A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Denommé-Pichon AS(1), Matalonga L(2), de Boer E(3), Jackson A(4), Benetti E(5),
Banka S(4), Bruel AL(6), Ciolfi A(7), Clayton-Smith J(4), Dallapiccola B(7),
Duffourd Y(6), Ellwanger K(8), Fallerini C(9), Gilissen C(10), Graessner H(8),
Haack TB(8), Havlovicova M(11), Hoischen A(12), Jean-Marçais N(13), Kleefstra
T(14), López-Martín E(15), Macek M(11), Mencarelli MA(16), Moutton S(17), Pfundt
R(3), Pizzi S(7), Posada M(15), Radio FC(7), Renieri A(18), Rooryck C(19), Ryba
L(11), Safraou H(6), Schwarz M(11), Tartaglia M(7), Thauvin-Robinet C(20),
Thevenon J(17), Tran Mau-Them F(6), Trimouille A(21), Votypka P(11), de Vries
BBA(3), Willemsen MH(3), Zurek B(8), Verloes A(22), Philippe C(6); Solve-RD
DITF-ITHACA; Solve-RD SNV-indel Working Group; Solve-RD Consortia; Orphanomix
Group; Vitobello A(6), Vissers LELM(3), Faivre L(23).

Collaborators: Abbott KM, Banka S, de Boer E, Ciolfi A, Clayton-Smith J,
Dallapiccola B, Denommé-Pichon AS, Faivre L, Gilissen C, Haack TB, Havlovicova
M, Hoischen A, Jackson A, Kerstjens M, Kleefstra T, Martín EL, Macek M Jr,
Matalonga L, Maystadt I, Morleo M, Nigro V, Pinelli M, Pizzi S, Posada M, Radio
FC, Renieri A, Riess O, Rooryck C, Ryba L, Agathe JS, Santen GWE, Schwarz M,
Tartaglia M, Thauvin C, Torella A, Trimouille A, Verloes A, Vissers L, Vitobello
A, Votypka P, Zguro K, Boer E, Cohen E, Danis D, Denommé-Pichon AS, Gao F,
Gilissen C, Horvath R, Johari M, Johanson L, Li S, Matalonga L, Morsy H, Nelson
I, Paramonov I, Te Paske IBAW, Robinson P, Savarese M, Steyaert W, Töpf A,
Trimouille A, van der Velde JK, Vandrovcova J, Vitobello A, Riess O, Haack TB,
Graessner H, Zurek B, Ellwanger K, Ossowski S, Demidov G, Sturm M,
Schulze-Hentrich JM, Schüle R, Xu J, Kessler C, Wayand M, Synofzik M, Wilke C,
Traschütz A, Schöls L, Hengel H, Lerche H, Kegele J, Heutink P, Brunner H,
Scheffer H, Hoogerbrugge N, Hoischen A, ‘t Hoen PAC, Vissers LELM, Gilissen C,
Steyaert W, Sablauskas K, de Voer RM, Kamsteeg EJ, van de Warrenburg B, van Os
N, Paske IT, Janssen E, de Boer E, Steehouwer M, Yaldiz B, Kleefstra T, Brookes
AJ, Veal C, Gibson S, Maddi V, Mehtarizadeh M, Riaz U, Warren G, Dizjikan FY,
Shorter T, Töpf A, Straub V, Bettolo CM, Manera JD, Hambleton S, Engelhardt K,
Clayton-Smith J, Banka S, Alexander E, Jackson A, Faivre L, Thauvin C, Vitobello
A, Denommé-Pichon AS, Duffourd Y, Bruel AL, Peyron C, Pélissier A, Beltran S,
Gut IG, Laurie S, Piscia D, Matalonga L, Papakonstantinou A, Bullich G, Corvo A,
Fernandez-Callejo M, Hernández C, Picó D, Paramonov I, Lochmüller H, Gumus G,
Bros-Facer V, Rath A, Hanauer M, Lagorce D, Hongnat O, Chahdil M, Lebreton E,
Stevanin G, Durr A, Davoine CS, Guillot-Noel L, Heinzmann A, Coarelli G, Bonne
G, Evangelista T, Allamand V, Nelson I, Ben Yaou R, Metay C, Eymard B, Cohen E,
Atalaia A, Stojkovic T, Macek M Jr, Turnovec M, Thomasová D, Kremliková RP,
Franková V, Havlovicová M, Lišková P, Doležalová P, Parkinson H, Keane T,
Freeberg M, Thomas C, Spalding D, Robinson P, Danis D, Robert G, Costa A, Patch
C, Hanna M, Houlden H, Reilly M, Vandrovcova J, Efthymiou S, Morsy H, Cali E,
Magrinelli F, Sisodiya SM, Rohrer J, Muntoni F, Zaharieva I, Sarkozy A,
Timmerman V, Baets J, de Vries G, De Winter J, Beijer D, de Jonghe P, Van de
Vondel L, De Ridder W, Weckhuysen S, Nigro V, Mutarelli M, Morleo M, Pinelli M,
Varavallo A, Banfi S, Torella A, Musacchia F, Piluso G, Ferlini A, Selvatici R,
Gualandi F, Bigoni S, Rossi R, Neri M, Aretz S, Spier I, Sommer AK, Peters S,
Oliveira C, Pelaez JG, Matos AR, José CS, Ferreira M, Gullo I, Fernandes S,
Garrido L, Ferreira P, Carneiro F, Swertz MA, Johansson L, van der Velde JK, van
der Vries G, Neerincx PB, Ruvolo D, Abbott KM, Kerstjens Frederikse WS,
Zonneveld-Huijssoon E, Roelofs-Prins D, van Gijn M, Köhler S, Metcalfe A,
Verloes A, Drunat S, Heron D, Mignot C, Keren B, Agathe JS, Rooryck C, Lacombe
D, Trimouille A, Capella G, Valle L, Holinski-Feder E, Laner A, Steinke-Lange V,
Cilio MR, Carpancea E, Depondt C, Lederer D, Sznajer Y, Duerinckx S, Mary S,
Macaya A, Cazurro-Gutiérrez A, Pérez-Dueñas B, Munell F, Jarava CF, Masó LB,
Marcé-Grau A, Colobran R, Hackman P, Johari M, Savarese M, Udd B, Hemelsoet D,
Dermaut B, Schuermans N, Poppe B, Verdin H, Osorio AN, Depienne C, Roos A,
Maystadt I, Cordts I, Deschauer M, Striano P, Zara F, Riva A, Iacomino M, Uva P,
Scala M, Scudieri P, Başak AN, Claeys K, Boztug K, Haimel M, W E G, Ruivenkamp
CAL, Natera de Benito D, Lochmüller H, Thompson R, Polavarapu K, Grimbacher B,
Zaganas I, Kokosali E, Lambros M, Evangeliou A, Spilioti M, Kapaki E, Bourbouli
M, Ciolfi A, Dallapiccola B, Pizzi S, Radio FC, Tartaglia M, Balicza P, Molnar
MJ, De la Paz MP, Sánchez EB, Martín EL, Delgado BM, Alonso García de la Rosa
FJ, Schröck E, Rump A, Mei D, Vetro A, Balestrini S, Guerrini R, Horvath R,
Chinnery PF, Ratnaike T, Gao F, Schon K, Maver A, Peterlin B, Münchau A, Lohmann
K, Herzog R, Pauly M, May P, Beeson D, Cossins J, Renieri A, Furini S, Fallerini
C, Benetti E, Afenjar A, Goldenberg A, Masurel A, Phan A, Dieux-Coeslier A,
Fargeot A, Guerrot AM, Toutain A, Molin A, Sorlin A, Putoux A, Jouret B, Laudier
B, Demeer B, Doray B, Bonniaud B, Isidor B, Gilbert-Dussardier B, Leheup B,
Reversade B, Paul C, Vincent-Delorme C, Neiva C, Poirsier C, Quélin C,
Chiaverini C, Coubes C, Francannet C, Colson C, Desplantes C, Wells C, Goizet C,
Lederer D, Sanlaville D, Amram D, Lehalle D, Geneviève D, Heron D, Lacombe D,
Gaillard D, Zivi E, Sarrazin E, Steichen E, Schaefer É, Lacaze E, Jacquemin E,
Bongers E, Kilic E, Colin E, Giuliano F, Prieur F, Laffargue F, Morice-Picard F,
Petit F, Cartault F, Feillet F, Baujat G, Morin G, Diene G, Journel H, Maystadt
I, Perthus I, Lespinasse J, Alessandri JL, Amiel J, Martinovic J, Delanne J,
Albuisson J, Lambert L, Perrin L, Ousager LB, Van Maldergem L, Pinson L, Ruaud
L, Samimi M, Bournez M, Bonnet-Dupeyron MN, Vincent M, Jacquemont ML,
Cordier-Alex MP, Gérard-Blanluet M, Willems M, Spodenkiewicz M, Doco-Fenzy M,
Rossi M, Renaud M, Fradin M, Mathieu M, Holder-Espinasse MH, Houcinat N, Hanna
N, Leperrier N, Chassaing N, Philip N, Boute O, Van Kien PK, Parent P, Bitoun P,
Sarda P, Vabres P, Jouk PS, Touraine R, El Chehadeh S, Whalen S, Marlin S,
Passemard S, Grotto S, Bellanger SA, Blesson S, Nambot S, Naudion S, Lyonnet S,
Odent S, Attie-Bitach T, Busa T, Drouin-Garraud V, Layet V, Bizaoui V, Cusin V,
Capri Y, Alembik Y.

Author information:
(1)Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD,
Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD
“Génétique des Anomalies du Développement,” FHU-TRANSLAD, University of
Burgundy, Dijon, France. Electronic address:
.
(2)CNAG-CRG, Centre for Genomic Regulation,” The Barcelona Institute of Science
and Technology, Barcelona, Spain.
(3)Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders
Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The
Netherlands.
(4)Manchester Centre for Genomic Medicine, University of Manchester, Manchester,
United Kingdom.
(5)MedBiotech Hub and Competence Center, Department of Medical Biotechnologies,
University of Siena, Siena, Italy.
(6)Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD,
Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD
“Génétique des Anomalies du Développement,” FHU-TRANSLAD, University of
Burgundy, Dijon, France.
(7)Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù,
IRCCS, Rome, Italy.
(8)Institute of Medical Genetics and Applied Genomics, University of Tübingen,
Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen,
Tübingen, Germany.
(9)MedBiotech Hub and Competence Center, Department of Medical Biotechnologies,
University of Siena, Siena, Italy; Medical Genetics, University of Siena, Siena,
Italy.
(10)Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud
Institute for Molecular Life Sciences, Radbound University, Nijmegen, The
Netherlands.
(11)Department of Biology and Medical Genetics, Second Faculty of Medicine of
Charles University and Motol University Hospital, Prague, Czech Republic.
(12)Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud
Institute for Molecular Life Sciences, Radbound University, Nijmegen, The
Netherlands; Department of Internal Medicine and Radboud Center for Infectious
Diseases, Radboudumc, Nijmegen, The Netherlands.
(13)INSERM UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD,
University of Burgundy, Dijon, France; Department of Genetics and Reference
Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and
GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France.
(14)Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders
Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The
Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh
Institute for Psychiatry, Venray, The Netherlands.
(15)Institute of Rare Diseases Research, Spanish Undiagnosed Rare Diseases Cases
Program (SpainUDP) & Undiagnosed Diseases Network International, Instituto de
Salud Carlos III, Madrid, Spain.
(16)Medical Genetics, Azienda Ospedaliero-Universitaria Senese, Siena, Italy.
(17)INSERM UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD,
University of Burgundy, Dijon, France.
(18)MedBiotech Hub and Competence Center, Department of Medical Biotechnologies,
University of Siena, Siena, Italy; Medical Genetics, University of Siena, Siena,
Italy; Medical Genetics, Azienda Ospedaliero-Universitaria Senese, Siena, Italy.
(19)MRGM INSERM U1211, University of Bordeaux, Medical Genetics Department,
Bordeaux University Hospital, Bordeaux, France.
(20)Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD,
Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD
“Génétique des Anomalies du Développement,” FHU-TRANSLAD, University of
Burgundy, Dijon, France; Department of Genetics and Reference Center for
Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI
Institute, Dijon Bourgogne University Hospital, Dijon, France.
(21)Molecular Genetics Laboratory, Medical Genetics Department, Bordeaux
University Hospital – Hôpital Pellegrin, Bordeaux, France.
(22)Department of Genetics, Assistance Publique-Hôpitaux de Paris – Université
de Paris, Paris, France; INSERM UMR 1141 “NeuroDiderot,” Hôpital Robert Debré,
Paris, France.
(23)INSERM UMR1231 GAD “Génétique des Anomalies du Développement,” FHU-TRANSLAD,
University of Burgundy, Dijon, France; Department of Genetics and Reference
Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and
GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France. Electronic
address: .

PURPOSE: Within the Solve-RD project (https://solve-rd.eu/), the European
Reference Network for Intellectual disability, TeleHealth, Autism and Congenital
Anomalies aimed to investigate whether a reanalysis of exomes from unsolved
cases based on ClinVar annotations could establish additional diagnoses. We
present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for
the failure of previous analyses, and lessons learned.
METHODS: Data from the first 3576 exomes (1522 probands and 2054 relatives)
collected from European Reference Network for Intellectual disability,
TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD
consortium by evaluating for the presence of single-nucleotide variant, and
small insertions and deletions already reported as (likely) pathogenic in
ClinVar. Variants were filtered according to frequency, genotype, and mode of
inheritance and reinterpreted.
RESULTS: We identified causal variants in 59 cases (3.9%), 50 of them also
raised by other approaches and 9 leading to new diagnoses, highlighting
interpretation challenges: variants in genes not known to be involved in human
disease at the time of the first analysis, misleading genotypes, or variants
undetected by local pipelines (variants in off-target regions, low quality
filters, low allelic balance, or high frequency).
CONCLUSION: The “ClinVar low-hanging fruit” analysis represents an effective,
fast, and easy approach to recover causal variants from exome sequencing data,
herewith contributing to the reduction of the diagnostic deadlock.

Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

DOI: 10.1016/j.gim.2023.100018
PMID: 36681873 [Indexed for MEDLINE]

Conflict of interest statement: Conflict of Interest The authors declare no
conflicts of interest.

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