Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Variant calling”

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 433 records · Page 24Linked to original sources
PubMed1980

[Classification of stomach and intestinal tumors].

Having compared world oncological literatures with his own series [about 1000 cases] of tumours of the stomach, small intestine, appendix, and large intestine [diagnosed bioptically as well as necroptically], the author recommends a simplification of the usual classification scheme on the grounds that mesenchymal and neuroectodermal tumours do not require any other scheme than for soft tissue tumours. Likewise, anal tumours so long as there are skin variants do not call for any independent classification. The author recommends the following classification of epithelial tumours: Adenoma: a] tubular; b] villous; c] other types. Adenomatoid processes: a] harmartoma polyp; b] heterotopia [gastric, intestinal, duodenal, endometriosis, others]; c] hyperplasia; d] precanceroses e] others. Carcinoma: a] tubular; b] diffuse; c] solid; d] others [in situ, intramucous, tubopapillary, gelatinous, adenosquamous, cloacogenic, in ulcere peptico, non-classifiable]. The other tumours are mostly difficult to distinguish from metastases, and should therefore be assessed individually.

Humans↗
PubMed1995

MHC class I expression and transport in a calnexin-deficient cell line.

The human leukemic cell line, CEM, and an NK-resistant variant of CEM, called CEM-NKR, were analyzed for protein differences by two-dimensional gel electrophoresis. One protein was found to be completely absent in CEM-NKR. This protein has been identified as calnexin. CEM-NKR also completely lacks calnexin RNA. Calnexin is thought to act as a molecular chaperone by assisting in the assembly and/or retention of MHC class I and many other membrane and secreted proteins. The surface expression of class I molecules on CEM-NKR was compared with CEM by several Abs. There was no significant class I expression differences between CEM and CEM-NKR using w6/32 (a conformational and beta 2-microglobulin-dependent mAb), HC-10 (a conformational and beta 2-microglobulin-independent mAb), and an anti-class I antiserum that reacts with native and denatured class I. The transport rate of class I in both cell lines was examined by pulse-chase experiments, immunoprecipitating class I with w6/32 and anti-class I antiserum. The results show that class I molecules in the calnexin-deficient cell line and its parent cell line are transported at similar rates. These results indicate that calnexin is not absolutely required for the viability of CEM or the transport and surface expression of human MHC class I molecules.

Biological Transport↗
PubMed1994

Low-grade myxoid chondrosarcoma of the temporal bone: differential diagnosis and report of two cases.

Skull base chondrosarcoma and chordoma are rare tumors that generally have a poor prognosis. In 1973, Heffelfinger et al described a chondroid variant of chordoma, called chondroid chordoma that was found to have a significantly better prognosis than classic chordoma. However, recent evidence suggests that many of the tumors diagnosed as chondroid chordoma may, in fact, be low-grade myxoid chondrosarcomas. This report presents the diagnosis and treatment of two cases of skull base tumor that were diagnosed preoperatively as schwannoma because they were thought initially to be centred on the jugular foramen. Initial histologic evaluation suggested chondroid chordoma, but immunohistologic techniques and a review of the literature led to a diagnosis of low-grade myxoid chondrosarcoma.

Adult↗
PubMed1997

Characterization of a CNS cell line, CAD, in which morphological differentiation is initiated by serum deprivation.

A CNS catecholaminergic cell line, Cath.a, was established by targeted oncogenesis in transgenic mice. Cath.a cells express neuronal properties but lack neuronal morphology. Here, we describe a variant of Cath.a, called CAD (Cath.a-differentiated), in which reversible morphological differentiation can be initiated by removal of serum or exogenously added protein from the medium. In serum- or protein-free media, CAD cells stop proliferating and extend long processes. Differentiated CAD cells can be maintained without serum or protein for at least 6 weeks. CAD cells are distinct from Cath.a cells; most significant, the original immortalizing oncogene, SV40 T antigen, was spontaneously lost. By immunostaining or immunoblotting, we show that CAD cells express neuron-specific proteins, such as class III beta-tubulin, GAP-43, SNAP-25, and synaptotagmin, but not GFAP. Ultrastructurally, processes from differentiated CAD cells have abundant parallel microtubules and intermediate filaments, and bear varicosities that contain both large dense-core vesicles/granules (120-160 nm) and smaller clear vesicles (60-80 nm). Additionally, CAD cells express enzymatically active tyrosine hydroxylase and accumulate L-DOPA. CAD cells exhibit biochemical and morphological characteristics of primary neurons and provide an unique tool for studying neuronal differentiation.

Animals↗
PubMed2004

Novel down-regulatory mechanism of the surface expression of the vasopressin V2 receptor by an alternative splice receptor variant.

In rat kidney, two alternatively spliced transcripts are generated from the V2 vasopressin receptor gene. The large transcript (1.2 kb) encodes the canonical V2 receptor, whereas the small transcript encodes a splice variant displaying a distinct sequence corresponding to the putative seventh transmembrane domain and the intracellular C terminus of the V2 receptor. This work showed that the small spliced transcript is translated in the rat kidney collecting tubules. However, the protein encoded by the small transcript (here called the V2b splice variant) is retained inside the cell, in contrast to the preferential surface distribution of the V2 receptor (here called the V2a receptor). Cells expressing the V2b splice variant do not exhibit binding to 3H-labeled vasopressin. Interestingly, we found that expression of the splice variant V2b down-regulates the surface expression of the V2a receptor, most likely via the formation of V2a.V2b heterodimers as demonstrated by co-immunoprecipitation and fluorescence resonance energy transfer experiments between the V2a receptor and the V2b splice variant. The V2b splice variant would then be acting as a dominant negative. The effect of the V2b splice variant is specific, as it does not affect the surface expression of the G protein-coupled interleukin-8 receptor (CXCR1). Furthermore, the sequence encompassing residues 242-339, corresponding to the C-terminal domain of the V2b splice variant, also down-regulates the surface expression of the V2a receptor. We suggest that some forms of nephrogenic diabetes insipidus are due to overexpression of the splice variant V2b, which could retain the wild-type V2a receptor inside the cell via the formation of V2a.V2b heterodimers.

Alternative Splicing↗
PubMed1989

Nasal cerebral heterotopia: the so-called nasal glioma or sequestered encephalocele and its variants.

Twenty two nasal cerebral heterotopias were compared with 11 nasal encephaloceles. No histological feature was found that would allow a communication with the brain to be confidently identified or excluded. Even laminated cerebral cortex with neurones and ependymal canals, suggestive of encephalocele, were found in heterotopias. Distinction required radiological and surgical evidence. However, CT scan could be misleading, in one infant suggesting a cribriform plate defect when none was found at craniotomy. Three children had multiple extracranial glial lesions, two with both heterotopia and encephalocele in the same patient. In a few older children it was extremely difficult to identify brain tissue because of marked replacement by fibrous tissue (up to 95%), leading to one misdiagnosis as fibroma, and considerable fibrosis occurred also in five of six recurrences and in a longstanding small encephalocele. In two heterotopias, cellularity in places approached that of low-grade neoplastic glioma. One nasopharyngeal heterotopia contained multiple mesenchymal tissues suggestive of teratoma. Two midline nasopharyngeal encephaloceles showed adjacent epithelium, possibly vestiges of Rathke's pouch.

Brain↗
PubMed2000

Histoid, a clinical variant of multibacillary leprosy: report from so-called nonendemic areas.

This is a hospital-based study of 25 biopsy-proven cases of histoid leprosy in the arid, northwest Rajasthan region of India. Over an 11-year span, a total of 893 new cases of leprosy were diagnosed at our institution. These 25 histoid cases thus make up 2.8% of our new patients. Various clinical and laboratory observations are summarized and compared to other published series.

Adolescent↗
PubMed2001

Dandy-Walker variant in Coffin-Siris syndrome.

We describe a five-month-old male infant with Coffin-Siris syndrome, the so-called Dandy-Walker variant (hypoplasia of the cerebellar vermis with cystic dilatation of the fourth ventricle, but without enlargement of the posterior fossa), and partial agenesis of the corpus callosum. Dandy-Walker malformation and mega cisterna magna, but not Dandy-Walker variant, have been reported in Coffin-Siris syndrome. The presence of Dandy-Walker variant in the infant we described confirms that the full continuum of the Dandy-Walker complex can occur in Coffin-Siris syndrome. The yet unidentified gene(s) for the syndrome may be related to the development of the hindbrain.

Cisterna Magna↗
PubMed2000

Improved sensitivity of PCR for diagnosis of human granulocytic ehrlichiosis using epank1 genes of Ehrlichia phagocytophila-group ehrlichiae.

The agent of human granulocytic ehrlichiosis (HGE), Ehrlichia phagocytophila, and Ehrlichia equi probably comprise variants of a single Ehrlichia species now called the Ehrlichia phagocytophila genogroup. These variants share a unique 153-kDa protein antigen with ankyrin repeat motifs encoded by the epank1 gene. The epank1 gene was investigated as an improved target for PCR diagnosis of HGE compared with the currently used 16S rRNA gene target. Primers for epank1 flanking a region that spans part of the 5' ankyrin repeat coding region and part of the unique 3' region were synthesized. Blood samples from 31 patients with suspected HGE who were previously tested by 16S rRNA gene (16S) PCR and indirect immunofluorescent antibody test (IFA) were retrospectively tested with the epank1 primers. Eleven patients were 16S PCR positive and had a seroconversion detected by IFA (group A), 10 patients were 16S PCR negative but had a seroconversion detected by IFA (group B), and 10 patients were 16S PCR negative and seronegative (group C). Ten of the 11 group A patients were epank1 PCR positive, all 10 of the group B patients were epank1 PCR positive, and all of the PCR-negative and seronegative patients (group C) were epank1 PCR negative. The epank1 primers are more sensitive than the previously used 16S rRNA gene primers and therefore may be more useful in diagnostic testing for HGE.

Ankyrin Repeat↗
PubMed2002

HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.

We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci.

Databases, Genetic↗
PubMed1984

[Clinico-morphological variants of myocardial hypertrophy in patients with ischemic heart disease and idiopathic myocarditis (problem of so-called secondary hypertrophic cardiomyopathy)].

The authors studied the clinicomorphological variants of left ventricle hypertrophy in dead patients with coronary heart disease (CHD) and idiopathic myocarditis (IM). Postmortem examination of CHD patients showed both the symmetrical and asymmetrical patterns of left ventricle hypertrophy. IM patients manifested the combined dilatation of the heart cavities and myocardial hypertrophy. It is pointed out that in CHD patients, the presence of a "giant" negative T wave with ST interval depression in chest leads is mostly an ECG-sign of the common CHD course. However, it may be also a manifestation of marked left ventricle hypertrophy, which should be considered in the diagnosis and treatment of patients. It is noted that IM with remarkable myocardial hypertrophy and the presence of a "giant" negative T wave and ST interval depression on the ECG may take a favourable course. The use of the term "secondary hypertrophic cardiomyopathy" is regarded as unwanted.

Aged↗
PubMed1990

[Antigenic expression in human choroid plexus carcinoma: report of 2 cases].

Primary neoplasms of choroid plexus are rare. Six morphological variants have been described: papillary, cystic, acinar, mucus-secreting, oncocytic, and anaplastic. The anaplastic variant, the so-called choroid plexus carcinoma, is the rarest of all and can metastasize. The differential diagnosis of the anaplastic variant of choroid plexus neoplasms with adenocarcinomas, melanomas and undifferentiated neoplasms can be troublesome chiefly in adults. The now large use of immunocytochemical techniques in tissue section has become a powerful tool in the analysis of cell lineages, tumoral and non-tumoral. Nevertheless, the choroid plexus neoplasms have shown a complex and a somewhat confusing pattern of antigenic expression. In two choroid plexus carcinomas (one localized in the right lateral ventricle from a boy of 1 year and 9 months old, and the other localized in the left lateral ventricle from a girl of 3 years old) the following antigens were searched (using the avidin-biotin-peroxidase complex): glial fibrillary acidic protein (GFAP) with monoclonal and polyclonal antibodies; cytokeratins of 40-50kDa, cytokeratins of 60-70kDA (callus cytokeratin), neuronal specific enolase (NSE) and S-100 protein with monoclonal antibodies. The two neoplasms showed immunoreactivity against NSE, S-100 protein and cytokeratin of 40-50kDA. The neoplasm of the boy exhibited glial differentiation having immunoreactivity against GFAP with monoclonal and polyclonal antibodies.

Antigens, Neoplasm↗
PubMed1993

Molecular analysis of a variant 18;22 translocation in a case of lymphocytic lymphoma.

We previously reported a 5' rearrangement of the BCL2 locus in a t(18;22) variant translocation found in a lymphocytic lymphoma. Primary structure analysis of both rearranged chromosomes confirmed the localization of the breakpoint in the so-called vcr region (for variant cluster region) that encompasses Z-DNA stretches 5' of the BCL2 locus, and in between J lambda 1 and C lambda 1 segments on the IGL locus. A 1,027 nucleotide segment from chromosome 22 was repeated on both derivative chromosomes 18q+ and 22q-. This segment contained an octanucleotide that was also present in the normal chromosome 18 close to the breakpoint. As a consequence of the translocation, a normal-sized BCL2 transcript was overexpressed in tumor cells.

Base Sequence↗
PubMed2000

[Hepatic arterial vascular anatomy and its variants].

PURPOSE: We investigated the frequency of anatomical variants of the hepatic artery, which can influence interventional angiographic procedures. MATERIAL AND METHODS: We reviewed 150 consecutive angiograms performed for the treatment of primary (112) or metastatic (38) liver tumors and evaluated the frequency of anatomical variants of the hepatic artery based on the classification proposed by Michels in 1955, which describes 10 variants. The so-called typical anatomy, which is in fact only found in 55% of cases, is indicated as type I. RESULTS: The typical anatomy (type I variant) was seen in 78 patients (52%) and variants were seen in the other 72 (48%). We found 15 type II variants (10%), 23 type III (15.5%), 1 type IV and 1 type V (0.6%), 3 type VI (2%), 1 type VII (0.6%) and finally 6 type IX (4%). There were no type VIII or X variants, but in 22 patients (14.7%) vascular anatomy did not fit Michaels' classification. DISCUSSION AND CONCLUSIONS: In our series the typical hepatic artery anatomy was found in 52%, which is in agreement with Michels' findings, while the frequency of the individual anatomical variants differed. Not all of the variants reported by Michels were seen in our series and we found 22 patients with different variants. Disagreement might be due to the fact that Michels' was an autoptic series while our patients were cancer patients only and thus variability could be at least partly accounted for by neoplastic neovascularization. We believe that thourough knowledge of the anatomical variants of the hepatic artery is fundamental to angiographic practice, in particular for interventional procedures, because such variants can influence the choice of vascular technique and of materials.

Angiography↗
PubMed1998

Replication of R6K gamma origin in vitro: discrete start sites for DNA synthesis dependent on pi and its copy-up variants.

The regulation of the plasmid R6K gamma origin (gamma ori) is accomplished through the ability of the pi protein to act as an initiator and inhibitor of replication. Hyperactive variants of this protein, called copy-up pi, allow four to tenfold increases of gamma ori plasmid DNA in vivo. The higher activity of copy-up pi variants could be explained by an increase in the initiator function, a decrease in the inhibitor activity, or a derepression of a more efficient mechanism of replication that can be used by wt pi (pi35. 0) only under certain conditions. We have compared the replication activities of wt pi35.0 and copy-up pi mutants in vitro, and analyzed the replication products. It is shown that copy-up variants are several-fold more active than wt pi35.0 in replication. This appears to be due to enhanced specific replication activity of copy-up mutants rather than elevated fractions of protein proficient in DNA binding. Furthermore, biochemical complementation revealed that pi200 (copy-up) is dominant over wt pi35.0. The elevated activity of copy-up pi is not caused by an increased rate of replisome assembly as inferred from in vitro replication assays in which the lag periods observed were similar to that of wt pi35.0. Moreover, only one round of semiconservative, unidirectional replication occurred in all the samples analyzed indicating that copy-up pi proteins do not initiate multiple rounds of DNA synthesis. Rather, a larger fraction of DNA template replicates in the presence of copy-up pi as determined by electron microscopy. Two clusters of discrete DNA synthesis start sites are mapped by primer extension near the stability (stb) locus of the gamma ori. We show that the start sites are the same in the presence of wt pi35.0 or copy-up proteins. This comparative analysis suggests that wt pi35.0 and copy-up variants utilize fundamentally similar mechanism(s) of replication priming.

Amino Acid Substitution↗
PubMed2005

[Chronic pancreatitis--pancreas cancer: influence of genetic factors].

Chronic pancreatitis: Only recently mutations in several genes were found in patients with chronic pancreatitis. In those with a familial chronic pancreatitis mutations of the cationic trypsinogen were identified and the variants N29I and R122H lead to an autosomal dominant disease. In this group of patients the mutation N34S of the trypsin inhibitor SPINK1 was detected. In so-called idiopathic pancreatitis both variants of the SPINK1 and of the CFTR (cystic fibrosis transmembrane conductance regular) were identified. Alterations in both genes were also found in patients with alcoholic chronic pancreatitis. The strongest risk factor for chronic pancreatitis were trypsinogen mutations N29I and R122H mutations. However, both SPINK1 and CFTR increased the risk for chronic pancreatitis to a higher level than alcohol consumption. A genetic investigation should be performed in familial disease and younger age, but also in patients without family history and higher age a mutation could be found. Pancreas cancer: In 10% of the patients with pancreas cancer other members of the family were affected from the disease. Some of them belong to well characterized familial syndroms like HNPCC or Peutz-Jeghers-syndrom. In a minority of the others a genetic factor may be found, too. In sporadic disease the development of the tumor is characterized by continued acquirement of genetic alterations described by the PanIN model (pancreatic intraepithelial neoplesia). This means that the evolution of the neoplasia progresses from normal tissue via epithelial hyperplasy (PanIN 1A), papillary hyperplasy without (PanIN 1B) and with dysplasy (PanIN 2) and carcinoma in situ (PanIN 3) to invasive pancreas cancer. The progression is associated with genetic alterations of the cells (mutations of ki-ras, p16, p53 etc.). This results in deterioration of control of the cell cycle and the apoptosis and explains the malignancy of the disease. These findings may be used in the future to develop newer therapeutic principles in order to improve the dismal prognosis of this disease.

Carrier Proteins↗
PubMed2001

[Evaluation of prognostic factors in breast cancer EC I-II and the importance of local recurrence].

OBJECTIVE: [corrected] We evaluated the prognostic factors in patients with breast cancer EC-I-II treated in the Instituto Nacional de Cancerología in Mexico and compared patients with or without local or/and systemic recurrence. METHOD: This is a retrospective study in patients treated with conservative surgery between 1983 and 1993 with a diagnosis of invasive breast cancer and tumors <4 cm All pathological variables were analyzed and we performed studies on c-erb.B2, P53, estrogene and progesterone receivers, cellular ploidy and cellular percentage on face "S" of the cellular cycle. All these variables were compared in two groups, one with recurrences and the other without recurrences, with the same symptoms and demographics characteristics. RESULTS: From 1270 patients with breast cancer EC I-II, 139 patients were submitted to conservative surgery, 14 patients of this group recurred and were compared with 32 patients that did not, out of a total of 46 patients. We found that SBR greater than five (P = 0.046), poor differentiated tumors (P = 0.04), tumors with vascular permeability (P = 0.020) and with intraductal characteristics of a comedocarcinoma (P = 0.004) had a worse prognosis and increased the risk of local recurrences. CONCLUSIONS: In patients with breast cancer the pathological variants are more important than the so called secondary prognostic variables. Besides the pathological variants, it is acceptable only the use of hormonal receptors and the presence of c-erb-b2.

Adenocarcinoma↗
PubMed2004

Frontal-striatal circuitry activated by human peak-interval timing in the supra-seconds range.

Functional magnetic resonance imaging (fMRI) was used to measure the location and intensity of brain activations when participants time an 11-s signal duration. The experiment evaluated six healthy adult male participants who performed the peak-interval timing procedure in variants of stimulus modality (auditory or visual) and condition (foreground or background: i.e., whether the presence or absence of the stimulus is the signal to be timed). The complete experimental design called for each signal variant to be used across four behavioral tasks presented in the following order: control, timing+motor, timing, and motor. In the control task, participants passively experienced the stimuli. The timing+motor and timing tasks were preceded by five fixed-time training trials in which participants learned the 11-s signal they would subsequently reproduce. In the timing+motor task, participants made two motor responses centered around their subjective estimate of the criterion time. For the timing task, participants were instructed to time internally without making a motor response. The motor task had participants make two cued responses that were not determined by the participant's sense of the passage of time. Neuroimaging data from the timing+motor and timing tasks showed activation of the frontal cortex, striatum and thalamus--none of which was apparent in the control or motor tasks. These results, combined with other peak-interval procedure data from drug and lesion studies in animals as well as behavioral results in human patient populations with striatal damage, support the involvement of frontal-striatal circuitry in human interval timing.

Acoustic Stimulation↗