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 721 records · Page 40Linked to original sources
PubMed1994

An endogenous glycosylphosphatidylinositol-specific phospholipase D releases basic fibroblast growth factor-heparan sulfate proteoglycan complexes from human bone marrow cultures.

Basic fibroblast growth factor (bFGF) is a hematopoietic cytokine that stimulates stromal and stem cell growth. It binds to a glycosylphosphatidylinositol (GPI)-anchored heparan sulfate proteoglycan on human bone marrow (BM) stromal cells. The bFGF-proteoglycan complex is biologically active and is released by addition of exogenous phosphatidylinositol-specific phospholipase C. In this study, we show the presence of an endogenous GPI-specific phospholipase D (GPI-PLD) that releases the bFGF-binding heparan sulfate proteoglycan and the variant surface glycoprotein (a model GPI-anchored protein) from BM cultures. An involvement of proteases in this process is unlikely, because released proteoglycan contained the GPI anchor component, ethanol-amine, and protease inhibitors did not diminish the release. The mechanism of release is likely to involve a GPI-PLD and not a GPI-specific phospholipase C, because the release of variant surface glycoprotein did not reveal an epitope called the cross-reacting determinant that is exposed by phospholipase C-catalyzed GPI anchor cleavage. In addition, phosphatidic acid (which is specifically a product of GPI-PLD-catalyzed anchor cleavage) was generated during the spontaneous release of the GPI-anchored variant surface glycoprotein. We also detected GPI-PLD-specific enzyme activity and mRNA in BM cells. Therefore, we conclude that an endogenous GPI-PLD releases bFGF-heparan sulfate proteoglycan complexes from human BM cultures. This mechanism of GPI anchor cleavage could be relevant for mobilizing biologically active bFGF in BM. An endogenous GPI-PLD could also release other GPI-anchored proteins important for hematopoiesis and other physiologic processes.

Adult↗
PubMed1988

The specificity of the interaction between the agretope of an antigen and an Ia-molecule can depend on the T cell clonotype.

A series of T cell clones was developed from (B10 x B10.BR)F1 mice immunized with the isolated A chain of pig insulin. The T cell clones show considerable diversity as defined by their distinct reactivities to pig, beef, sheep and horse insulins in combination with the same syngeneic Ab alpha Ak beta molecules. These species variants of insulin differ from each other only in amino acid residues in position A8, A9 or A10 within the so-called A chain loop and responsiveness of mice to these variants is under Ir gene control. A detailed analysis of the stimulatory capacity of various insulin/Ia combinations including inhibition experiments with anti-Ia- and -L3T4 antibodies led to the following interpretation: the amino acid residues A8-A10 are involved in the interaction of the insulin A chain with the Ia molecules. This region can, therefore, be regarded as part of the agretope. Structural variations within this region can modify the stimulatory potency of the insulin variants. However, whether a particular amino acid substitution results in an enhancement or a reduction of the response depends on the fine specificity of the T cell clone involved. Thus, an interaction of Ia molecules with antigen cannot solely account for the functional specificity of an agretope, rather this also depends on the structure of the particular T cell receptor that participates in recognition.

Animals↗
PubMed2026

Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.

MOTIVATION: Focal oncogene amplification is a key driver of tumor progression. Remarkably, the increased pathology depends on the context-whether the amplification is extrachromosomal (ecDNA) or intrachromosomal. EcDNA amplifications promote heterogeneity, therapy resistance, and poor prognosis. Focal intrachromosomal amplifications often arise through breakage-fusion-bridge (BFB) cycles, which produce highly rearranged but stable chromosomes. Distinguishing BFB from ecDNA remains challenging due to overlapping genomic signatures. To address this, we present BFBArchitect, a computational method leveraging long-read Oxford Nanopore data to identify BFB sequences consistent with both copy number and structural variations. RESULTS: We provide a novel combinatorial characterization of BFB, which naturally leads to an integer linear programming (ILP) optimization. The ILP optimization generates a BFB sequence that best explains experimentally observed copy numbers and foldback structural variants. We implement this idea in a tool called BFBArchitect, which achieves near-perfect accuracy in distinguishing BFB from non-BFB structures in extensive simulations as well as on 18 validated tumor samples. Moreover, it generates sequence-level BFB reconstructions that provide mechanistic insights into BFB formation, including repair mechanisms with template switching and other structural variants, and recapture of telomere for stabilization. AVAILABILITY AND IMPLEMENTATION: BFBArchitect is available at https://github.com/AmpliconSuite/BFBArchitect.

Sequence Analysis, DNA↗
PubMed1985

Unilocular cystic sebaceous lymphadenoma of the parotid gland.

A unique variant of the sebaceous lymphadenoma, so-called unilocular cystic sebaceous lymphadenoma or lymphoepithelial cyst with sebaceous differentiation, occurred in the parotid gland of a 38-year-old man. Morphologic evidence to support the lymph node-salivary gland inclusion derivation of this tumor is presented and its taxonomic relationship to the parotid lymphoepithelial cyst and Warthin's tumor is discussed.

Adult↗
PubMed1991

Fine-needle aspiration biopsy of malignant melanoma: a cytologic and immunocytochemical analysis.

The immunoreactivity of alcohol-fixed cell blocks from 15 fine-needle aspiration (FNA) specimens of malignant melanoma was investigated using monoclonal antibodies to keratin and vimentin intermediate filaments, melanoma cytoplasmic antigen (HMB-45), and S-100, as well as polyclonal antibodies to S-100. The results were compared with the immunoprofiles obtained using formalin-fixed surgical specimens from 10 of the same patients. In all cases, immunostaining for keratin was negative and immunostaining for vimentin was positive. Immunostaining for HMB-45 was positive in 13/15 aspirates and in 9/10 surgical specimens. Immunostaining for S-100 protein showed the greatest variability in staining, with 5/15 fine needle aspiration biopsies and 9/10 surgical specimens being positive using the polyclonal antibody and only 1/15 FNA specimens and 7/10 surgical specimens being positive using the monoclonal S-100 reagent. Our findings indicate that immunocytochemical studies can be very useful as an adjunct in the FNA diagnosis of melanoma. Also included in our series is an unusual variant of malignant melanoma, the so-called signet ring melanoma. Given the location of the anal verge, the use of immunocytochemical markers was essential in establishing the correct diagnosis in this case. While S-100 protein is of limited value as a marker of melanoma in alcohol-fixed FNA specimens, a definitive diagnosis of malignant melanoma can be made using a panel of antibodies including keratin, vimentin, and HMB-45.

Adult↗
PubMed1998

Multiple-pulse mixing sequences that selectively enhance chemical exchange or cross-relaxation peaks in high-resolution NMR spectra.

Rotating-frame NMR experiments which either emphasize or suppress cross relaxation, and which simultaneously suppress TOCSY, COSY, and zero-quantum peaks in NMR spectra, are presented and analyzed. The new experiments rely on mixing sequences which follow naturally from the transverse-ROESY (Tr-ROESY) sequence of Hwang and Shaka, and which are applicable to larger molecules in solution (spin diffusion limit). In the first variant a modified Tr-ROESY sequence, called multiple-pulse ROESY (MP-ROESY), is used to enhance cross-relaxation peak intensity compared to Tr-ROESY; in the second, called phase-modulated CLEAN chemical exchange (CLEANEX-PM), cross-relaxation peaks are greatly attenuated. The two methods are thus complementary: MP-ROESY is used to observe Overhauser peaks, and CLEANEX-PM is used to eliminate them, permitting clear observation of chemical exchange peaks alone. The new techniques are examined by theory and experiment. Practical guidelines that will result in high-quality spectra are given, including the judicious use of continuous weak static magnetic field gradients.

Magnetic Resonance Spectroscopy↗
PubMed1983

Genetic localization and sequential electrophoresis of glucose-6-phosphate dehydrogenase in Drosophila melanogaster.

Studies were undertaken to investigate two critical aspects of the glucose-6-phosphate dehydrogenase polymorphism in Drosophila melanogaster. The first investigation unequivocally maps the genetic site of the G6PD locus to the X chromosome. The second study subjects a set of isochromosomal lines to sequential electrophoresis in an attempt to uncover common molecular heterogeneity within the global polymorphism, assuming that this variation may have gone undetected under conventional electrophoretic conditions. The genetic site was mapped following the segregation of the two common electrophoretic alleles, a so-called null allele, and two rare electrophoretic variants. From the pooled results, the Zw locus mapped to 62.9 on the X chromosome relative to the flanking markers car (at 62.5) and sw (at 64.7). A set of 126 iso-X chromosomal lines of diverse geographic origin was subjected to sequential electrophoresis under three different acrylamide conditions in addition to the conventional starch electrophoretic system. No additional variation beyond the common diallele polymorphism was seen.

Alleles↗
PubMed1988

Lymphoid follicular proctitis. A condition different from ulcerative proctitis?

A heterogeneous group is formed by patients presenting with clinical features suggestive of inflammatory bowel disease limited to the rectum and whose rectal biopsies show lymphoid follicular hyperplasia of the mucosa. All these cases are traditionally considered as one variant of chronic ulcerative colitis, so-called ulcerative proctitis. Twenty such cases were critically assessed on clinical, endoscopic, and histologic grounds, as well as on response to treatment and follow-up data. While 11 patients showed clinicopathologic features consistent with typical chronic ulcerative colitis, the other nine patients appeared to form a different group, for which the term "lymphoid follicular proctitis" seemed justified. Lymphoid follicular proctitis was, overall, characterized by rectal bleeding, a congested and granular mucosa without ulceration, abnormal and coalescing hyperplastic lymphoid follicles without acute inflammation, and failure to respond to local steroid therapy. The nature of lymphoid follicular proctitis is uncertain at present but seems unrelated to chronic ulcerative colitis.

Adolescent↗
PubMed1980

The priming effect of glucose in soil sterilized by gamma-radiation and reinoculated with Cellulomonas sp.

Mineralization of native organic matter and U-14C-glucose was followed by measuring the formation of CO2 and its radioactivity in chernozem soil presterilized by gamma-radiation and inoculated with a washed suspension of Cellulomonas sp. cells. The introduced bacteria mineralized the soil organic component to a higher extent in variants enriched with glucose. This so-called priming effect of glucose was observed also in the presence of chloramphenicol, inhibiting the growth of the bacteria. The increased mineralization of the native soil organic fraction was also detected in samples that were not enriched with glucose when the bacterial suspension was first disintegrated ultrasonically and the material then used for the inoculation. Possible participation of phenomena of the type of cometabolism and activation of cell membrane transport mechanisms on the occurrence of the priming effect of glucose in the soil is discussed.

Actinomycetales↗
PubMed2006

Somnambulistic sexual behaviour (sexsomnia).

Somnambulism or sleepwalking is a viable defence on the basis of automatism. The behaviours that occur during sleepwalking can be highly complex and include sexual behaviour of all types. Somnambulistic sexual behaviour (also called sexsomnia, sleep sex) is considered a variant of sleepwalking disorder as the overwhelming majority of people with Sexsomnia have a history of parasomnia and a family history of sleepwalking. Sexual behaviour during a sleep automatism can vary from explicit sexual vocalisations, to violent masturbation, to complex sexual acts including anal, oral and vaginal penetration. A recent case in England is reported where the defendant was acquitted on 3 charges of rape on the basis of automatism due to somnambulistic sexual behaviour.

Adult↗
PubMed1997

Neuronal complexity loss in temporal lobe epilepsy: effects of carbamazepine on the dynamics of the epileptogenic focus.

Analysis methods derived from the theory of non-linear dynamics have been shown to provide new information about the complex spatio-temporal behaviour of neuronal networks involved in temporal lobe epilepsy. To test whether day to day alterations in neuronal complexity are influenced by changes in serum level of carbamazepine (CBZ), a moving-window correlation dimension analysis was applied to electrocorticographic and stereoelectroencephalographic recordings of 10 patients with unilateral temporal lobe epilepsy. Data sets (n = 78) were obtained from interictal states at subsequent days during the presurgical evaluation with strongly variant CBZ serum levels. The so-called neuronal complexity loss L* was used to quantify the change of dimensionality in brain electrical activity recorded under different levels of medication. We found a significant inverse relationship between L* and CBZ serum level spatially restricted to the primary epileptogenic area. This finding can be assumed to reflect the mechanism of action of CBZ attributed to an inhibition of sustained high-frequency firing of bursting neurons.

Adult↗
PubMed1997

Cyclin D1 (PRAD1) alternative transcript b: full-length cDNA cloning and expression in breast cancers.

The cyclin D1/PRAD1 protooncogene is a key regulator of the G1 phase of the cell cycle and has been incriminated in the pathogenesis of a variety of primary human tumors. Recently, part of a novel alternatively spliced cyclin D1 transcript, called transcript b, has been identified. This variant transcript showed a failure of splicing at the 3' end of exon 4 and as a result, the expected protein product is altered at its C-terminus. Because of similar transcript sizes, previous Northern analyses would not have been expected to distinguish the two variants, and the relative levels of the two cyclin D1 transcripts in human tumors is unknown. To elucidate the role of cyclin D1 transcript b, we have isolated cDNA clones of this variant transcript from human breast cancer cell lines and report the sequence of the entire coding region of the cDNA. The protein predicted from the cDNA sequence consists of 274 amino acid residues and lacks a PEST sequence in its C-terminus. Examination of the levels of the two alternative cyclin D1 transcripts in primary breast cancers and breast cancer cell lines by Northern blot analysis and reverse transcription-polymerase chain reaction (RT-PCR) assays showed that the variant transcript b is indeed expressed in primary breast cancers and breast cancer cell lines, but the level of transcript b is dramatically lower than that of the originally reported transcript a of the cyclin D1 gene. In breast cancers, oncogenic overexpression of cyclin D1 mRNA appears to consist overwhelmingly of transcript a, and the role of transcript b, if any, in oncogenesis remains to be established. Science Ireland Ltd.

Alternative Splicing↗
PubMed1997

A diminished role for hydrogen bonds in antifreeze protein binding to ice.

The most abundant isoform (HPLC-6) of type I antifreeze protein (AFP1) in winter flounder is a 37-amino-acid-long, alanine-rich, alpha-helical peptide, containing four Thr spaced 11 amino acids apart. It is generally assumed that HPLC-6 binds ice through a hydrogen-bonding match between the Thr and neighboring Asx residues to oxygens atoms on the {2021} plane of the ice lattice. The result is a lowering of the nonequilibrium freezing point below the melting point (thermal hysteresis). HPLC-6, and two variants in which the central two Thr were replaced with either Ser or Val, were synthesized. The Ser variant was virtually inactive, while only a minor loss of activity was observed in the Val variant. CD, ultracentrifugation, and NMR studies indicated no significant structural changes or aggregation of the variants compared to HPLC-6. These results call into question the role of hydrogen bonds and suggest a much more significant role for entropic effects and van der Waals interactions in binding AFP to ice.

Amino Acid Sequence↗
PubMed2000

HAM: a new epitope-tag for in vivo protein labeling.

The ability to metabolically label proteins with 35S-methionine is critical for the analysis of protein synthesis and turnover. Despite the importance of this approach, however, efficient labeling of proteins in vivo is often limited by a low number of available methionine residues, or by deleterious side-effects associated with protein overexpression. To overcome these limitations, we have created a methionine-rich variant of the widely used HA tag, called HAM, for use with ectopically expressed proteins. Here we describe the development of a series of vectors, and corresponding antisera, for the expression and detection of HAM-tagged proteins in mammalian cells. We show that the HAM tag dramatically improves the sensitivity of 35S-methionine labeling, and permits the analysis of Myc oncoprotein turnover even when HAM-tagged Myc is expressed at levels comparable to that of the endogenous protein. Because of the improved sensitivity provided by the HAM tag, the vectors and antisera described here should be useful for the analysis of protein synthesis and destruction at physiological levels of protein expression.

Amino Acid Sequence↗
PubMed2002

CD44H is expressed by cells of the oligodendrocyte lineage and by oligodendrogliomas in humans.

CD44, a family of cell surface glycoproteins involved in cell-cell and cell-extracellular matrix adhesion, is widely expressed in the white matter of the normal brain and in astrocytic gliomas under its standard form (CD44s also called CD44H). On the other hand, several variants have been found in brain metastases and rarely found in gliomas. We have investigated by immunohistochemistry CD44H and CD44v6 expression in 28 oligodendrogliomas. All tumors were CD44v6 negative whereas nearly all tumors were immunolabelled with anti-CD44H antibody. Immunostaining increased in parallel with grade and was particulary strong around vessels and in tumoral subpial nodules. Western blot analysis showed that oligodendrogliomas expressed the same 80-kDa CD44 isoform as normal brain. Since gliomas may arise from a dividing progenitor cell, we also studied CD44H expression during the oligodendrocyte lineage in vitro in parallel with specific markers of the O-2A cells. Precursor cells (PSA-NCAM positive), O-2A progenitor cells, as well as preoligodendrocytes (A2B5 positive cells) and immature oligodendrocytes (O4 positive cells), coexpressed CD44H. Our data showed that CD44H is expressed by cells of the oligodendrocyte lineage in vitro and by oligodendrogliomas in vivo especially in sites of dissemination such as subpial spaces. This suggests that CD44H could play a role in migration of tumor cells in oligodendrocytic tumors.

Animals↗
PubMed2004

A novel neuronal-specific splice variant of Type I phosphatidylinositol 4-phosphate 5-kinase isoform gamma.

Type I PIPkins (phosphatidylinositol 4-phosphate 5-kinases) are the enzymes that catalyse the major cellular route of synthesis of PtdIns(4,5) P2, and three isoforms (alpha, beta and gamma) with several splice variants have been found to date. In the present paper, we describe the discovery of a novel splice variant of the gamma isoform, which we call PIPkin Igammac, and which is characterized by the inclusion of a 26-amino-acid insert near the C-terminus. Its transcript appears to be selectively expressed in brain, where it locates in the neurons of restricted regions, such as cerebellum, hippocampus, cortex and olfactory bulb, as indicated by in situ hybridization studies. Overexpression of two different catalytically inactive constructs of PIPkin Igammac in rat cerebellar granule cells causes a progressive loss of their neuronal processes, whereas equivalent kinase-dead versions of PIPkin Igammaa did not induce any such effect, suggesting the possible existence of a specific PtdIns(4,5) P2 pool synthesized by PIPkin Igammac, which is involved in the maintenance of some neuronal cellular processes.

Alternative Splicing↗
PubMed2000

Alternative splicing generates a family of putative secreted and membrane-associated MUC4 mucins.

The MUC4 mucin gene encodes a putative membrane-anchored mucin with predicted size of 930 kDa, for its 26.5-kb allele. It is composed of two regions, the 850-kDa mucin-type subunit MUC4alpha and the 80-kDa membrane-associated subunit MUC4beta. In this study, we cloned and characterized unique MUC4 cDNA sequences that differ from the originally published sequence. Eight alternative splice events located downstream of the central large tandem repeat array generated eight new, distinct cDNAs. The deduced sequences of these MUC4 cDNAs (sv1-MUC4 to sv8-MUC4, the full length cDNA being called sv0-MUC4) provided seven distinct variants, five secreted forms and two membrane-associated forms. Furthermore, two other alternative splicing events located on both sides of the tandem repeat array created two variants, MUC4/Y and MUC4/X, both lacking the central tandem repeat. Therefore, MUC4 can be expressed in three distinct forms, one membrane-bound, one secreted, and one lacking the hallmark feature of mucin, the tandem repeat array. Although no specific function has yet been discovered for the family of proteins putatively produced from the unique MUC4 gene, we suspect that the MUC4 proteins may be implicated in the integrity and renewal of the epithelium.

Alleles↗
PubMed1999

Molecular evolution of the thermosensitive PAb1620 epitope of human p53 by DNA shuffling.

Conformational stability of the p53 protein is an absolute necessity for its physiological function as a tumor suppressor. Recent in vitro studies have shown that wild-type p53 is a highly temperature-sensitive protein at the structural and functional levels. Upon heat treatment at 37 degrees C, p53 loses its wild-type (PAb1620(+)) conformation and its ability to bind DNA, but can be stabilized by different classes of ligands. To further investigate the thermal instability of p53, we isolated p53 mutants resistant to heat denaturation. For this purpose, we applied a recently developed random mutagenesis technique called DNA shuffling and screened for p53 variants that could retain reactivity to the native conformation-specific anti-p53 antibody PAb1620 upon thermal treatment. After three rounds of mutagenesis and screening, mutants were isolated with the desired phenotype. The isolated mutants were translated in vitro in either Escherichia coli or rabbit reticulocyte lysate and characterized biochemically. Mutational analysis identified 20 amino acid residues in the core domain of p53 (amino acids 101-120) responsible for the thermostable phenotype. Furthermore, the thermostable mutants could partially protect the PAb1620(+) conformation of tumor-derived p53 mutants from thermal unfolding, providing a novel approach for restoration of wild-type structure and possibly function to a subset of p53 mutants in tumor cells.

Animals↗