Pitfalls in genetic testing: the story of missed SCN1A mutations

Tania Djémié¹, Sarah Weckhuysen², Sarah von Spiczak³, Gemma L Carvill⁴, Johanna Jaehn³, Anna-Kaisa Anttonen⁵, Eva Brilstra⁶, Hande S Caglayan⁷, Carolien G de Kovel⁶, Christel Depienne⁸, Eija Gaily⁹, Elena Gennaro¹⁰, Beatriz G Giraldez¹¹, Padhraig Gormley¹², Rosa Guerrero-López¹³, Renzo Guerrini¹⁴, Eija Hämäläinen¹⁵, Corinna Hartmann³, Laura Hernandez-Hernandez¹⁶, Helle Hjalgrim¹⁷, Bobby P C Koeleman⁶, Eric Leguern⁸, Anna-Elina Lehesjoki¹⁸, Johannes R Lemke¹⁹, Costin Leu²⁰, Carla Marini¹⁴, Jacinta M McMahon²¹, Davide Mei¹⁴, Rikke S Møller¹⁷, Hiltrud Muhle³, Candace T Myers⁴, Caroline Nava⁸, Jose M Serratosa¹¹, Sanjay M Sisodiya¹⁶, Ulrich Stephani³, Pasquale Striano²², Marjan J A van Kempen⁶, Nienke E Verbeek⁶, Sunay Usluer⁷, Federico Zara²³, Aarno Palotie²⁴, Heather C Mefford⁴, Ingrid E Scheffer²⁵, Peter De Jonghe²⁶, Ingo Helbig²⁷, Arvid Suls²⁸; EuroEPINOMICS‐RES Dravet working group

Affiliations

¹ Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium.
² Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Centre de reference épilepsies raresEpilepsy unit, AP-HP Groupe hospitalier Pitié-SalpêtrièreParis75013France.
³ Department of Neuropediatrics University Medical Center Schleswig-Holstein Kiel Germany.
⁴ Division of Genetic Medicine Department of Pediatrics University of Washington Seattle Washington 98195 USA.
⁵ Folkhälsan Institute of GeneticsHelsinkiFinland; Medical and Clinical GeneticsUniversity of HelsinkiHelsinkiFinland; Helsinki University HospitalHelsinkiFinland.
⁶ Department of Medical Genetics University Medical Center Utrecht Utrecht The Netherlands.
⁷ Department of Molecular Biology and Genetics Bogaziçi University Istanbul Turkey.
⁸ Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Département de génétiqueAP-HP, hôpital Pitié-Salpêtrière47/83boulevard de l'HôpitalParis75013France.
⁹ Department of Pediatric Neurology Helsinki University Hospital Helsinki Finland.
¹⁰ Laboratory of Genetics E.O. Ospedali Galliera Genova Italy.
¹¹ Neurology Laboratory and Epilepsy UnitDepartment of NeurologyInstituto de Investigatión Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de MadridMadridSpain; IIS-Fundación Jiménez Díaz and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)MadridSpain.
¹² Psychiatric and Neurodevelopmental Genetics UnitMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts02114USA; Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Wellcome Trust Sanger InstituteHinxtonUnited Kingdom.
¹³ IIS-Fundación Jiménez Díaz and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Madrid Spain.
¹⁴ Pediatric Neurology and Neurogenetics Unit and Laboratories A. Meyer Children's Hospital-University of Florence Florence Italy.
¹⁵ Wellcome Trust Sanger InstituteHinxtonUnited Kingdom; Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland.
¹⁶ Department of Clinical and Experimental EpilepsyNIHR University College London Hospitals Biomedical Research CentreUCL Institute of NeurologyLondonUnited Kingdom; The Epilepsy SocietyChalfont-St-PeterBucksUnited Kingdom.
¹⁷ Department of NeurologyDanish Epilepsy CentreDianalundDenmark; Institute for Regional Health researchUniversity of Southern DenmarkOdenseDenmark.
¹⁸ Folkhälsan Institute of GeneticsHelsinkiFinland; Research Programs UnitMolecular NeurologyUniversity of HelsinkiHelsinkiFinland.
¹⁹ Institute of Human Genetics University of Leipzig Leipzig Germany.
²⁰ Department of Clinical and Experimental Epilepsy NIHR University College London Hospitals Biomedical Research Centre UCL Institute of Neurology London United Kingdom.
²¹ Epilepsy Research Centre Department of Medicine University of Melbourne Austin Health Melbourne Australia.
²² Pediatric Neurology and Muscular Diseases Unit Department of Neurosciences Rehabilitation Ophthalmology Genetics and Maternal and Child Health University of Genoa 'G. Gaslini' Institute Genova Italy.
²³ Laboratory of Neurogenetics Department of Neurosciences Giannina Gaslini Institute Genova Italy.
²⁴ Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland.
²⁵ Epilepsy Research CentreDepartment of MedicineUniversity of MelbourneAustin HealthMelbourneAustralia; Department of PaediatricsUniversity of Melbourne and Royal Children's HospitalParkvilleVictoria3052Australia; Florey Institute of Neuroscience and Mental HealthMelbourneVictoria3084Australia.
²⁶ Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; Division of NeurologyAntwerp University HospitalAntwerpBelgium.
²⁷ Department of NeuropediatricsUniversity Medical Center Schleswig-HolsteinKielGermany; Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA.
²⁸ Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; GENOMEDCenter for Medical GeneticsUniversity of AntwerpAntwerpBelgium.

PMID: 27465585
PMCID: PMC4947864
DOI: 10.1002/mgg3.217

Pitfalls in genetic testing: the story of missed SCN1A mutations

Tania Djémié et al. Mol Genet Genomic Med. 2016.

. 2016 Apr 14;4(4):457-64.

doi: 10.1002/mgg3.217. eCollection 2016 Jul.

Authors

Affiliations

¹ Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium.
² Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Centre de reference épilepsies raresEpilepsy unit, AP-HP Groupe hospitalier Pitié-SalpêtrièreParis75013France.
³ Department of Neuropediatrics University Medical Center Schleswig-Holstein Kiel Germany.
⁴ Division of Genetic Medicine Department of Pediatrics University of Washington Seattle Washington 98195 USA.
⁵ Folkhälsan Institute of GeneticsHelsinkiFinland; Medical and Clinical GeneticsUniversity of HelsinkiHelsinkiFinland; Helsinki University HospitalHelsinkiFinland.
⁶ Department of Medical Genetics University Medical Center Utrecht Utrecht The Netherlands.
⁷ Department of Molecular Biology and Genetics Bogaziçi University Istanbul Turkey.
⁸ Sorbonne universitésUPMC université Paris 0691-105boulevard de l'HôpitalParis75013France; ICM, CNRS UMR 7225, Inserm U 112747/83, boulevard de l'HôpitalParis75013France; Département de génétiqueAP-HP, hôpital Pitié-Salpêtrière47/83boulevard de l'HôpitalParis75013France.
⁹ Department of Pediatric Neurology Helsinki University Hospital Helsinki Finland.
¹⁰ Laboratory of Genetics E.O. Ospedali Galliera Genova Italy.
¹¹ Neurology Laboratory and Epilepsy UnitDepartment of NeurologyInstituto de Investigatión Sanitaria-Fundación Jiménez Díaz, Universidad Autónoma de MadridMadridSpain; IIS-Fundación Jiménez Díaz and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)MadridSpain.
¹² Psychiatric and Neurodevelopmental Genetics UnitMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts02114USA; Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Wellcome Trust Sanger InstituteHinxtonUnited Kingdom.
¹³ IIS-Fundación Jiménez Díaz and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Madrid Spain.
¹⁴ Pediatric Neurology and Neurogenetics Unit and Laboratories A. Meyer Children's Hospital-University of Florence Florence Italy.
¹⁵ Wellcome Trust Sanger InstituteHinxtonUnited Kingdom; Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland.
¹⁶ Department of Clinical and Experimental EpilepsyNIHR University College London Hospitals Biomedical Research CentreUCL Institute of NeurologyLondonUnited Kingdom; The Epilepsy SocietyChalfont-St-PeterBucksUnited Kingdom.
¹⁷ Department of NeurologyDanish Epilepsy CentreDianalundDenmark; Institute for Regional Health researchUniversity of Southern DenmarkOdenseDenmark.
¹⁸ Folkhälsan Institute of GeneticsHelsinkiFinland; Research Programs UnitMolecular NeurologyUniversity of HelsinkiHelsinkiFinland.
¹⁹ Institute of Human Genetics University of Leipzig Leipzig Germany.
²⁰ Department of Clinical and Experimental Epilepsy NIHR University College London Hospitals Biomedical Research Centre UCL Institute of Neurology London United Kingdom.
²¹ Epilepsy Research Centre Department of Medicine University of Melbourne Austin Health Melbourne Australia.
²² Pediatric Neurology and Muscular Diseases Unit Department of Neurosciences Rehabilitation Ophthalmology Genetics and Maternal and Child Health University of Genoa 'G. Gaslini' Institute Genova Italy.
²³ Laboratory of Neurogenetics Department of Neurosciences Giannina Gaslini Institute Genova Italy.
²⁴ Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts02142USA; Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland.
²⁵ Epilepsy Research CentreDepartment of MedicineUniversity of MelbourneAustin HealthMelbourneAustralia; Department of PaediatricsUniversity of Melbourne and Royal Children's HospitalParkvilleVictoria3052Australia; Florey Institute of Neuroscience and Mental HealthMelbourneVictoria3084Australia.
²⁶ Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; Division of NeurologyAntwerp University HospitalAntwerpBelgium.
²⁷ Department of NeuropediatricsUniversity Medical Center Schleswig-HolsteinKielGermany; Division of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA.
²⁸ Neurogenetics groupDepartment of Molecular GeneticsVIBAntwerpBelgium; Laboratory of NeurogeneticsInstitute Born-BungeUniversity of AntwerpAntwerpBelgium; GENOMEDCenter for Medical GeneticsUniversity of AntwerpAntwerpBelgium.

PMID: 27465585
PMCID: PMC4947864
DOI: 10.1002/mgg3.217

Abstract

Background: Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next-generation sequencing (NGS). No single mutation detection technique is however perfect in identifying all mutations. Therefore, we wondered to what extent inconsistencies between Sanger sequencing and NGS affect the molecular diagnosis of patients. Since mutations in SCN1A, the major gene implicated in epilepsy, are found in the majority of Dravet syndrome (DS) patients, we focused on missed SCN1A mutations.

Methods: We sent out a survey to 16 genetic centers performing SCN1A testing.

Results: We collected data on 28 mutations initially missed using Sanger sequencing. All patients were falsely reported as SCN1A mutation-negative, both due to technical limitations and human errors.

Conclusion: We illustrate the pitfalls of Sanger sequencing and most importantly provide evidence that SCN1A mutations are an even more frequent cause of DS than already anticipated.

Keywords: Dravet syndrome; Sanger sequencing; epilepsy; genetic screening; next‐generation sequencing.

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Comment in

Genetic Testing Requires NGS and Sanger Methodologies.
Jennings LJ, Kirschmann D. Jennings LJ, et al. Pediatr Neurol Briefs. 2016 Sep;30(9):36. doi: 10.15844/pedneurbriefs-30-9-1. Pediatr Neurol Briefs. 2016. PMID: 27651130 Free PMC article.

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Pitfalls in genetic testing: the story of missed SCN1A mutations

Affiliations

Pitfalls in genetic testing: the story of missed SCN1A mutations

Authors

Affiliations

Abstract

Comment in

References

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