No detection of atypical one-base deletion of CALR exon 9 with fragment analysis: A molecular trap to avoid

Gastrointestinale Stromatumoren (GIST), an denen in Deutschland jährlich etwa 1250 Menschen neu erkranken, entstehen aus mesenchymalen, interstitiellen Stammzellen im Bereich des Auerbach-Plexus, weit überwiegend aufgrund spezifischer Mutationen im Gen des KIT-, seltener auch des PDGF-Rezeptors (Platelet Derived Growth Factor), die zur Selbstaktivierung der Rezeptoren führen. Die meisten KIT-Mutationen liegen im Exon 11 (ca. 65%) oder Exon 9 (ca. 15%). Da Chemo- und Strahlentherapie keine Wirksamkeit erzielen, stellte die Entwicklung der Tyrosinkinase-Inhibitoren (TKI) Imatinib und Sunitinib laut Prof. Jörg Thomas Hartmann, Tübingen, einen deutlichen Fort-schritt dar: Sie unterbrechen die Selbstaktivierung der Rezeptoren, indem sie diese in-trazellulär blockieren.

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Fragment Analysis Process for the Joint Trauma Analysis and Prevention of Injury in Combat Program

10.21236/ada550813 ◽

2011 ◽

Author(s):

Karen Pizzolato

Keyword(s):

Fragment Analysis ◽

Analysis Process ◽

Joint Trauma

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Screening for Plasminogen Mutations in Hereditary Angioedema Patients

Genes ◽

10.3390/genes12030402 ◽

2021 ◽

Vol 12 (3) ◽

pp. 402

Author(s):

Henriette Farkas ◽

Anna Dóczy ◽

Edina Szabó ◽

Lilian Varga ◽

Dorottya Csuka

Keyword(s):

Gene Mutation ◽

Hereditary Angioedema ◽

Unknown Origin ◽

Factor Xii ◽

Gene Encoding ◽

New Techniques ◽

Ex Post ◽

Appropriate Therapy ◽

Exon 9 ◽

Serping1 Gene

Hereditary angioedema (HAE) is a rare disease belonging to the group of bradykinin-mediated angioedemas, characterized by recurring edematous episodes involving the subcutaneous and/or submucosal tissues. Most cases of HAE are caused by mutations in the SERPING1 gene encoding C1-inhibitor (C1-INH-HAE); however, mutation analysis identified seven further types of HAE: HAE with Factor XII mutation (FXII-HAE), with plasminogen gene mutation (PLG-HAE), with angiopoietin-1 gene mutation (ANGPT1-HAE), with kininogen-1 gene mutation (KNG1-HAE), with a myoferlin gene mutation (MYOF-HAE), with a heparan sulfate-glucosamine 3-sulfotransferase 6 (HS3ST6) mutation, and hereditary angioedema of unknown origin (U-HAE). We sequenced DNA samples stored from 124 U-HAE patients in the biorepository for exon 9 of the PLG gene. One of the 124 subjects carried the mutation causing a lysine to glutamic acid amino acid exchange at position 330 (K330E). Later, the same PLG mutation was identified in the patient’s son. The introduction of new techniques into genetic testing has increased the number of genes identified. As shown by this study, a biorepository creates the means for the ex-post analysis of recently identified genes in stored DNA samples of the patients. This makes the diagnosis more accurate with the possibility of subsequent family screening and the introduction of appropriate therapy.

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Quantitative Evaluation of CFTR Pre-mRNA Splicing Dependent on the (TG)mTn Poly-Variant Tract

Diagnostics ◽

10.3390/diagnostics11020168 ◽

2021 ◽

Vol 11 (2) ◽

pp. 168

Author(s):

Manuela Sterrantino ◽

Andrea Fuso ◽

Silvia Pierandrei ◽

Sabina Maria Bruno ◽

Giancarlo Testino ◽

...

Keyword(s):

Cystic Fibrosis ◽

Transmembrane Conductance Regulator ◽

Functional Effect ◽

Transmembrane Conductance ◽

Therapeutic Consequences ◽

Clinical Consequences ◽

Exon 9 ◽

The Many ◽

Cystic Fibrosis Transmembrane ◽

Exon 10

Genetic analysis in cystic fibrosis (CF) is a difficult task. Within the many causes of variability and uncertainty, a major determinant is poor knowledge of the functional effect of most DNA variants of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. In turn, knowledge of the effect of a CFTR variant has dramatic diagnostic, prognostic and, in the era of CF precision medicine, also therapeutic consequences. One of the most challenging CFTR variants is the (TG)mTn haplotype, which has variable functional effect and controversial clinical consequences. The exact quantification of the anomalous splicing of CFTR exon 10 (in the HGVS name; exon 9 in the legacy name) and, consequently, of the residual wild-type functional CFTR mRNA, should be mandatory in clinical assessment of patients with potentially pathological haplotype of this tract. Here, we present a real time-based assay for the quantification of the proportion of exon 10+/exon 10− CFTR mRNA, starting from nasal brushing. Our assay proved rapid, economic and easy to perform. Specific primers used for this assay are either disclosed or commercially available, allowing any laboratory to easily perform it. A simplified analysis of the data is provided, facilitating the interpretation of the results. This method helps to enhance the comprehension of the genotype–phenotype relationship in CF and CFTR-related disorders (CFTR-RD), crucial for the diagnosis, prognosis and personalized therapy of CF.

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Small Non-Coding RNAome of Ageing Chondrocytes

International Journal of Molecular Sciences ◽

10.3390/ijms21165675 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5675

Author(s):

Panagiotis Balaskas ◽

Jonathan A. Green ◽

Tariq M. Haqqi ◽

Philip Dyer ◽

Yalda A. Kharaz ◽

...

Keyword(s):

Quantitative Polymerase Chain Reaction ◽

Differential Expression Analysis ◽

Cartilage Tissue ◽

Pcr Analysis ◽

Small Rna Sequencing ◽

High Grade ◽

Human Cartilage ◽

Fragment Analysis ◽

Qrt Pcr ◽

Age Related

Ageing is a leading risk factor predisposing cartilage to osteoarthritis. However, little research has been conducted on the effect of ageing on the expression of small non-coding RNAs (sncRNAs). RNA from young and old chondrocytes from macroscopically normal equine metacarpophalangeal joints was extracted and subjected to small RNA sequencing (RNA-seq). Differential expression analysis was performed in R using package DESeq2. For transfer RNA (tRNA) fragment analysis, tRNA reads were aligned to horse tRNA sequences using Bowtie2 version 2.2.5. Selected microRNA (miRNAs or miRs) and small nucleolar RNA (snoRNA) findings were validated using real-time quantitative Polymerase Chain Reaction (qRT-PCR) in an extended cohort of equine chondrocytes. tRNA fragments were further investigated in low- and high-grade OA human cartilage tissue. In total, 83 sncRNAs were differentially expressed between young and old equine chondrocytes, including miRNAs, snoRNAs, small nuclear RNAs (snRNAs), and tRNAs. qRT-PCR analysis confirmed findings. tRNA fragment analysis revealed that tRNA halves (tiRNAs), tiRNA-5035-GluCTC and tiRNA-5031-GluCTC-1 were reduced in both high grade OA human cartilage and old equine chondrocytes. For the first time, we have measured the effect of ageing on the expression of sncRNAs in equine chondrocytes. Changes were detected in a number of different sncRNA species. This study supports a role for sncRNAs in ageing cartilage and their potential involvement in age-related cartilage diseases.

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Primary and Secondary Kinase Genotypes Correlate With the Biological and Clinical Activity of Sunitinib in Imatinib-Resistant Gastrointestinal Stromal Tumor

Journal of Clinical Oncology ◽

10.1200/jco.2007.15.7461 ◽

2008 ◽

Vol 26 (33) ◽

pp. 5352-5359 ◽

Cited By ~ 463

Author(s):

Michael C. Heinrich ◽

Robert G. Maki ◽

Christopher L. Corless ◽

Cristina R. Antonescu ◽

Amy Harlow ◽

...

Keyword(s):

Growth Factor Receptor ◽

Progression Free Survival ◽

Clinical Results ◽

Clinical Activity ◽

Wild Type ◽

Mutational Status ◽

Imatinib Resistant ◽

Exon 9 ◽

Exon 11 ◽

The Impact

PurposeMost gastrointestinal stromal tumors (GISTs) harbor mutant KIT or platelet-derived growth factor receptor α (PDGFRA) kinases, which are imatinib targets. Sunitinib, which targets KIT, PDGFRs, and several other kinases, has demonstrated efficacy in patients with GIST after they experience imatinib failure. We evaluated the impact of primary and secondary kinase genotype on sunitinib activity.Patients and MethodsTumor responses were assessed radiologically in a phase I/II trial of sunitinib in 97 patients with metastatic, imatinib-resistant/intolerant GIST. KIT/PDGFRA mutational status was determined for 78 patients by using tumor specimens obtained before and after prior imatinib therapy. Kinase mutants were biochemically profiled for sunitinib and imatinib sensitivity.ResultsClinical benefit (partial response or stable disease for ≥ 6 months) with sunitinib was observed for the three most common primary GIST genotypes: KIT exon 9 (58%), KIT exon 11 (34%), and wild-type KIT/PDGFRA (56%). Progression-free survival (PFS) was significantly longer for patients with primary KIT exon 9 mutations (P = .0005) or with a wild-type genotype (P = .0356) than for those with KIT exon 11 mutations. The same pattern was observed for overall survival (OS). PFS and OS were longer for patients with secondary KIT exon 13 or 14 mutations (which involve the KIT-adenosine triphosphate binding pocket) than for those with exon 17 or 18 mutations (which involve the KIT activation loop). Biochemical profiling studies confirmed the clinical results.ConclusionThe clinical activity of sunitinib after imatinib failure is significantly influenced by both primary and secondary mutations in the predominant pathogenic kinases, which has implications for optimization of the treatment of patients with GIST.

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