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1. Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability

Author

Zelia Corradi, Mubeen Khan, Rebekkah Hitti-Malin, Ketan Mishra, Laura Whelan, Stéphanie S. Cornelis, Carel B. Hoyng, Kati Kämpjärvi, Caroline C.W. Klaver, Petra Liskova, Heidi Stöhr, Bernhard H.F. Weber, Sandro Banfi, G. Jane Farrar, Dror Sharon, Jana Zernant, Rando Allikmets, Claire-Marie Dhaenens, and Frans P.M. Cremers

Subjects
ABCA4, ABCA4-associated retinopathies, missing heritability, smMIPs sequencing, deep-intronic variants, Genetics, QH426-470
Abstract

Summary: The ABCA4 gene is the most frequently mutated Mendelian retinopathy-associated gene. Biallelic variants lead to a variety of phenotypes, however, for thousands of cases the underlying variants remain unknown. Here, we aim to shed further light on the missing heritability of ABCA4-associated retinopathy by analyzing a large cohort of macular dystrophy probands. A total of 858 probands were collected from 26 centers, of whom 722 carried no or one pathogenic ABCA4 variant, while 136 cases carried two ABCA4 alleles, one of which was a frequent mild variant, suggesting that deep-intronic variants (DIVs) or other cis-modifiers might have been missed. After single molecule molecular inversion probes (smMIPs)-based sequencing of the complete 128-kb ABCA4 locus, the effect of putative splice variants was assessed in vitro by midigene splice assays in HEK293T cells. The breakpoints of copy number variants (CNVs) were determined by junction PCR and Sanger sequencing. ABCA4 sequence analysis solved 207 of 520 (39.8%) naive or unsolved cases and 70 of 202 (34.7%) monoallelic cases, while additional causal variants were identified in 54 of 136 (39.7%) probands carrying two variants. Seven novel DIVs and six novel non-canonical splice site variants were detected in a total of 35 alleles and characterized, including the c.6283-321C>G variant leading to a complex splicing defect. Additionally, four novel CNVs were identified and characterized in five alleles. These results confirm that smMIPs-based sequencing of the complete ABCA4 gene provides a cost-effective method to genetically solve retinopathy cases and that several rare structural and splice altering defects remain undiscovered in Stargardt disease cases.

Published
2023
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2. Generation of VCCRIi001-A, a human induced pluripotent stem cell line, from a patient with spontaneous coronary artery dissection

Author

Ketan Mishra, Keerat Junday, Claire M.Y. Wong, Andrea Y. Chan, Stephanie Hesselson, David W. Muller, Siiri E. Iismaa, Ashish Mehta, and Robert M. Graham

Subjects
Biology (General), QH301-705.5
Abstract

Spontaneous coronary artery dissection (SCAD) is a non-atherosclerotic form of coronary artery disease of unknown cause that predominantly affects women (>90%; mean age 44–55 years) and can be fatal. The finding of familial clustering, including the concordant involvement of monozygotic twins, and its association with the PHACTR1/EDN1 genetic locus, indicate a genetic predisposition to its pathophysiology. A human induced pluripotent stem cell line (hiPSC) was generated from a patient who had survived an episode of SCAD. This disease-specific hiPSC line will be useful for the study of SCAD after differentiation into blood vessel-forming cells. Keywords: SCAD, Induced pluripotent stem cells, Disease modeling, Cardiovascular biology, Reprogramming

Published
2019
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3. Exploring the Genetic Architecture of Spontaneous Coronary Artery Dissection Using Whole-Genome Sequencing

Author

Ingrid Tarr, Stephanie Hesselson, Siiri E. Iismaa, Emma Rath, Steven Monger, Michael Troup, Ketan Mishra, Claire M.Y. Wong, Pei-Chen Hsu, Keerat Junday, David T. Humphreys, David Adlam, Tom R. Webb, Anna A. Baranowska-Clarke, Stephen E. Hamby, Keren J. Carss, Nilesh J. Samani, Monique Bax, Lucy McGrath-Cadell, Jason C. Kovacic, Sally L. Dunwoodie, Diane Fatkin, David W.M. Muller, Robert M. Graham, and Eleni Giannoulatou

Subjects
Coronary Vessel Anomalies, Humans, Female, General Medicine, Vascular Diseases, Acute Coronary Syndrome
Abstract

Background: Spontaneous coronary artery dissection (SCAD) is a cause of acute coronary syndrome that predominantly affects women. Its pathophysiology remains unclear but connective tissue disorders (CTD) and other vasculopathies have been observed in many SCAD patients. A genetic component for SCAD is increasingly appreciated, although few genes have been robustly implicated. We sought to clarify the genetic cause of SCAD using targeted and genome-wide methods in a cohort of sporadic cases to identify both common and rare disease-associated variants. Methods: A cohort of 91 unrelated sporadic SCAD cases was investigated for rare, deleterious variants in genes associated with either SCAD or CTD, while new candidate genes were sought using rare variant collapsing analysis and identification of novel loss-of-function variants in genes intolerant to such variation. Finally, 2 SCAD polygenic risk scores were applied to assess the contribution of common variants. Results: We identified 10 cases with at least one rare, likely disease-causing variant in CTD-associated genes, although only one had a CTD phenotype. No genes were significantly associated with SCAD from genome-wide collapsing analysis, however, enrichment for TGF (transforming growth factor)-β signaling pathway genes was found with analysis of 24 genes harboring novel loss-of-function variants. Both polygenic risk scores demonstrated that sporadic SCAD cases have a significantly elevated genetic SCAD risk compared with controls. Conclusions: SCAD shares some genetic overlap with CTD, even in the absence of any major CTD phenotype. Consistent with a complex genetic architecture, SCAD patients also have a higher burden of common variants than controls.

Published
2023

5. ABCA4 c.859-25A>G, a Frequent Palestinian Founder Mutation Affecting the Intron 7 Branchpoint, Is Associated With Early-Onset Stargardt Disease

Author

Zelia Corradi, Manar Salameh, Mubeen Khan, Elise Héon, Ketan Mishra, Rebekkah J. Hitti-Malin, Yahya AlSwaiti, Alice Aslanian, Eyal Banin, Brian P. Brooks, Wadih M. Zein, Robert B. Hufnagel, Susanne Roosing, Claire‐Marie Dhaenens, Dror Sharon, Frans P. M. Cremers, and Alaa AlTalbishi

Subjects
Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Mutation, Humans, Stargardt Disease, ATP-Binding Cassette Transporters, Cone-Rod Dystrophies, Introns, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Arabs, Pedigree
Abstract

Contains fulltext : 251966.pdf (Publisher’s version ) (Open Access) PURPOSE: The effect of noncoding variants is often unknown in the absence of functional assays. Here, we characterized an ABCA4 intron 7 variant, c.859-25A>G, identified in Palestinian probands with Stargardt disease (STGD) or cone-rod dystrophy (CRD). We investigated the effect of this variant on the ABCA4 mRNA and retinal phenotype, and its prevalence in Palestine. METHODS: The ABCA4 gene was sequenced completely or partially in 1998 cases with STGD or CRD. The effect of c.859-25A>G on splicing was investigated in silico using SpliceAI and in vitro using splice assays. Homozygosity mapping was performed for 16 affected individuals homozygous for c.859-25A>G. The clinical phenotype was assessed using functional and structural analyses including visual acuity, full-field electroretinography, and multimodal imaging. RESULTS: The smMIPs-based ABCA4 sequencing revealed c.859-25A>G in 10 Palestinian probands from Hebron and Jerusalem. SpliceAI predicted a significant effect of this putative branchpoint-inactivating variant on the nearby intron 7 splice acceptor site. Splice assays revealed exon 8 skipping and two partial inclusions of intron 7, each having a deleterious effect. Additional genotyping revealed another 46 affected homozygous or compound heterozygous individuals carrying variant c.859-25A>G. Homozygotes shared a genomic segment of 59.6 to 87.9 kb and showed severe retinal defects on ophthalmoscopic evaluation. CONCLUSIONS: The ABCA4 variant c.859-25A>G disrupts a predicted branchpoint, resulting in protein truncation because of different splice defects, and is associated with early-onset STGD1 when present in homozygosity. This variant was found in 25/525 Palestinian inherited retinal dystrophy probands, representing one of the most frequent inherited retinal disease-causing variants in West-Bank Palestine.

Published
2022

6. Association of the PHACTR1/EDN1 Genetic Locus With Spontaneous Coronary Artery Dissection

Author

David Adlam, Timothy M. Olson, Nicolas Combaret, Jason C. Kovacic, Siiri E. Iismaa, Abtehale Al-Hussaini, Megan M. O'Byrne, Sara Bouajila, Adrien Georges, Ketan Mishra, Peter S. Braund, Valentina d’Escamard, Siying Huang, Marios Margaritis, Christopher P. Nelson, Mariza de Andrade, Daniella Kadian-Dodov, Catherine A. Welch, Stephani Mazurkiewicz, Xavier Jeunemaitre, Claire Mei Yi Wong, Eleni Giannoulatou, Michael Sweeting, David Muller, Alice Wood, Lucy McGrath-Cadell, Diane Fatkin, Sally L. Dunwoodie, Richard Harvey, Cameron Holloway, Jean-Philippe Empana, Xavier Jouven, Jeffrey W. Olin, Rajiv Gulati, Marysia S. Tweet, Sharonne N. Hayes, Nilesh J. Samani, Robert M. Graham, Pascal Motreff, Nabila Bouatia-Naji, Loïc Belle, Patrick Dupouy, Pierre Barnay, Nicolas Meneveau, Martine Gilard, Gilles Rioufol, Grégoire Range, Philippe Brunel, Nicolas Delarche, Emmanuelle Filippi, Louis Le Bivic, Brahim Harbaoui, Hakim Benamer, Guillaume Cayla, Olivier Varenne, Stephane Peggy Manzo-Silberman, Johanne Silvain, Christian Spaulding, Christophe Caussin, Edouard Gerbaud, Yann Valy, René Koning, Thibault Lhermusier, Stanislas Champin, Emmanuel Salengro, Arnaud Fluttaz, Amer Zabalawi, Yves Cottin, Emmanuel Teiger, Christophe Saint-Etienne, Grégory Ducrocq, Stéphanie Marliere, Emmanuel Boiffard, Pierre Aubry, Jean Louis Georges, Didier Bresson, Fabien De Poli, Gaëtan Karrillon, Vincent Roule, Laurent Bali, Mathieu Valla, Antoine Gerbay, David Houpe, Olivier Dubreuil, Arsène Monnier, Norbert Mayaud, Aurélie Manchuelle, Philippe Commeau, Marc Bedossa, Majid Nikpay, Anuj Goel, Hong-Hee Won, Leanne M. Hall, Christina Willenborg, Stavroula Kanoni, Danish Saleheen, Theodosios Kyriakou, Jemma C. Hopewell, Thomas R. Webb, Lingyao Zeng, Abbas Dehghan, Maris Alver, Sebastian M. Armasu, Kirsi Auro, Andrew Bjonnes, Daniel I. Chasman, Shufeng Chen, Ian Ford, Nora Franceschini, Christian Gieger, Christopher Grace, Stefan Gustafsson, Jie Huang, Shih-Jen Hwang, Yun Kyoung Kim, Marcus E. Kleber, King Wai Lau, Xiangfeng Lu, Yingchang Lu, Leo P. Lyytikäinen, Evelin Mihailov, Alanna Morrison, Natalia Pervjakova, Liming Qu, Lynda M. Rose, Elias Salfati, Richa Saxena, Markus Scholz, Albert V. Smith, Emmi Tikkanen, Andre Uitterlinden, Xueli Yang, Weihua Zhang, Wei Zhao, Paul S. de Vries, Natalie R. van Zuydam, Sonia S. Anand, Lars Bertram, Frank Beutner, George Dedoussis, Philippe Frossard, Dominique Gauguier, Alison H. Goodall, Omri Gottesman, Marc Haber, Bok-Ghee Han, Jianfeng Huang, Shapour Jalilzadeh, Thorsten Kessler, Inke R. König, Lars Lannfelt, Wolfgang Lieb, Lars Lind, Cecilia M. Lindgren, Maisa Lokki, Patrik K. Magnusson, Nadeem H. Mallick, Narinder Mehra, Thomas Meitinger, Fazal-ur-Rehman Memon, Andrew P. Morris, Markku S. Nieminen, Nancy L. Pedersen, Annette Peters, Loukianos S. Rallidis, Asif Rasheed, Maria Samuel, Svati H. Shah, Juha Sinisalo, Kathleen E. Stirrups, Stella Trompet, Laiyuan Wang, Khan S. Zaman, Diego Ardissino, Eric Boerwinkle, Ingrid B. Borecki, Erwin P. Bottinger, Julie E. Buring, John C. Chambers, Rory Collins, L Adrienne Cupples, John Danesh, Ilja Demuth, Roberto Elosua, Stephen E. Epstein, Tõnu Esko, Mary F. Feitosa, Oscar H. Franco, Maria Grazia Franzosi, Christopher B. Granger, Dongfeng Gu, Vilmundur Gudnason, Alistair S. Hall, Anders Hamsten, Tamara B. Harris, Stanley L. Hazen, Christian Hengstenberg, Albert Hofman, Erik Ingelsson, Carlos Iribarren, J Wouter Jukema, Pekka J. Karhunen, Bong-Jo Kim, Jaspal S. Kooner, Iftikhar J. Kullo, Terho Lehtimäki, Ruth J. Loos, Olle Melander, Andres Metspalu, Winfried März, Colin N. Palmer, Markus Perola, Thomas Quertermous, Daniel J. Rader, Paul M. Ridker, Samuli Ripatti, Robert Roberts, Veikko Salomaa, Dharambir K. Sanghera, Stephen M. Schwartz, Udo Seedorf, Alexandre F. Stewart, David J. Stott, Joachim Thiery, Pierre A. Zalloua, Christopher J. O'Donnell, Muredach P. Reilly, Themistocles L. Assimes, John R. Thompson, Jeanette Erdmann, Robert Clarke, Hugh Watkins, Sekar Kathiresan, Ruth McPherson, Panos Deloukas, Heribert Schunkert, Martin Farrall, Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, Mayo Clinic [Rochester], Service de Cardiologie Maladies Vasculaires [CHU Clermont-Ferrand], CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Icahn School of Medicine at Mount Sinai [New York] (MSSM), Victor Chang Cardiac Research Institute, University of New South Wales [Sydney] (UNSW), St. Vincent’s Clinical School [Sydney, Australia], UNSW Faculty of Medicine [Sydney], University of New South Wales [Sydney] (UNSW)-University of New South Wales [Sydney] (UNSW), Department of Health Sciences Research [Mayo Clinic] (HSR), Mayo Clinic, Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), Service de génétique [CHU HEGP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Department of Cardiovascular Medicine, Mayo Clinic, Hôpital Universitaire Carémeau [Nîmes] (CHU Nîmes), and Centre Hospitalier Universitaire de Nîmes (CHU Nîmes)

Subjects
Adult, Male, medicine.medical_specialty, Myocardial infarction, Coronary Vessel Anomalies, Fibromuscular dysplasia, 030204 cardiovascular system & hematology, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Internal medicine, medicine, Prevalence, Fibromuscular Dysplasia, Humans, 030212 general & internal medicine, Vascular Diseases, Artery dissection, MESH: Australia, United Kingdom, USA, Coronary Vessel Anomalies / epidemiology, Endothelin-1 / genetics, Microfilament proteins / genetics, Genetic association, Aged, Endothelin-1, business.industry, Microfilament Proteins, Australia, Cardiovascular disease in women, Middle Aged, medicine.disease, R1, United States, 3. Good health, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Genetic Loci, Case-Control Studies, Cardiology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Female, France, Cardiology and Cardiovascular Medicine, Scad, business
Abstract

Background: \ud Spontaneous coronary artery dissection (SCAD) is an increasingly recognized cause of acute coronary syndromes (ACS) afflicting predominantly younger to middle-aged women. Observational studies have reported a high prevalence of extracoronary vascular anomalies, especially fibromuscular dysplasia (FMD) and a low prevalence of coincidental cases of atherosclerosis. PHACTR1/EDN1 is a genetic risk locus for several vascular diseases, including FMD and coronary artery disease, with the putative causal noncoding variant at the rs9349379 locus acting as a potential enhancer for the endothelin-1 (EDN1) gene.\ud \ud Objectives: \ud This study sought to test the association between the rs9349379 genotype and SCAD.\ud \ud Methods: \ud Results from case control studies from France, United Kingdom, United States, and Australia were analyzed to test the association with SCAD risk, including age at first event, pregnancy-associated SCAD (P-SCAD), and recurrent SCAD.\ud \ud Results: \ud The previously reported risk allele for FMD (rs9349379-A) was associated with a higher risk of SCAD in all studies. In a meta-analysis of 1,055 SCAD patients and 7,190 controls, the odds ratio (OR) was 1.67 (95% confidence interval [CI]: 1.50 to 1.86) per copy of rs9349379-A. In a subset of 491 SCAD patients, the OR estimate was found to be higher for the association with SCAD in patients without FMD (OR: 1.89; 95% CI: 1.53 to 2.33) than in SCAD cases with FMD (OR: 1.60; 95% CI: 1.28 to 1.99). There was no effect of genotype on age at first event, P-SCAD, or recurrence.\ud \ud Conclusions: \ud The first genetic risk factor for SCAD was identified in the largest study conducted to date for this condition. This genetic link may contribute to the clinical overlap between SCAD and FMD.

Published
2019

7. Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Author

Ymkje M. Hettinga, Karsten Hufendiek, Jacek P. Szaflik, Ian M. MacDonald, Isabelle Meunier, Marcela D. Mena, Kaoru Fujinami, Mubeen Khan, Eyal Banin, Elfride De Baere, G. Jane Farrar, Adrian Dockery, Rianne Miller, Tamar Ben-Yosef, Manar Salameh, L. Ingeborgh van den Born, Anna M Tracewska, Sandro Banfi, Caroline C W Klaver, John N. De Roach, Carmen Ayuso, Sabine Defoort, Damjan Glavač, Ulrich Kellner, Juliana Maria Ferraz Sallum, Claire-Marie Dhaenens, Stéphanie S. Cornelis, Bernhard H. F. Weber, Klaus Rüther, Jennifer A. Thompson, Bernard Puech, Raj Ramesar, Aurore Devos, Lisa Roberts, Herbert Jägle, Osvaldo L. Podhajcer, Hadas Newman, Bohdan Kousal, Femke Bults, Marta Del Pozo-Valero, Marc Pieterse, Laura Whelan, Xavier Zanlonghi, Alaa AlTalbishi, Francesca Simonelli, Marloes Steehouwer, Caroline Thuillier, Frans P.M. Cremers, Andrea L Vincent, Smaragda Kamakari, Ana Fakin, Anna Matynia, Dror Sharon, Ketan Mishra, Mariana Vallim Salles, Heidi Stöhr, Miriam Bauwens, Petra Liskova, Esmee H. Runhart, Buhle Ntozini, Georg Spital, Carel B. Hoyng, Takaaki Hayashi, Terri L. McLaren, Martine van Zweeden, Lubica Dudakova, Camiel J. F. Boon, Christian Gilissen, Jacquie Greenberg, Monika Ołdak, Tina M. Lamey, Yahya AlSwaiti, Alexander Hoischen, Marianthi Karali, Michael B. Gorin, Ophthalmology, ANS - Complex Trait Genetics, Khan, Mubeen, Cornelis, Stéphanie S, Pozo-Valero, Marta Del, Whelan, Laura, Runhart, Esmee H, Mishra, Ketan, Bults, Femke, Alswaiti, Yahya, Altalbishi, Alaa, De Baere, Elfride, Banfi, Sandro, Banin, Eyal, Bauwens, Miriam, Ben-Yosef, Tamar, Boon, Camiel J F, van den Born, L Ingeborgh, Defoort, Sabine, Devos, Aurore, Dockery, Adrian, Dudakova, Lubica, Fakin, Ana, Farrar, G Jane, Sallum, Juliana Maria Ferraz, Fujinami, Kaoru, Gilissen, Christian, Glavač, Damjan, Gorin, Michael B, Greenberg, Jacquie, Hayashi, Takaaki, Hettinga, Ymkje M, Hoischen, Alexander, Hoyng, Carel B, Hufendiek, Karsten, Jägle, Herbert, Kamakari, Smaragda, Karali, Marianthi, Kellner, Ulrich, Klaver, Caroline C W, Kousal, Bohdan, Lamey, Tina M, Macdonald, Ian M, Matynia, Anna, Mclaren, Terri L, Mena, Marcela D, Meunier, Isabelle, Miller, Rianne, Newman, Hada, Ntozini, Buhle, Oldak, Monika, Pieterse, Marc, Podhajcer, Osvaldo L, Puech, Bernard, Ramesar, Raj, Rüther, Klau, Salameh, Manar, Salles, Mariana Vallim, Sharon, Dror, Simonelli, Francesca, Spital, Georg, Steehouwer, Marloe, Szaflik, Jacek P, Thompson, Jennifer A, Thuillier, Caroline, Tracewska, Anna M, van Zweeden, Martine, Vincent, Andrea L, Zanlonghi, Xavier, Liskova, Petra, Stöhr, Heidi, Roach, John N De, Ayuso, Carmen, Roberts, Lisa, Weber, Bernhard H F, Dhaenens, Claire-Marie, and Cremers, Frans P M

Subjects
DEEP-INTRONIC VARIANTS, Proband, smMIP, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], ABCA4, RPE65, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Macular Degeneration, Exon, 0302 clinical medicine, Missing heritability problem, purl.org/becyt/ford/3.2 [https], Medicine and Health Sciences, smMIPs, MUTATION, Genetics (clinical), Genetics, variants, 0303 health sciences, structural, biology, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Genomics, DYSTROPHY, Pedigree, 3. Good health, Stargardt disease, MATERNAL UNIPARENTAL ISODISOMY, purl.org/becyt/ford/3 [https], RETINAL, CHROMOSOME-1, PATIENT, STRUCTURAL VARIANTS, Deep sequencing, 03 medical and health sciences, SDG 3 - Good Health and Well-being, deep-intronic variants, REVEALS, medicine, Humans, 030304 developmental biology, REPAIR, deep-intronic variant, structural variants, medicine.disease, GENE, Introns, Uniparental Isodisomy, Mutation, 030221 ophthalmology & optometry, biology.protein, ATP-Binding Cassette Transporters, Transcriptome
Abstract

Purpose: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. Methods: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. Results: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. Conclusion: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases. Fil: Khan, Mubeen. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Cornelis, Stéphanie S.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Del Pozo Valero, Marta. Hospital Universitario Fundación Jiménez Díaz; España. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Whelan, Laura. Trinity College; Estados Unidos Fil: Runhart, Esmee H.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Mishra, Ketan. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Bults, Femke. Radboud University Nijmegen Medical Centre; Países Bajos Fil: AlSwaiti, Yahya. St John of Jerusalem Eye Hospital Group; Palestina (ANP) Fil: AlTalbishi, Alaa. St John of Jerusalem Eye Hospital Group; Palestina (ANP) Fil: De Baere, Elfride. University of Ghent; Bélgica Fil: Banfi, Sandro. Seconda Universita Degli Studi Di Napoli; Italia Fil: Banin, Eyal. The Hebrew University of Jerusalem; Israel Fil: Bauwens, Miriam. University of Ghent; Bélgica Fil: Ben Yosef, Tamar. The Ruth And Bruce Rappaport Faculty Of Medicine; Israel Fil: Boon, Camiel J. F.. Leiden University. Leiden University Medical Center; Países Bajos Fil: van den Born, L. Ingeborgh. Rotterdam Ophthalmic Institute; Países Bajos Fil: Defoort, Sabine. Universite Lille; Francia Fil: Devos, Aurore. Universite Lille; Francia Fil: Dockery, Adrian. Trinity College; Estados Unidos Fil: Dudakova, Lubica. Charles University and General University Hospital; República Checa Fil: Fakin, Ana. Charles University and General University Hospital; República Checa Fil: Farrar, G. Jane. Trinity College; Estados Unidos Fil: Ferraz Sallum, Juliana Maria. Universidade Federal de Sao Paulo; Brasil Fil: Fujinami, Kaoru. UCL Institute of Ophthalmology; Reino Unido Fil: Gilissen, Christian. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Glavac, Damjan. University of Ljubljana; Eslovenia Fil: Gorin, Michael B.. University of California at Los Angeles. School of Medicine; Estados Unidos Fil: Greenberg, Jacquie. University of Cape Town; Sudáfrica Fil: Hayashi, Takaaki. The Jikei University School of Medicine; Japón Fil: Hettinga, Ymkje M.. Bartiméus Diagnostic Center for Complex Visual Disorders; Países Bajos Fil: Hoischen, Alexander. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Hoyng, Carel B.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Hufendiek, Karsten. University Eye Hospital Hannover Medical School; Alemania Fil: Jägle, Herbert. University Regensburg; Alemania Fil: Kamakari, Smaragda. OMMA Ophthalmological Institute of Athens; Grecia Fil: Karali, Marianthi. Seconda Universita Degli Studi Di Napoli; Italia Fil: Kellner, Ulrich. No especifíca; Fil: Klaver, Caroline C. W.. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Kousal, Bohdan. Charles University and General University Hospital; República Checa Fil: Lamey, Tina M.. University of Western Australia; Australia Fil: MacDonald, Ian M.. University of Alberta; Canadá Fil: Matynia, Anna. University of California at Los Angeles. School of Medicine; Estados Unidos Fil: McLaren, Terri L.. University of Western Australia; Australia Fil: Mena, Marcela D.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Meunier, Isabelle. Université Montpellier II; Francia Fil: Miller, Rianne. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Newman, Hadas. Universitat Tel Aviv; Israel Fil: Ntozini, Buhle. University of Cape Town; Sudáfrica Fil: Oldak, Monika. No especifíca; Fil: Pieterse, Marc. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Podhajcer, Osvaldo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Puech, Bernard. Universite Lille; Francia Fil: Ramesar, Raj. University of Cape Town; Sudáfrica Fil: Rüther, Klaus. No especifíca; Fil: Salameh, Manar. No especifíca; Fil: Salles, Mariana Vallim. Universidade de Sao Paulo; Brasil Fil: Sharon, Dror. The Hebrew University of Jerusalem; Israel Fil: Simonelli, Francesca. Seconda Universita Degli Studi Di Napoli; Italia Fil: Spital, Georg. No especifíca; Fil: Steehouwer, Marloes. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Szaflik, Jacek P.. No especifíca; Fil: Thompson, Jennifer A.. No especifíca; Fil: Thuillier, Caroline. Universite Lille; Francia Fil: Tracewska, Anna M.. No especifíca; Fil: van Zweeden, Martine. Radboud University Nijmegen Medical Centre; Países Bajos Fil: Vincent, Andrea L.. University of Auckland; Nueva Zelanda Fil: Zanlonghi, Xavier. No especifíca; Fil: Liskova, Petra. Charles University and General University Hospital; República Checa Fil: Stöhr, Heidi. Universitat Regensburg; Alemania Fil: De Roach, John N.. University of Western Australia; Australia Fil: Ayuso, Carmen. Hospital Universitario Fundación Jiménez Díaz; España Fil: Roberts, Lisa. University of Cape Town; Sudáfrica Fil: Weber, Bernhard H. F.. Universitat Regensburg; Alemania Fil: Dhaenens, Claire Marie. Universite Lille; Francia Fil: Cremers, Frans P. M.. Radboud University Nijmegen Medical Centre; Países Bajos

Published
2020
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8. Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming

Author

Margeaux Hodgson-Garms, Ethan Ford, Joseph Chen, Jahnvi Pflueger, Jacob M. Paynter, Carmel M. O’Brien, Cheng Huang, Susan K. Nilsson, Ketan Mishra, Christian M. Nefzger, Andrew L. Laslett, Natasha Jansz, Xiaodong Liu, Sarah M. Williams, Fernando J. Rossello, Ralf B. Schittenhelm, Hun S. Chy, Anja S Knaupp, Marnie E. Blewitt, Jose M. Polo, Ryan Lister, and Jaber Firas

Subjects
Pluripotent Stem Cells, 0301 basic medicine, Somatic cell, Cellular differentiation, Cell Differentiation, Cell Biology, Computational biology, Fibroblasts, Biology, Cellular Reprogramming, Biochemistry, Web tool, Embryonic stem cell, Genomic Instability, Kruppel-Like Factor 4, 03 medical and health sciences, 030104 developmental biology, KLF4, Humans, Induced pluripotent stem cell, Molecular Biology, Cell potency, Reprogramming, Biotechnology
Abstract

Recent reports on the characteristics of naive human pluripotent stem cells (hPSCs) obtained using independent methods differ. Naive hPSCs have been mainly derived by conversion from primed hPSCs or by direct derivation from human embryos rather than by somatic cell reprogramming. To provide an unbiased molecular and functional reference, we derived genetically matched naive hPSCs by direct reprogramming of fibroblasts and by primed-to-naive conversion using different naive conditions (NHSM, RSeT, 5iLAF and t2iLGöY). Our results show that hPSCs obtained in these different conditions display a spectrum of naive characteristics. Furthermore, our characterization identifies KLF4 as sufficient for conversion of primed hPSCs into naive t2iLGöY hPSCs, underscoring the role that reprogramming factors can play for the derivation of bona fide naive hPSCs.

Published
2017

9. Resolving the dark matter of ABCA4 for 1,054 Stargardt disease probands through integrated genomics and transcriptomics

Author

Carel B. Hoyng, Yahya AlSwaiti, Lubica Dudakova, Alexander Hoischen, Lisa Roberts, Christian Gilissen, Michael B. Gorin, Marc Pieterse, Isabelle Meunier, Damjan Glavač, Jacek P. Szaflik, Andrea L Vincent, Dror Sharon, Xavier Zanlonghi, Martine van Zweeden, Monika Ołdak, Bernard Puech, Camiel J. F. Boon, Femke Bults, Anna M. Tracewska, Marloes Steehouwer, Caroline C W Klaver, Jacquie Greenberg, Hadas Newman, Bohdan Kousal, Miriam Bauwens, Bernard H.F. Weber, Smaragda Kamakari, G. Jane Farrar, Eyal Banin, Elfride De Baere, Jennifer A. Thompson, Adrian Dockery, Marcela D. Mena, Tamar Ben-Yosef, Manar Salameh, Laura Whelan, Tina M. Lamey, L. Ingeborgh van den Born, Ana Fakin, Frans P.M. Cremers, Klaus Rüther, Buhle Ntozini, Sandro Banfi, Claire-Marie Dhaenens, Raj Ramesar, Georg Spital, Osvaldo L. Podhajcer, Heidi Stöhr, Ulrich Kellner, Esmee H. Runhart, Herbert Jägle, John N. De Roach, Kaoru Fujinami, Marta Del Pozo-Valero, Takaaki Hayashi, Juliana Maria Ferraz Sallum, Petra Liskova, Terri L. McLaren, Karsten Hufendiek, Marianthi Karali, Stéphanie S. Cornelis, Sabine Defoort, Ymkje M. Hettinga, Francesca Simonelli, Alaa AlTabishi, Mubeen Khan, Caroline Thuillier, Anna Matynia, Carmen Ayuso, Ketan Mishra, Mariana Vallim Salles, Ian M. MacDonald, Aurore Devos, and Rianne Miller

Subjects
Genetics, 0303 health sciences, Sequence analysis, Genomics, Biology, medicine.disease, DNA sequencing, Stargardt disease, 03 medical and health sciences, Exon, 0302 clinical medicine, Missing heritability problem, 030221 ophthalmology & optometry, medicine, Coding region, Gene, 030304 developmental biology
Abstract

Missing heritability in human diseases represents a major challenge. Although whole-genome sequencing enables the analysis of coding and non-coding sequences, substantial costs and data storage requirements hamper its large-scale use to (re)sequence genes in genetically unsolved cases. The ABCA4 gene implicated in Stargardt disease (STGD1) has been studied extensively for 22 years, but thousands of cases remained unsolved. Therefore, single molecule molecular inversion probes were designed that enabled an automated and cost-effective sequence analysis of the complete 128-kb ABCA4 gene. Analysis of 1,054 unsolved STGD and STGD-like probands resulted in bi-allelic variations in 448 probands. Twenty-seven different causal deep-intronic variants were identified in 117 alleles. Based on in vitro splice assays, the 13 novel causal deep-intronic variants were found to result in pseudo-exon (PE) insertions (n=10) or exon elongations (n=3). Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions that were accompanied by flanking exon deletions. Structural variant analysis revealed 11 distinct deletions, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. Integrated complete gene sequencing combined with transcript analysis, identified pathogenic deep-intronic and structural variants in 26% of bi-allelic cases not solved previously by sequencing of coding regions. This strategy serves as a model study that can be applied to other inherited diseases in which only one or a few genes are involved in the majority of cases.

Published
2019
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10. Production of High-Titer Lentiviral Particles for Stable Genetic Modification of Mammalian Cells

Author

Michael R, Larcombe, Jan, Manent, Joseph, Chen, Ketan, Mishra, Xiaodong, Liu, and Christian M, Nefzger

Subjects
Mice, HEK293 Cells, Genetic Vectors, Lentivirus, Gene Transfer Techniques, Animals, Humans, Polyethyleneimine, Fibroblasts, Cell Line, Plasmids, Polyethylene Glycols
Abstract

Lentiviral gene transfer technologies exploit the natural efficiency of viral transduction to integrate exogenous genes into mammalian cells. This provides a simple research tool for inducing transgene expression or endogenous gene knockdown in both dividing and nondividing cells. This chapter describes an improved protocol for polyethylenimine (PEI)-mediated multi-plasmid transfection and polyethylene glycol (PEG) precipitation to generate and concentrate lentiviral vectors.

Published
2019

11. Production of High-Titer Lentiviral Particles for Stable Genetic Modification of Mammalian Cells

Author

Michael R. Larcombe, Xiaodong Liu, Joseph Chen, Christian M. Nefzger, Ketan Mishra, and Jan Manent

Subjects
0301 basic medicine, Polyethylenimine, Gene knockdown, Transgene, technology, industry, and agriculture, Endogeny, Transfection, Polyethylene glycol, Cell biology, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, 0302 clinical medicine, chemistry, 030220 oncology & carcinogenesis, PEG ratio, Gene
Abstract

Lentiviral gene transfer technologies exploit the natural efficiency of viral transduction to integrate exogenous genes into mammalian cells. This provides a simple research tool for inducing transgene expression or endogenous gene knockdown in both dividing and nondividing cells. This chapter describes an improved protocol for polyethylenimine (PEI)-mediated multi-plasmid transfection and polyethylene glycol (PEG) precipitation to generate and concentrate lentiviral vectors.

Published
2019

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