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At least 199 records · Page 11Linked to original sources
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↗
PubMed2004

Rapid individual identification by minisatellite variant repeat (MVR)-PCR at D1S8 locus using "exponential law".

We describe an efficient and simple minisatellite variant repeat mapping by PCR (MVR-PCR) method based on the assignment of the tandem array of 29 bp repeating units into a-type, t-type and 0-type (a rarely appearing unamplified unit), from the first repeat unit position (code position 0) of 293 bp in D1S8 locus. After microchip electrophoresis of PCR product amplified from the target DNA of a human hair root, each rung of the ladder at the position of 293 + 29 n bp (n: code position) was detected and the type of repeating unit was determined, i.e., aa, a0, tt, t0, at and 00. The peak area of the rungs from PCR product decreased with increase in code position. We found for the first time that the logarithmic plots of the peak area against the code position showed a linear relationship, which implied that peak areas decrease exponentially. The present method was successfully applied to identify 37 individuals using only a hair root as a biological specimen. This "exponential law" is expected to be an effective tool in forensic science.

Base Sequence↗
PubMed1984

Identification of beta variant hemoglobins by DNA restriction endonuclease mapping.

An alternative method for identifying beta variant hemoglobins is described. Computer analysis of restriction sites was used to predict which beta variants could be detected by DNA mapping. 61 of 217 variants were shown to have changes in restriction fragment patterns which were useful markers for the abnormal hemoglobin. A further 25 could be identified by polyacrylamide electrophoresis. Implications of DNA analysis in diagnosis of variant hemoglobins are discussed.

Base Sequence↗
PubMed1986

Ultrathin-layer polyacrylamide gel isoelectric focusing for the identification of hemoglobin variants.

An ultrathin-layer polyacrylamide gel isoelectric focusing method for typing hemoglobin is described. This method, which uses Pharmalyte pH 6.7-7.7 and an electrode wick distance of 5.0 cm, clearly resolves the A, F, S, C and a number of rare variant allelic products. The technique is ideal for rapid screening of a large number of fresh blood and/or bloodstained samples.

Blood Protein Electrophoresis↗
PubMed2005

Identification of novel variant, 1484delG in the 3'UTR of H3F3B, a member of the histone 3B replacement family, in ovarian tumors.

Previous studies have implicated the chromosomal region at 17q25 as harboring tumor suppressor genes based on the frequent loss of heterozygosity (LOH) observed in epithelial ovarian cancers (EOC). RT-PCR validation of Affymetrix GeneChip expression of H3F3B, a member of the 3B histone family that maps to 17q25.1, revealed a doublet band in cDNA from one of four EOC cell lines, OV90. In contrast to three other EOC cell lines (TOV81D, TOV112D and TOV21G) and primary cultures derived from normal ovarian surface epithelial cells (NOSE), sequence analysis of the cDNA revealed a deletion of G at position 1484 of the transcribed sequence which is located within the 3'UTR of H3F3B. OV90 was derived from ascites fluid of an undifferentiated adenocarcinoma of ovarian origin. The variant allele was identified in 1 of 65 (2%) healthy women with no prior history of cancer and in 5 participants with ovarian tumors comprising of 4 of 79 (5%) malignant EOC, none of 10 low malignancy potential tumors, and 1 of 8 (13%) benign tumors. All carriers of the variant alleles were heterozygous and tumor samples did not exhibit preferential LOH of the normal allele. The variant allele was identified in EOC samples of clear cell (1 of 20), mucinous (1 of 8), mixed cell (1 of 3) and undifferentiated (1 of 2) histopathological subtypes but none of 34 serous or 12 endometrioid subtype tumors. One of 3 mucinous benign tumors also harbored the variant allele. The functional significance of the variant is unknown, however its presence in rare subtypes of ovarian epithelial tumors warrants further investigation.

3' Untranslated Regions↗
PubMed1996

Polymerase chain reaction for diagnosis and identification of distinct variants of Crimean-Congo hemorrhagic fever virus in the United Arab Emirates.

Viral hemorrhagic fever has re-emerged in the United Arab Emirates (UAE) since November 1993. Genomic RNA of Crimean-Congo hemorrhagic virus (C-CHFV) was detected by a newly developed, nested reverse transcriptase polymerase chain reaction (RT-PCR) in the sera of four (25.0%) of 16 suspected cases of viral hemorrhagic fever. The RT-PCR was based on oligonucleotide primers deducted from the small RNA segment encoding the nucleoprotein of the virus. By comparison with a nucleotide sequence of a C-CHFV isolate from a Chinese sheep, a divergence of 10.0-11.8% was detected in the C-CHFV variants causing the UAE outbreak. In the four positive sera, three phylogenetically distinct C-CHFV variants were amplified and confirmed by direct sequencing of the PCR fragments. These C-CHFV sequences were obtained directly from sera of infected humans without prior propagation in cell culture. The RT-PCR allows rapid detection of genomic C-CHFV RNA in clinical specimens and study of the molecular epidemiology of this infection.

Amino Acid Sequence↗
PubMed1998

A new nonamyloid transthyretin variant, G101S, detected by electrospray ionization/mass spectrometry. Mutations in brief no. 201. Online.

Familial amyloidotic polyneuropathy is caused by transthyretin (TTR) variants. The identification of new variants with and without amyloidosis may help to clarify the mechanism of amyloid fibril formation. We detected several variant TTRs from patients with and without symptoms of amyloidosis using mass spectrometry (MS). TTR was isolated by mixing test serum with anti-transthyretin antiserum, and the generated immunoprecipitate was analyzed by high performanced liquid chromatography/electrospray ionization (HPLC/ESI) MS. Variant TTRs showed extra peaks in addition to normal TTR peaks. A variant found in nonamyloid group was sequenced by HPLC/ESI tandem MS using peptides obtained by protelytic digestion of TTR and by DNA analysis. The structure was new, [G101S], and was found in a 74 years old Japanese male. This mutation results from substitution in a CpG hot spot. The substitution in the surface loop, 98-102, between F and G b-strands may not cause amyloid formation.

Aged↗
PubMed2002

Systematic identification of splice variants in human P/Q-type channel alpha1(2.1) subunits: implications for current density and Ca2+-dependent inactivation.

P/Q-type (Ca(v)2.1) calcium channels support a host of Ca2+-driven neuronal functions in the mammalian brain. Alternative splicing of the main alpha1A (alpha1(2.1)) subunit of these channels may thereby represent a rich strategy for tuning the functional profile of diverse neurobiological processes. Here, we applied a recently developed "transcript-scanning" method for systematic determination of splice variant transcripts of the human alpha1(2.1) gene. This screen identified seven loci of variation, which together have never been fully defined in humans. Genomic sequence analysis clarified the splicing mechanisms underlying the observed variation. Electrophysiological characterization and a novel analytical paradigm, termed strength-current analysis, revealed that one focus of variation, involving combinatorial inclusion and exclusion of exons 43 and 44, exerted a primary effect on current amplitude and a corollary effect on Ca2+-dependent channel inactivation. These findings significantly expand the anticipated scope of functional diversity produced by splice variation of P/Q-type channels.

Alternative Splicing↗
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↗
PubMed1986

Inherited thrombocytopenia, elevated serum IgA and renal disease: identification as a variant of the Wiskott-Aldrich syndrome.

A kindred with X-linked hereditary thrombocytopenia in association with elevated serum IgA and a mild nephropathy is described. Thirteen males with thrombocytopenia were identified in three generations amongst 49 family members who were available for screening. Serious infective sequelae were absent but five patients had suffered from severe eczema since infancy. The platelet volume as measured by an automated counter and electron microscopy was reduced compared with normal and in vitro tests demonstrated minor abnormalities of immune function in three patients. The disorder is identified as a novel variant of the Wiskott-Aldrich syndrome and comparisons are made with previously described kindreds showing different patterns of expression.

Adult↗
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↗
PubMed1984

Identification of genetic variants in erythrocyte lysate by two-dimensional gel electrophoresis.

Two-dimensional gel electrophoresis followed by silver-staining has been employed to study 27 red cell lysates for genetic variation. Forty-six polypeptides selected without respect to variability were considered suitable for scoring. Only 23 of the total of 1,242 polypeptides could not be scored unambiguously. Of the remaining 1,219 polypeptides, 38 exhibited the combination of a normal and a variant polypeptide. All variants were present in either the father or the mother of the subjects. The observed index of heterozygosity was 3.1% +/- 0.5%.

Adult↗
PubMed1994

Isolation, characterization, and chromosomal localization of the porcine calcitonin receptor gene. Identification of two variants of the receptor generated by alternative splicing.

The gene encoding the calcitonin receptor (CTR) was isolated from a porcine kidney epithelial cell line (LLC-PK1) genomic library and found to span approximately 70 kilobases. Analysis of the gene sequence revealed that the CTR mRNA encompasses 14 exons with 12 exons encoding the protein. Two splicing acceptor sites separated by 48 nucleotides were found in intron 7. The expression of two mRNA species in LLC-PK1 cells was subsequently confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and DNA sequencing. In LLC-PK1 cells the mRNA encoding the shorter CTR (CTR-1a) is approximately 1,000 times more abundant than the longer variant (CTR-1b), as estimated by the competitive RT-PCR. The transcription initiation site of the CTR gene was mapped by primer extension, S1 nuclease, and RT-PCR analysis. The proximal promoter region of 500 base pair is GC-rich (66%) and CpG-rich (CpG/GpC ratio 0.71). Transient transfection of CTR gene promoter-luciferase chimeras in LLC-PK1 cells led to the expression of luciferase activity. The CTR gene was mapped to chromosome band 9q11-q12.

Alternative Splicing↗
PubMed1996

[Identification of a variant D(IVa) with anti-D in serum].

The first D(IVa) variant described so far in Spain is presented. This variant was identified, by means of a commercial monoclonal antibodies panel, in a RhD positive patient with anti-D in her serum. Differential diagnosis is discussed and the clinical relevance of identifying these variants is commented.

Antibodies, Monoclonal↗