Abstract Accurate classification of genetic variants is crucial for clinical decision-making in hereditary cancer. In Spain, genetic diagnostic laboratories have traditionally approached this task ...independently due to the lack of a dedicated resource. Here we present SpadaHC, a web-based database for sharing variants in hereditary cancer genes in the Spanish population. SpadaHC is implemented using a three-tier architecture consisting of a relational database, a web tool and a bioinformatics pipeline. Contributing laboratories can share variant classifications and variants from individuals in Variant Calling Format (VCF) format. The platform supports open and restricted access, flexible dataset submissions, automatic pseudo-anonymization, VCF quality control, variant normalization and liftover between genome builds. Users can flexibly explore and search data, receive automatic discrepancy notifications and access SpadaHC population frequencies based on many criteria. In February 2024, SpadaHC included 18 laboratory members, storing 1.17 million variants from 4306 patients and 16 343 laboratory classifications. In the first analysis of the shared data, we identified 84 genetic variants with clinically relevant discrepancies in their classifications and addressed them through a three-phase resolution strategy. This work highlights the importance of data sharing to promote consistency in variant classifications among laboratories, so patients and family members can benefit from more accurate clinical management. Database URL: https://spadahc.ciberisciii.es/
The aim of this review is to provide an updated overview of hereditary hearing loss, with special attention to the etiological diagnosis of sensorineural hearing loss, the genes most frequently ...mutated in our environment, the techniques available for their analysis and the clinical implications of genetic diagnosis. More than 60% of childhood sensorineural hearing loss is genetic. In adults, the percentage of hereditary hearing loss is unknown. Genetic testing is the highest yielding test for evaluating patients with sensorineural hearing loss. The process of genetic counselling is intended to inform patients and their families of the medical, psychological and familial implications of genetic diseases, as well as the risks, benefits and limitations of genetic testing. The implementation of any genetic analysis must be always preceded by an appropriate genetic counselling process.
Background
Next‐generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding ...in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies.
Methods
Next‐generation sequencing libraries enriched in the exons of 215 cancer genes (97 for therapy selection and 148 for predisposition, with 30 informative for both applications), as well as selected introns from 17 genes involved in drug‐related rearrangements, were prepared from 39 tumors (paraffin‐embedded tissues/cytologies), 36 germline samples (blood) and 10 cell lines using hybrid capture. Analysis of NGS results was performed with specifically developed bioinformatics pipelines.
Results
The platform detects single‐nucleotide variants (SNVs) and insertions/deletions (indels) with sensitivity and specificity >99.5% (allelic frequency ≥0.1), as well as copy‐number variants (CNVs) and rearrangements. Somatic testing identified tailored approved targeted drugs in 35/39 tumors (89.74%), showing a diagnostic yield comparable to that of leading commercial platforms. A somatic EGFR p.E746_S752delinsA mutation in a mediastinal metastasis from a breast cancer prompted its anatomopathologic reassessment, its definite reclassification as a lung cancer and its treatment with gefitinib (partial response sustained for 15 months). Testing of 36 germline samples identified two pathogenic mutations (in CDKN2A and BRCA2). We propose a strategy for interpretation and reporting of results adaptable to the aim of the request, the availability of tumor and/or normal samples and the scope of the informed consent.
Conclusion
With an adequate methodology, it is possible to translate to the clinical practice the latest advances in precision oncology, integrating under the same platform the identification of somatic and germline genomic alterations.
This work describes the development, validation and clinical application of a novel molecular diagnostics platform based on targeted NGS, specifically designed to comprehensively identify, in a single test, both (1) somatic alterations linked to sensitivity or resistance to approved cancer therapies and (2) germline mutations predisposing to familial cancer. We also propose an innovative framework for analysis, interpretation and reporting of results, which adapts to different combinatorial situations regarding the nature of the request, the availability of tumor/normal samples and the scope of the informed consent. The analytical sensitivity and specificity of the platform for detecting SNVs and indels are >99.5% and its application to patient samples identified targeted therapeutic opportunities, revealed one case of misdiagnosis and detected germline pathogenic mutations.
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has frequent alterations in few genes (KRAS, CDKN2A/TP53/SMAD4) and extensive heterogeneity of cancer drivers beyond. The expectation that mutational ...landscapes of rare drivers could explain phenotypic diversity has -with few exceptions- not come true. Likewise, PDAC metastasis is not understood, and comparisons of primary/metastasis pairs did not find recurrently mutated “metastasis genes”. Here we show that key aspects of PDAC biology are defined by gene-dosage variation of PDAC signature genes, evolving along distinct evolutionary routes. We found increased gene dosage of the initiating KRAS mutation (KRASMUT-iGD) in human PDAC precursors. Mouse models revealed the importance of KrasMUT-iGD for both, early progression and metastasis, rationalizing the high frequency of PDAC dissemination at diagnosis. To overcome limitations posed to gene dosage studies by PDAC´s stroma-richness, we developed murine cell culture resources comprising 135 primaries/metastases. Integrative analyses of their genomes, transcriptomes and tumor phenotypes, combined with human studies and functional analyses revealed a series of additional KrasMUT-dosage effects: different KrasMUT-levels define distinct cellular morphologies, histopathologies and clinical outcomes, with highest KrasMUT-expression underlying the most aggressive undifferentiated phenotypes. We also observed KrasMUT-dosage-associated cellular plasticity, including epithelial-to-mesenchymal transition. Mechanistically, oncogenic dosage-variation is linked to distinct evolutionary routes, characterized by defined types/states of tumor-suppressor alterations: Phylogenetic tracking studies revealed convergent evolution of KrasMUT-iGD-gains, with dependence on prior homozygous Cdkn2a- or Trp53-loss. By contrast, in Cdkn2aHET cancers, amplifications of known and novel oncogenes (Myc, Yap1, Nfkb2) collaborate with KrasMUT-HET to drive progression, yet with lower metastatic potential. These results also reveal oncogene-selective/context-dependent Cdkn2a-haploinsufficiency, for which Tgfβ pathway alterations provide permissiveness. Our study uncovers universal principles underlying PDAC biology and phenotypic diversification. It describes evolutionary trajectories, identifies their genetic hallmarks and shows how oncogenic dosage-variation is differentially licensed along individual routes to control critical disease characteristics, including early progression, histopathology, metastasis, cellular plasticity and clinical aggressiveness.
Citation Format: Sebastian Mueller, Thomas Engleitner, Roman Maresch, Magdalena Zukowska, Sebastian Lange, Thorsten Kaltenbacher, Björn Konukiewitz, Rupert Öllinger, Maximilian Zwiebel, Alex Strong, Hsi-Yu Yen, Ruby Banerjee, Sandra Louzada, Beiyuan Fu, Barbara Seidler, Juliana Götzfried, Kathleen Schuck, Zonera Hassan, Nina Schönhuber, Sabine Klein, Christian Veltkamp, Mathias Friedrich, Lena Rad, Maxim Barenboim, Christoph Ziegenhain, Julia Hess, Oliver M. Dovey, Stefan Eser, Swati Parekh, Fernando Constantino-Casas, Jorge de la Rosa, Marta I. Sierra, Mario Fraga, Julia Mayerle, Günter Klöppel, Roland M. Schmid, Juan Cadiñanos, Pentao Liu, George Vassiliou, Wilko Weichert, Katja Steiger, Wolfgang Enard, Fengtang Yang, Kristian Unger, Günter Schneider, Ignacio Varela, Allan Bradley, Dieter Saur, Roland Rad. Evolutionary trajectories and KRAS gene dosage define pancreatic cancer phenotypes abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 391.
Hasta ahora no existían evidencias de la presencia de ninguna de las especies del género Limonium en la provincia de Burgos, a pesar de que sí lo están en algunas provincias limítrofes como ...Cantabria, Vizcaya, La Rioja, Soria, Segovia y Ávila. También aportamos la tercera cita de Sonchus maritimus L. para Burgos.
Hasta ahora no existían evidencias de la presencia de ninguna de las especies del género Limonium en la provincia de Burgos, a pesar de que sí lo están en algunas provincias limítrofes como ...Cantabria, Vizcaya, La Rioja, Soria, Segovia y Ávila. También aportamos la tercera cita de Sonchus maritimus L. para Burgos. ABSTRACT : Until now there was no evidence of the presence of any of the species of the genus Limonium in the province of Burgos, even though they are in a number of neighbouring provinces such as Cantabria, Vizcaya, La Rioja, Soria, Segovia and Avila. We also contribute the third citation of Sonchus maritimus L. for Burgos.
Sensorineural hearing loss (SNL) is the most prevalent sensory deficit in our environment. The next generation genomic sequencing (NGS) allows to obtain an etiological diagnosis in a high percentage ...of patients. Our pilot study shows the results of the systematic application of NGS in a Childhood Hearing Loss Unit, as well as its implications in the clinical management of patients and their families.
We included 27 patients diagnosed with SNH between 2014 and 2017, in which an environmental cause was ruled out. The genetic test consisted of a panel of genes analyzed by NGS (OTOgenics™ panel). This panel has been designed to include genes associated with sensorineural or mixed hearing loss, early onset or late, syndromic and non-syndromic, regardless of their inheritance pattern.
A genetic diagnosis was obtained in 56% (15/27) of the patients (62% in the case of bilateral HNS). 5/27 (19%) presented pathogenic variants in the GJB2 gene and the rest variants pathogenic and/or probably pathogenic in other genes associated with isolated HNS (PR2 × 2, TECTA and STRC), with syndromic HNS (CHD7, GATA3, COL4A5, MITF and SOX10) or with syndromic and non-syndromic HNS (BSND, ACTG1 and CDH23).
The etiological diagnosis of SNL is a challenge in clinical practice. Our series demonstrates that it is possible to implement genetic diagnosis in the daily routine and that this information has prognostic and therapeutic implications.
La hipoacusia neurosensorial (HNS) es el déficit sensorial más prevalente en nuestro medio. La secuenciación genómica de nueva generación (NGS) permite obtener un diagnóstico etiológico en un alto porcentaje de pacientes. Nuestro estudio piloto muestra los resultados de la aplicación sistemática de la NGS en una Unidad de Hipoacusia Infantil, así como sus implicaciones en el manejo clínico de los pacientes y sus familiares.
Se incluyeron 27 pacientes diagnosticados de HNS entre 2014 y 2017 en los que se descartó una causa ambiental. El test genético consistió en un panel de genes analizados mediante NGS (panel OTOgenics™). Este panel ha sido diseñado para incluir genes asociados con hipoacusia neurosensorial o mixta, de inicio precoz o tardío, sindrómica y no sindrómica, independientemente de su patrón de herencia.
Se obtuvo un diagnóstico genético en el 56% (15/27) de los pacientes (62% en el caso de las HNS bilaterales). 5/27 (19%) presentaron variantes patogénicas en el genGJB2 y el resto variantes patogénicas y/o probablemente patogénicas en otros genes asociados con HNS aislada (PR2 × 2, TECTA y STRC), con HNS sindrómicas (CHD7, GATA3, COL4A5, MITF y SOX10) o con HNS sindrómicas y no sindrómicas (BSND, ACTG1 y CDH23).
El diagnóstico etiológico de la HNS supone un desafío en la práctica clínica. Nuestra serie demuestra que es posible implementar el diagnóstico genético en la rutina asistencial y que esta información tiene implicaciones pronósticas y terapéuticas.
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