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At least 37 records · Page 2Linked to original sources
PubMed2025

Identification of pathogenic variants in six Chinese families with keratoconus of autosomal dominant inheritance: pathogenicity analysis and variable phenotype.

PURPOSE: Keratoconus (KC) is a bilateral, asymmetric disease causing corneal thinning, irregular astigmatism, and vision decline, with unclear etiology. This study aims to investigate pathogenic variants of candidate genes in Chinese KC families via whole exome sequencing (WES). METHODS: The Pentacam 3D anterior segment analysis system was applied for keratectasia detection, and the Corvis ST was used for corneal biomechanics measurement. Probands from KC families were screened via WES and further verified in other family members through Sanger sequencing. Additionally, qPCR was used to validate copy number variants and identify pathogenic gene loci. The identified variants were then classified according to the Standards and Guidelines for the Interpretation of Sequence Variants published by the American College of Medical Genetics and Genomics (ACMG). Finally, STRING protein-protein interaction (PPI) networks analysis was performed to investigate interactions among candidate gene-related proteins. RESULTS: Using WES, four heterozygous missense variants were detected in the ZNF469, KRT12, COL8A2, and COL18A1 genes: c.4384G > A: p.Asp1462Asn, c.1229T > G:p.Val410Gly, c.505A > G:p.Ile169Val, and c.1159G > A:p.Gly387Arg. Additionally, a heterozygous frameshift variant was detected in the PMS2 gene: c.1551_1572del:p.Ser517Argfs*71. The affected parents carried the same variants as the probands verified by Sanger sequencing. A copy number variant was detected in the DPP6 gene: seq[GRCh38] dup(7)(q36.2q36.2) chr7:g.153782360_ 153982491dup. According to ACMG guidelines, ZNF469, KRT12, COL8A2, and COL18A1 gene variants are Likely Pathogenic; PMS2 and DPP6 gene variants are Pathogenic. STRING analysis highlights a tightly interconnected network centered on COL8A2, involving COL18A1, FN1, ZNF469, and KRT12. DPP6 was involved in KC via affecting FN1. In four of six autosomal dominant KC (adKC) families, affected parents had the same variants as probands but milder phenotypes. CONCLUSION: In this study, six novel variants in ZNF469, KRT12, COL8A2, COL18A1, PMS2, and DPP6 were linked to adKC. Family phenotypes showed variable expressivity with irregular dominance inheritance. Abnormal KC-related gene protein expression may contribute to corneal structural instability. This study broadened KC genetic screening candidates and suggested genetic testing could aid early KC diagnosis and intervention.

Adult↗
PubMed1991

DNase activity in Costa Rican crotaline snake venoms: quantification of activity and identification of electrophoretic variants.

DNase activity of Costa Rican crotaline snake venoms from the genera Bothrops, Crotalus and Lachesis was quantified by an enzymodiffusion method on agarose/DNA gels containing ethidium bromide. The reaction is detected as a ring lacking fluorescence when gels are visualized under u.v. light. Electrophoresis of non-fluorescent areas demonstrated DNA degradation. All of the venoms had DNase activity, B. schlegelii being most active. Venoms from B. schlegelii and B. asper induced an inner hyper-fluorescent ring in addition to the external non-fluorescent ring, probably caused by the formation of complexes between DNA and highly basic proteins present in these venoms. In order to study the number of electrophoretic DNase variants, venoms were separated by analytical isoelectric focusing on polyacrylamide minigels, proteins were transferred to nitrocellulose paper and the paper was placed over an agarose gel containing DNA. Then the agarose gel was stained with ethidium bromide and the bands of DNase activity were visualized under u.v. light. All the venoms tested, as well as commercial DNase showed several bands with DNase activity. The majority of venom DNase variants have basic pIs although bands with acidic pIs were also present in B. godmani and L. muta venoms. No major differences in the DNase electrophoretic pattern were observed between individual venoms of adult B. asper specimens nor between lyophilized and frozen venoms.

Crotalid Venoms↗
PubMed1986

Species variants of cathepsin L and their immunological identification.

Cathepsin L variants purified from sheep and ox liver are shown to have similar catalytic properties to those from rat, rabbit and man with regard to activity against the substrate benzyloxycarbonyl-Phe-Arg-7-(4-methyl)coumarylamide and inhibition by benzyloxycarbonyl-Phe-Phe-diazomethane, thus identifying cathepsin L in these species for the first time. All five variants of cathepsin L are shown to be immunologically related by their interaction with antibodies raised to the human enzyme. Sheep liver was found to yield more enzyme than any other species, suggesting that this tissue is a good source of cathepsin L. Cathepsin S, a closely related enzyme, could not be detected in livers of any of these species.

Animals↗
PubMed1977

Restoration of hemoglobin function in stored EDTA blood. Application in identification of hemoglobin variants with abnormal oxygen affinity.

The incubation of stored blood in a mixture of inosine, pyruvate, glucose, and phosphate restores the O2 affinity of hemoglobin to physiologic levels, as measured by the configuration of the dissociation curve and the P50. This regeneration of normal hemoglobin function not only is consistent for samples anticoagulated with EDTA and stored eight days at 4 C but also is demonstrable for at least 19 days of 4 C storage of EDTA-anticoagulated whole blood. This regeneration procedure is simple to perform and makes it possible to measure reliably O2 affinity in blood samples transmitted by mail.

Blood Preservation↗
PubMed1992

Genotyping of Chlamydia trachomatis from a trachoma-endemic village in the Gambia by a nested polymerase chain reaction: identification of strain variants.

Direct amplification of the major outer membrane protein (MOMP) gene by polymerase chain reaction (PCR) was used to identify Chlamydia trachomatis in eye swabs from clinically active cases of endemic trachoma in a Gambian village. Chlamydial DNA was detected in 51% of 96 subjects with clinically active disease and in 5% of 37 clinically negative individuals. The PCR detection was combined with typing, using nested primers to variable sequences (VS) 1, 2, and 4 of the MOMP genes to distinguish between trachoma genotypes A, B, and C, respectively. Genotypes A and B were detected in the village, with some individuals harboring both genotypes within the same eye. DNA sequencing revealed strain variants of both genotypes. Typing of genotype and strain variants is now in progress to study trachoma transmission within the village.

Bacterial Outer Membrane Proteins↗
PubMed1985

Identification of multiple variants of fast muscle troponin T in the chicken using monoclonal antibodies.

Two monoclonal antibodies, T1/7 and T1/61, have been prepared which are specific for chicken fast muscle troponin T. Both are of the IgG gamma 1 subclass. Both antibodies cross-react strongly with human fast and chicken cardiac troponin T, but while T1/7 reacts weakly with rabbit fast troponin T, T1/61 does not. The antibodies can be used for fibre typing of both chicken and human muscle. The antibodies have been used to identify fast troponin T on two-dimensional maps of proteins from a variety of chicken muscles by electrophoretic transfer to nitrocellulose followed by immunoperoxidase staining. Using this technique five variant forms of fast troponin T have been identified. Two variants, fBT1 and fBT2, are expressed in breast muscle, while the other three, fLT1, fLT2 and fLT3 are expressed in leg muscle. Of the leg muscle variants, fLT1 and fLT2 correspond to the two forms described previously [Wilkinson, J.M., Moir, A.J.G. and Waterfield, M.D. (1984) Eur. J. Biochem. 143, 47-56]. The third variant, fLT3, has not been described before and is expressed in muscles which have a high content of slow fibres. In addition to these clearly defined variant forms immunostaining reveals multiple minor variants of troponin T present in leg muscle which may reflect complex RNA processing of the troponin T gene transcript.

Animals↗
PubMed1991

Isolation and identification of a variant of bluetongue virus serotype 11 from a ram in a bluetongue outbreak in western Texas.

A field strain of bluetongue virus was isolated from a blood sample of a ram during an outbreak of bluetongue in November 1985 in western Texas. In this bluetongue outbreak at least 25 of the 2,000 sheep were infected. Isolation was made by intravenous inoculation of 11-day-old embryonated chicken eggs. The serotype was identified as serotype 11 by serum neutralization tests. The genomic pattern on sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) of the new isolate is similar to that of bluetongue virus prototype 11. Comparisons were also made with proteins labeled in vivo with [3H]leucine and separated by SDS-PAGE. We conclude that this virus belongs to serotype 11, with slight differences in both genome and protein electrophoretic patterns.

Animals↗
PubMed1990

Identification of two variant short chain acyl-coenzyme A dehydrogenase alleles, each containing a different point mutation in a patient with short chain acyl-coenzyme A dehydrogenase deficiency.

Two distinct mutant alleles of the precursor (p) short chain acyl-CoA dehydrogenase (SCAD) gene were identified in a SCAD-deficient patient (YH2065) using the polymerase chain reaction to amplify cDNA synthesized from total RNA from her fibroblasts. Cells from this patient had previously been shown to synthesize a labile variant SCAD in contrast to the normal stability of variant SCADs in two other SCAD-deficient cell lines (Naito, E., Y. Indo, and K. Tanaka. 1989. J. Clin. Invest. 84:1671-1674). In the present study, both mutant alleles of YH2065 were found to contain a C----T transition, one at position 136 and the other at position 319 of the coding region of pSCAD cDNA. Clones of cDNA amplified from this region showed only one of the C----T transitions, indicating that each mutation was derived from different pSCAD alleles. Each of these mutations altered a known restriction endonuclease site, and restriction analysis of additional cDNA clones from amplified mutant cDNA and Southern blotting of mutant genomic DNA confirmed the presence of two unique mutant alleles in YH2065, indicating YH2065 is a compound heterozygote. These C----T transitions result in the substitution of Arg-22 and Arg-83 of the mature SCAD with Trp and Cys, respectively.

Acyl-CoA Dehydrogenases↗
PubMed2026

Identification of candidate variants in plasma associated with early versus late disease progression under anti-PD-1 therapy in metastatic NSCLC.

BACKGROUND: Immune checkpoint inhibitors (ICIs), including anti-programmed cell death protein 1 (anti-PD-1) antibodies, have significantly improved outcomes in patients with metastatic non-small cell lung cancer (mNSCLC). However, substantial heterogeneity exists in clinical benefit, with some patients exhibiting early progression (EP) and others late progression (LP). To date, no biomarkers of EP versus LP disease have been implemented in clinical practice. Circulating tumor DNA (ctDNA) analysis represents a minimally invasive strategy for identifying such biomarkers. In this proof-of-concept study, we evaluated the performance of the TruSight Oncology 500 ctDNA (TSO500 ctDNA) panel and explored its feasibility to identify candidate variants associated with early and late disease progression under anti-PD-1 therapy. METHODS: Baseline ctDNA from eight mNSCLC patients treated with pembrolizumab was extracted and sequenced using the TSO500 ctDNA assay, a 523-gene targeted next-generation sequencing panel. Patients were classified according to their response as LP or EP. Variant calling was performed using the DRAGEN Bio-IT platform, and variants were annotated and clinically interpreted using the Clinical Genomics Workspace (CGW; PierianDx) according to Association for Molecular Pathology (AMP)/American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines. Survival outcomes were assessed using Kaplan-Meier and log-rank tests. Performance of ctDNA variants was evaluated using receiver operating characteristic (ROC) curve analysis, and multi-gene models were assessed using leave-one-out cross-validation with penalized logistic regression. RESULTS: All patients harbored detectable variants, including SNVs (100%), MNVs (87.5%), deletions (75%), and insertions (62.5%). Tier I variants were identified in 37.5% of patients, while all cases showed tier II and multiple tier III alterations. TP53 variants were associated with poorer outcomes under anti-PD-1 therapy. Individual gene alterations in TP53, ERBB3, SMC1A or LATS1 showed moderate discriminatory performance between LP and EP patients; however, combination of mutated genes improved apparent discrimination. Notably, specific two-gene combinations (SMC1A + LATS1 or ERBB3 + LATS1) showed the highest discriminatory performance between LP and EP patients in this exploratory cohort. CONCLUSIONS: This study demonstrates the feasibility and analytical performance of the TSO500 ctDNA panel and provides hypothesis-generating evidence that plasma gene variants may be useful to evaluate early versus late disease progression in patients with mNSCLC receiving immunotherapy.

TruSight Oncology 500↗
PubMed1990

Identification of metaplastic variants generated by transfection of a nonmetastatic rat mammary epithelial cell line with DNA from a metastatic rat mammary cell line.

The rat mammary 37 epithelial cell line yields non-metastasizing adenomas in syngeneic rats. On cellular DNA transfection, a series of cell lines have been isolated that grow in drug-selective medium. Representative transfected cell lines all yield tumors in rats that consist predominantly of spindle cells, but two also contain epithelial-like cells and glandlike elements (C18P, C19P). Immunocytochemical staining for milk fat globule membrane antigens, human callus keratin, and laminin confirms the identity of the epithelial cells and suggests a (myo)epithelial origin for the spindle cells. Some of the transfected cell lines also generate well-differentiated metaplastic elements in their tumors. One cell line (CT4-41) produces rhabdomyoblastic and possibly smooth-muscle-related elements; two (C18P, C19P) produce squamous metaplasia and sebaceous elements; and two (CL1-31, C11P) produce cartilaginous elements. The identities of the heterologous elements are confirmed by immunocytochemical staining for myoglobin, actin (CT4-41), keratin (C18P, C19P), type II collagen, and type II keratan sulfate (CL1-31). Those cell lines that have acquired the ability to metastasize from subcutaneous sites (CT4-41, C18P) reproduce the same metaplastic elements in their metastases. Thus, a cloned mammary epithelial cell line can be made to generate many of the well-differentiated, heterologous elements observed in human breast carcinomas, and this change is often associated with the rat cells acquiring metastatic properties.

Animals↗
PubMedDate not supplied

Peptide mapping using thermospray LC/MS detection: rapid identification of hemoglobin variants.

A rapid and easily interpreted method for peptide mapping is demonstrated with hemoglobin A and three variants. Digests of the globin chains are generated in columns containing immobilized trypsin. The resulting protein fragments are resolved by reverse phase HPLC and then analyzed by thermospray mass spectrometry. The entire process is carried out on-line. The result is a chromatographic trace which is two dimensional; in addition to the standard elution pattern, the individual mass spectra collected for each peak contain information about their identity and their purity. In two of the variants used, hemoglobin C and hemoglobin Baylor, the exact nature of the amino acid substitution could be determined unambiguously in a single analysis, from the masses of the new tryptic peptides observed. In the third case, hemoglobin S, the mass of the peptide containing the amino acid replacement is consistent with two separate sites of substitution. This ambiguity was resolved in a second analysis, using immobilized carboxypeptidase Y, prior to mass spectral analysis. The resulting partial digest permits reconstruction of the critical sequence region and correct assignment of the allelic site.

Amino Acid Sequence↗
PubMed1987

Identification of molecular variants of p210bcr-abl in chronic myelogenous leukemia.

The aberrant abl protein product of a chronic myelogenous leukemia (CML) blast crisis cell line (K562) and of five Philadelphia chromosome-positive CML patients in blast crisis were analyzed by an immune complex kinase assay using two antipeptide sera generated against the hydrophilic domain of v-abl and a region within the third exon of the breakpoint cluster region (bcr) respectively. Both the anti-abl and anti-bcr sera detected a 210 kd band in extracts derived from K562 cells and from two CML patients with myeloid blast crisis. p210 was detected by the anti-abl but not the anti-bcr sera in three CML patients with myeloid (one patient) and lymphoid (two patients) blast crisis, indicating the absence of bcr exon 3 in this protein. Southern blot analysis on DNA derived from one of the patients in the latter group was consistent with the break on chromosome 22 occurring 5' to bcr exon 3. Our observations demonstrate that the Philadelphia translocation results in the generation of a chimeric bcr-abl protein with at least two molecular variants, both of which are enzymatically active as protein kinases.

Blast Crisis↗
PubMed1979

[A case of succinylcholine apnea. Identification of genetic variants].

A report of a case of prolonged apnoea after succicurarium in a female patient with abnormal pseudo-cholinesterases is followed by a presentation of a study of pseudo-cholinesterases in 12 members of the family. The value of the use of 4 tests of inhibition of cholinesterase activity in determining the genotype of an individual is emphasised.

Apnea↗
PubMed1991

[Diagnosis of familial amyloid polyneuropathy--gene analysis with primer-directed enzymatic amplification of DNA, isolation of plasma variant prealbumin and immunohistochemical identification of tissue amyloid protein].

Type I familial amyloid polyneuropathy (FAP) is an autosomal dominant hereditary generalized amyloidosis characterized by polyneuropathy and autonomic nerve failure. The main component of the amyloid fibril protein in this disorder has been shown to be a variant prealbumin with a single substitution of a methionine residue for valine at position 30. In the present study we have investigated 19 patients with FAP aged 31 to 67 and an asymptomatic family member using gene analysis with primer-directed enzymatic amplification (PCR) of DNA, isolation of plasma variant prealbumin and immunohistochemical identification of tissue amyloid protein. All patients and a symptom-free boy in the affected family had the mutant prealbumin gene showing abnormal DNA fragments by treatment with restriction endonuclease Bal I, and plasma variant prealbumin was also detected in all of them by reverse-phase high performance liquid chromatography. Rectum biopsies obtained from 9 patients showed amyloid deposits which were specifically immunostained by anti-human prealbumin antiserum. However, an asymptomatic carrier at the age of 16 showed no rectal amyloid deposition. Recent studies of FAP have disclosed that the expression of type I FAP is closely associated with the gene mutation of prealbumin. Accordingly, a simple and rapid method to detect this gene abnormality using PCR technique is considered to be very useful for diagnosis of type I FAP and can also provide valuable information for the genetic counselling of the family members at risk.

Adolescent↗
PubMed1992

Thyroxine-binding globulin variant (TBG-Kumamoto): identification of a point mutation and genotype analysis of its family.

Thyroxine-binding globulin (TBG) is the major thyroid hormone transport protein. Several inherited TBG variants resulting in partial or complete TBG deficiencies have been shown to be caused by either one or two nucleotide substitutions, or one nucleotide deletion in the coding regions of the TBG gene. In this report, a Japanese female patient (proband) with hyperthyroid state, whose lower TBG levels did not return to normal under the euthyroid state after treatment was examined. Genomic DNA samples from the proband with thyroxine-binding globulin deficiency (termed TBG-Kumamoto) and her family were subjected to the polymerase chain reaction, and the generated DNA fragments were sequenced. A single nucleotide substitution in the codon for the amino acid 363 of native TBG molecule (CCT to CTT) was found, resulting in the replacement of proline by leucine. It was revealed that the proband was a heterozygote and her father was a hemizygote. The mutation was confirmed by the allele-specific amplification of genomic DNAs from the proband and her father using oligonucleotide primers of normal or mutant residues at the 3' position in the polymerase chain reaction. These results indicate that the abnormality of TBG-Kumamoto is the consequence of this mutation. Genetically, this point mutation observed in TBG-Kumamoto might be classified as a new type of TBG deficiency.

Adult↗
PubMed1989

[A simplified method of determining the serologic variants of Yersinia enterocolitica].

Identification of the serological variants according to G. Wauters et al. involves examination of one strain in the agglutination test with 32 sera, and to specify a number of serological variants, investigations with monosera are necessary. Six group sera are suggested for the determination of the minimal set of monovalent sera necessary for the identification of the tested strain serological variant. Employment of group sera considerably simplifies the serologic identification of the strains. The selected serum titers help obtain a clear-cut agglutination on the glass within 1 min. A set of 6 group and 31 monoreceptor sera has been prepared. Since serovariants O10 and O34 have been found antigenically identical, serum O34 has not been included in the set. A table for the determination of the serological variant from the results of the agglutination test is offered.

Microbiological Techniques↗