants are outlined.

Factor VIII

CAKL: Commutative algebra k-mer learning of genomics.

Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fundamental tool in algebraic geometry and number theory, has rarely been used in data and biological sciences. In this study, we introduce commutative algebra k-mer learning (CAKL) as the first-ever nonlinear algebraic framework for analyzing genomic sequences. CAKL bridges between commutative algebra, algebraic topology, combinatorics, and machine learning to establish a new mathematical paradigm for comparative genomic analysis. We evaluate its effectiveness on three tasks-genetic variant identification, phylogenetic tree analysis, and viral genome classification-typically requiring alignment-based, alignment-free, and machine-learning approaches, respectively. Across eleven datasets, CAKL outperforms five state-of-the-art sequence analysis methods, particularly in viral classification, and maintains stable predictive accuracy as dataset size increases, underscoring its scalability and robustness. This work ushers in a new era in commutative algebraic data analysis and learning.

Journal Article

[Epithelial tumors of the liver (histology, histogenesis, classification)].

Under study were 120 epithelial hepatic tumors. The problems of histology, histogenesis, classification, morphogenesis of hepatic tumors are being under consideration from the point of view of modern oncology with due account of tumor progression and its development in tumor field. Various trends of differentiation with isolation of histologic variants of epithelial tumors of the liver have been shown. The histological classification is suggested.

Adenocarcinoma