The term "arrhythmia" refers to any change from the normal sequence of electrical impulses. Tachycardia, an abnormally fast resting heart rate (>100 beats per minute, bpm), can be asymptomatic or severe and clinically characterized by dizziness, breathlessness, sudden weakness and palpitations in the chest. Single nucleotide variants (SNVs) are one of the major causes of cardiac conduction defects. The discovery of SNVs in novel genes associated with cardiac phenotypes has been enormously implemented thanks to the advent of Next Generation Sequencing (NGS) techniques, in particular Whole-Exome Sequencing (WES) and, more recently, Whole-Genome Sequencing (WGS). This thesis project adopted a "family-based” WES approach to study three kindreds showing cardiac conduction diseases. Our bionformatic pipeline included different steps of NGS data filtering: 1) in silico panel(s); 2) inheritance model (according to each specific pedigree); 3) variant prioritization. By using this approach, we identified three potential causative genes: KCNK1, FGF13, and SCN2A. KCNK1 (encoding for a potassium channel highly expressed in the brain and heart) and FGF13 (encoding for a fibroblast growth factor causing cardiac dysfunction when deleted in mice) have never been associated with known diseases in humans. So far, SCN2A de novo variants has been uniquely related to neurophenotypes (i.e. epileptic encephalopathy, ataxia, and benign seizures); however, considering that the gene encodes for a voltage-gated sodium channel, we hypothesized that tachycardia might represent a phenotypic expansion of SCN2A. This study lays the initial groundwork for further functional studies on the candidate genes (especially KCNK1 and FGF13) based on cellular and animal models.
Con il termine "aritmia" si intende un qualsiasi cambiamento rispetto alla normale sequenza di impulsi elettrici. La tachicardia, caratterizzata da una rapida e anormale frequenza cardiaca a riposo (> 100 battiti al minuto, bpm), può essere asintomatica o grave e clinicamente caratterizzata da vertigini, mancanza di respiro, debolezza improvvisa e palpitazioni al petto. Le varianti a singolo nucleotide (SNV) sono una delle principali cause di difetti della conduzione cardiaca. La scoperta di SNV in nuovi geni associati ai fenotipi cardiaci è stata enormemente implementata grazie all'avvento delle tecniche di Next Generation Sequencing (NGS), in particolare Whole-Exome Sequencing (WES) e, più recentemente, Whole-Genome Sequencing (WGS). Questo progetto di tesi ha adottato un approccio WES "basato sulla famiglia" per studiare tre parenti che mostrano malattie della conduzione cardiaca. La nostra pipeline bionformatica comprendeva diverse fasi di filtraggio dei dati NGS: 1) pannelli in silico; 2) modello di ereditarietà (secondo ciascuna genealogia) 3) prioritizzazione delle varianti. Utilizzando questo approccio, abbiamo identificato tre potenziali geni causativi: KCNK1, FGF13 e SCN2A. KCNK1 (codificante per un canale del potassio altamente espresso nel cervello e nel cuore) e FGF13 (codificante per un fibroblasto fattore di crescita che causa disfunzione cardiaca quando eliminato nei topi) non sono mai state associate a malattie note negli esseri umani. Finora, le varianti de novo di SCN2A sono state unicamente correlate ai neurofenotipi (cioè encefalopatia epilettica, atassia e convulsioni benigne); tuttavia, considerando che codifica per un canale del sodio voltaggio-dipendente, abbiamo ipotizzato che la tachicardia potrebbe rappresentare un'espansione fenotipica di SCN2A. Questo studio pone le basi iniziali per ulteriori studi funzionali sui geni candidati (in particolare KCNK1 e FGF13) basati su modelli cellulari e animali.
Family-based whole-exome sequencing per l'identificazione di nuovi geni malattia ed espansione del fenotipo in patologie cardiache
MUIA', CARLA
2019/2020
Abstract
The term "arrhythmia" refers to any change from the normal sequence of electrical impulses. Tachycardia, an abnormally fast resting heart rate (>100 beats per minute, bpm), can be asymptomatic or severe and clinically characterized by dizziness, breathlessness, sudden weakness and palpitations in the chest. Single nucleotide variants (SNVs) are one of the major causes of cardiac conduction defects. The discovery of SNVs in novel genes associated with cardiac phenotypes has been enormously implemented thanks to the advent of Next Generation Sequencing (NGS) techniques, in particular Whole-Exome Sequencing (WES) and, more recently, Whole-Genome Sequencing (WGS). This thesis project adopted a "family-based” WES approach to study three kindreds showing cardiac conduction diseases. Our bionformatic pipeline included different steps of NGS data filtering: 1) in silico panel(s); 2) inheritance model (according to each specific pedigree); 3) variant prioritization. By using this approach, we identified three potential causative genes: KCNK1, FGF13, and SCN2A. KCNK1 (encoding for a potassium channel highly expressed in the brain and heart) and FGF13 (encoding for a fibroblast growth factor causing cardiac dysfunction when deleted in mice) have never been associated with known diseases in humans. So far, SCN2A de novo variants has been uniquely related to neurophenotypes (i.e. epileptic encephalopathy, ataxia, and benign seizures); however, considering that the gene encodes for a voltage-gated sodium channel, we hypothesized that tachycardia might represent a phenotypic expansion of SCN2A. This study lays the initial groundwork for further functional studies on the candidate genes (especially KCNK1 and FGF13) based on cellular and animal models.È consentito all'utente scaricare e condividere i documenti disponibili a testo pieno in UNITESI UNIPV nel rispetto della licenza Creative Commons del tipo CC BY NC ND.
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https://hdl.handle.net/20.500.14239/12818