Whole Exome Sequencing Reveals a Large Genetic Heterogeneity and Revisits the Causes of Hypertrophic Cardiomyopathy
2019; Wolters Kluwer; Volume: 12; Issue: 5 Linguagem: Inglês
10.1161/circgen.119.002500
ISSN2574-8300
AutoresKarine Nguyen, Stéphane Roche, Erwan Donal, Sylvie Odent, Jean‐Christophe Eicher, Laurence Faivre, Gilles Millat, David Salgado, Jean-Pierre Desvignes, Cécile Lavoûte, Julie Haentjens, Émilie Consolino, Alexandre Janin, Mathieu Cérino, Patricia Réant, Caroline Rooryck, Philippe Charron, Pascale Richard, Anne‐Claire Casalta, Nicolas Michel, Frédérique Magdinier, Christophe Béroud, Nicolas Lévy, Gilbert Habib,
Tópico(s)Williams Syndrome Research
ResumoHomeCirculation: Genomic and Precision MedicineVol. 12, No. 5Whole Exome Sequencing Reveals a Large Genetic Heterogeneity and Revisits the Causes of Hypertrophic Cardiomyopathy Free AccessLetterPDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citationsPermissions ShareShare onFacebookTwitterLinked InMendeleyReddit Jump toFree AccessLetterPDF/EPUBWhole Exome Sequencing Reveals a Large Genetic Heterogeneity and Revisits the Causes of Hypertrophic CardiomyopathyExperience of a Multicentric Study of 200 French Patients Karine Nguyen, MD, PhD, Stéphane Roche, PhD, Erwan Donal, MD, PhD, Sylvie Odent, MD, PhD, Jean-Christophe Eicher, MD, Laurence Faivre, MD, PhD, Gilles Millat, PhD, David Salgado, PhD, Jean-Pierre Desvignes, BS, Cécile Lavoute, PhD, Julie Haentjens, PhD, Émilie Consolino, MSc, Alexandre Janin, PharmD, PhD, Mathieu Cerino, PharmD, Patricia Réant, MD, PhD, Caroline Rooryck, MD, PhD, Philippe Charron, MD, PhD, Pascale Richard, PharmD, PhD, Anne-Claire Casalta, MD, Nicolas Michel, MD, Frédérique Magdinier, PhD, Christophe Béroud, PharmD, PhD, Nicolas Lévy, MD, PhD and Gilbert Habib, MD, PhD Karine NguyenKarine Nguyen Karine Nguyen, MD, PhD, Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, 264 Rue St Pierre, 13385 Marseille Cedex 05, France. Email E-mail Address: [email protected] Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Stéphane RocheStéphane Roche Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Erwan DonalErwan Donal Service de Cardiologie (E.D.), CHU de Rennes, University of Rennes, France. , Sylvie OdentSylvie Odent Service de Génétique Clinique, IGDR (Institut de Génétique et développement de Rennes) (S.O.), CHU de Rennes, University of Rennes, France. , Jean-Christophe EicherJean-Christophe Eicher Centre de Compétences des Cardiomyopathies (J.-C.E.), Hôpital d'Enfants, CHU de Dijon, France , Laurence FaivreLaurence Faivre Centre de Génétique (L.F.), Hôpital d'Enfants, CHU de Dijon, France , Gilles MillatGilles Millat Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, France (G.M., A.J.). , David SalgadoDavid Salgado Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Jean-Pierre DesvignesJean-Pierre Desvignes Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Cécile LavouteCécile Lavoute Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Julie HaentjensJulie Haentjens Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Émilie ConsolinoÉmilie Consolino Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Alexandre JaninAlexandre Janin Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, France (G.M., A.J.). , Mathieu CerinoMathieu Cerino Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Patricia RéantPatricia Réant Service de Cardiologie (P. Réant), CHU de Bordeaux, France. , Caroline RooryckCaroline Rooryck Service de Génétique Médicale (C.R.), CHU de Bordeaux, France. , Philippe CharronPhilippe Charron Centre de référence pour les maladies cardiaques héréditaires, APHP, Hôpital Pitié-Salpêtrière, Sorbonne Universités, INSERM UMR_S 1166 and ICAN Institute, Paris, France (P.C.). , Pascale RichardPascale Richard Service de Biochimie Métabolique, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Unité de Cardiogénétique et myogénétique, Paris, France (P. Richard). , Anne-Claire CasaltaAnne-Claire Casalta , Nicolas MichelNicolas Michel , Frédérique MagdinierFrédérique Magdinier Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Christophe BéroudChristophe Béroud Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). , Nicolas LévyNicolas Lévy Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, Marseille, France. Aix Marseille University, INSERM, Marseille Medical Genetics, Faculté de Médecine, France (K.N., S.R., D.S., J.-P.D., M.C., F.M., C.B., N.L.). and Gilbert HabibGilbert Habib Originally published21 May 2019https://doi.org/10.1161/CIRCGEN.119.002500Circulation: Genomic and Precision Medicine. 2019;12:e002500Hypertrophic cardiomyopathy (HCM), the most common hereditary heart disease, is autosomal dominant with incomplete penetrance and variability. Heterozygous mutations in 5 sarcomeric genes (MYBPC3, MYH7, TNNT2, TNNI3, and MYL2), estimated to account for 50% to 70% of HCM cases, are routinely screened for diagnosis, genetic counseling, predictive testing, and targeted follow-up of mutation carriers.1 Secondary HCM cases caused by Fabry disease and transthyretin hereditary amyloidosis, which require specific therapies, remain underdiagnosed.2The HYPERGEN study evaluated the diagnostic value of whole exome sequencing (WES) in HCM compared with targeted sequencing of the 5 sarcomeric genes. Two hundred unrelated patients with newly diagnosed isolated HCM were enrolled in 5 French centers (Marseille, Bordeaux, Paris, Dijon, and Rennes). An institutional review committee approved the study. All subjects gave informed consent for genetic studies. HCM echocardiographic diagnosis was considered definite in presence of left ventricular hypertrophy (maximal wall thickness ≥15 mm in sporadic or >13 mm in familial cases) without dilatation or any other cardiac or systemic disease. The patient cohort included 132 men and 68 women (mean age, 55 years; range, 19–91; 86.5% above 40; 66% sporadic cases).WES was performed on the NGS Illumina HiSeq2500 platform using Agilent SureSelect V6 technology (Genwiz, United States). Bioinformatic analyses were performed in our laboratory using prediction software and comparison to mutation databases.3 We retained exonic and intronic variants whose frequencies were lower than 1% and predicted as pathogenic or likely pathogenic.4 The first step of WES data analysis consisted of searching for mutations in a virtual panel of 167 genes involved in cardiomyopathies and other various hereditary diseases. WES identified 418 variants located in 101 genes among the 167 genes (Figure [A]). Besides TTN (titin), which carried the largest number of variants (n=88), the most frequently mutated genes were MYBPC3 (n=57, 13.6%), MYH7 (n=16, 3.8%), FLNC (n=14, 3.3%), RYR2 (n=10, 2.4%), SCN5A (n=10, 2.4%), ANK2 (n=8, 1.9%), and CTNNA3 (n=7, 1.7%); MYH6, TNNT2, DSP, LAMA4, and NEBL (n=6 each gene, 1.4% each); and 88 other genes (total n=178, 42.6%). Only 1 variant was found in MYL2 (0.2%) and none in TNNI3. Overall, 65 variants (15.5% of all, 19.7% with TTN excluded) were located in 19 arrhythmia genes. The most prevalent genes were the sarcomeric genes with 96 variants in 10 genes (23%) among which the 5 most frequent sarcomeric genes accounted for 80 variants (19.1%).Download figureDownload PowerPointFigure. Mutations found by WES and diagnostic rate of targeted sequencing of 5 sarcomeric genes. A, Distribution of variants (n=418). Top, The relative frequencies of genes carrying variants is presented, according to the gene function. In blue, the 4 sarcomeric genes among the 5 genes expected to be the most frequently associated with hypertrophic cardiomyopathy (HCM), because of the absence of mutations in TNNI3 in this cohort. Green corresponds to a larger panel of 60 genes involved in various hereditary cardiac diseases. In gray, other genes involved in hereditary cardiac or systemic diseases. B, Diagnostic rate for the targeted sequencing of the 5 sarcomeric genes in the 5 French centers of the HYPERGEN study (top) and mutation detection rate in sporadic and familial cases of HCM (bottom). Lyz indicates lysosomal; X, other; and WES, whole exome sequencing.Four variants in the GLA gene (Fabry disease) were identified in 4 patients, among which were the same benign polymorphism p.Asp313Tyr in 3 patients and a novel heterozygous c.931dupC (p.Leu311Profs*4) pathogenic mutation in 1 woman presenting with isolated HCM and no extracardiac features. Accordingly, the plasmatic Lyso-GL3 biomarker was abnormal (10.6, normal≤1.8 ng/mL) and confirmed Fabry disease. The well-known p.Val50Met mutation in the TTR gene was identified in 1 patient showing isolated HCM, confirming transthyretin cardiac amyloidosis.Interestingly, 4 variants (1%) in the FBN1 gene were found in 4 patients, among which 1 was previously reported as a disease-causing mutation in Marfan syndrome, and all the patients had other variants in other genes. We also identified 4 variants in 2 novel genes (ROCK1 and ROCK2) belonging to the Rho kinases family and not previously associated with any cardiac phenotype. All occurred in combination with variants in other genes, including MYBPC3 and FBN1. Forty-six patients (23%) carried a single variant, whereas 129 (64.5%) carried >1 variant (from 2 to 7 variants).Altogether, after targeted sequencing of the 5 sarcomeric genes, 70 patients (35%) had a diagnosis of a pathogenic mutation, whereas, by WES, 175 patients (87.5%) carried at least 1 pathogenic or likely pathogenic mutation within the 167 genes (Figure [B]). Among the 130 patients with no mutation identified by the standard approach, WES detected at least 1 mutation in 105/130 patients (80.7%). Among the 70 patients with 1 mutation, WES detected additional mutations in 53/70 patients (75.7%).Considering a larger targeted panel of 60 genes involved in various cardiomyopathies and arrhythmias, currently proposed to be screened as a second step of the diagnostic strategy after sequencing of the 5 sarcomeric genes, the diagnostic rate reached 79% of patients (158/200) with identification of at least 1 mutation. In 25 patients (12.5%), neither targeted sequencing nor analysis of the WES virtual panel detected any mutation. Beyond the 167 genes in the WES virtual panel, further analysis of WES data is needed to identify potential new genes.In conclusion, the HYPERGEN study validated the yield of WES in HCM. WES detected additional mutations in patients with 1 mutation identified by targeted sequencing, suggesting larger genetic heterogeneity than previously thought, and perhaps oligogenism.5 WES confirmed the prominent involvement of MYBPC3 and MYH71 but also showed unexpected frequency of mutations in TTN and FLNC as well as in SCN5A, RYR2, and other ion channel genes, suggesting overlap between HCM and arrhythmia genes. Familial segregation studies will refine the interpretation of variants' pathogenicity and will be the next step of the HYPERGEN project.The data that support the findings of this study are available from the corresponding author upon reasonable request.AcknowledgmentsWe are indebted to all patients for participating in this study. We are thankful to Caroline Sawka, MSc, Geoffrey Bertolone, MSc, and Amandine Baurand, MSc for providing clinical data and samples.Sources of FundingThis study was financially supported by SANOFI GENZYME SA (contract number C01550).DisclosuresNone.Footnotes*Drs Lévy and Habib contributed equally as last authors.Karine Nguyen, MD, PhD, Département de génétique médicale, APHM, Hôpital d'enfants de la Timone, 264 Rue St Pierre, 13385 Marseille Cedex 05, France. Email karine.[email protected]frReferences1. Richard P, et al; EUROGENE Heart Failure Project. Hypertrophic cardiomyopathy: distribution of disease genes, spectrum of mutations, and implications for a molecular diagnosis strategy.Circulation. 2003; 107:2227–2232. doi: 10.1161/01.CIR.0000066323.15244.54LinkGoogle Scholar2. Hagège AA, et al; FOCUS Study Investigators. Screening patients with hypertrophic cardiomyopathy for Fabry disease using a filter-paper test: the FOCUS study.Heart. 2011; 97:131–136. doi: 10.1136/hrt.2010.200188CrossrefMedlineGoogle Scholar3. Salgado D, et al. UMD-Predictor: a high-throughput sequencing compliant system for pathogenicity prediction of any human cDNA substitution.Hum Mutat. 2016; 37:439–446. doi: 10.1002/humu.22965CrossrefMedlineGoogle Scholar4. Richards S, et al; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.Genet Med. 2015; 17:405–424. doi: 10.1038/gim.2015.30CrossrefMedlineGoogle Scholar5. Li L, et al. A potential oligogenic etiology of hypertrophic cardiomyopathy: a classic single-gene disorder.Circ Res. 2017; 120:1084–1090. doi: 10.1161/CIRCRESAHA.116.310559LinkGoogle Scholar Previous Back to top Next FiguresReferencesRelatedDetailsCited By Christian S, Cirino A, Hansen B, Harris S, Murad A, Natoli J, Malinowski J and Kelly M (2022) Diagnostic validity and clinical utility of genetic testing for hypertrophic cardiomyopathy: a systematic review and meta-analysis, Open Heart, 10.1136/openhrt-2021-001815, 9:1, (e001815), Online publication date: 1-Apr-2022. 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May 2019Vol 12, Issue 5 Advertisement Article InformationMetrics © 2019 American Heart Association, Inc.https://doi.org/10.1161/CIRCGEN.119.002500PMID: 31112424 Originally publishedMay 21, 2019 Keywordsgenetic counselingwhole exome sequencingdilatationamyloidosisFabry diseasePDF download Advertisement SubjectsCardiomyopathyClinical StudiesGeneticsHypertrophy
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