High diagnostic yield of direct Sanger sequencing in the diagnosis of neuronal ceroid lipofuscinoses

Abdulhakim Jilani; Diana Matviychuk; Susan Blaser; Sarah Dyack; Jean Mathieu; Asuri N Prasad; Chitra Prasad; Lianna Kyriakopoulou; Saadet Mercimek-Andrews

doi:10.1002/jmd2.12057

High diagnostic yield of direct Sanger sequencing in the diagnosis of neuronal ceroid lipofuscinoses

JIMD Rep. 2019 Sep 3;50(1):20-30. doi: 10.1002/jmd2.12057. eCollection 2019 Nov.

Authors

Abdulhakim Jilani¹, Diana Matviychuk², Susan Blaser³, Sarah Dyack⁴, Jean Mathieu⁵, Asuri N Prasad⁶, Chitra Prasad⁷, Lianna Kyriakopoulou^{2

8}, Saadet Mercimek-Andrews^{1

9

10}

Affiliations

¹ Division of Clinical and Metabolic Genetics, Department of Paediatrics University of Toronto, The Hospital for Sick Children Toronto Ontario Canada.
² Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine The Hospital for Sick Children Toronto Ontario Canada.
³ Division of Neuroradiology, Department of Medical Imaging University of Toronto, The Hospital for Sick Children Toronto Ontario Canada.
⁴ Division of Medical Genetics, Department of Pediatrics, IWK Health Centre University of Dalhouise Halifax Nova Scotia Canada.
⁵ Neuromuscular Disease Clinic University of Sherbrooke Quebec Canada.
⁶ Division of Clinical Neurosciences, Department of Paediatrics, Schulich School of Medicine and Dentistry Western University London Ontario Canada.
⁷ Division of Medical Genetics, Department of Paediatrics, Schulich School of Medicine & Dentistry Western University London Ontario Canada.
⁸ Department of Paediatric Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada.
⁹ Genetics and Genome Biology Program, Research Institute The Hospital for Sick Children Toronto Ontario Canada.
¹⁰ Institute of Medical Sciences University of Toronto Toronto Ontario Canada.

Abstract

Background: Neuronal ceroid lipofuscinoses are neurodegenerative disorders. To investigate the diagnostic yield of direct Sanger sequencing of the CLN genes, we reviewed Molecular Genetics Laboratory Database for molecular genetic test results of the CLN genes from a single clinical molecular diagnostic laboratory.

Methods: We reviewed electronic patient charts. We used consent forms and Research Electronic Data Capture questionnaires for the patients from outside of our Institution. We reclassified all variants in the CLN genes.

Results: Six hundred and ninety three individuals underwent the direct Sanger sequencing of the CLN genes for the diagnosis of neuronal ceroid lipofuscinoses. There were 343 symptomatic patients and 350 family members. Ninety-one symptomatic patients had molecular genetic diagnosis of neuronal ceroid lipofuscinoses including CLN1 (PPT1) (n = 10), CLN2 (TPP1) (n = 33), CLN3 (n = 17), CLN5 (n = 7), CLN6 (n = 10), CLN7 (MFSD8) (n = 10), and CLN8 (n = 4) diseases. The diagnostic yield of direct Sanger sequencing of CLN genes was 27% in symptomatic patients. We report detailed clinical and investigation results of 33 NCL patients. Juvenile onset CLN1 (PPT1) and adult onset CLN6 diseases were nonclassical phenotypes.

Conclusion: In our study, the diagnostic yield of direct Sanger sequencing was close to diagnostic yield of whole exome sequencing. Developmental regression, cognitive decline, visual impairment and cerebral and/or cerebellar atrophy in brain MRI are significant clinical and neuroimaging denominators to include NCL in the differential diagnosis.

Keywords: CLN genes; developmental regression; epilepsy; neuronal ceroid lipofuscinoses; visual loss.