Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS

Haloom Rafehi; David J Szmulewicz; Mark F Bennett; Nara L M Sobreira; Kate Pope; Katherine R Smith; Greta Gillies; Peter Diakumis; Egor Dolzhenko; Michael A Eberle; María García Barcina; David P Breen; Andrew M Chancellor; Phillip D Cremer; Martin B Delatycki; Brent L Fogel; Anna Hackett; G Michael Halmagyi; Solange Kapetanovic; Anthony Lang; Stuart Mossman; Weiyi Mu; Peter Patrikios; Susan L Perlman; Ian Rosemergy; Elsdon Storey; Shaun R D Watson; Michael A Wilson; David S Zee; David Valle; David J Amor; Melanie Bahlo; Paul J Lockhart

doi:10.1016/j.ajhg.2019.05.016

Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS

Am J Hum Genet. 2019 Jul 3;105(1):151-165. doi: 10.1016/j.ajhg.2019.05.016. Epub 2019 Jun 20.

Authors

Haloom Rafehi¹, David J Szmulewicz², Mark F Bennett³, Nara L M Sobreira⁴, Kate Pope⁵, Katherine R Smith⁶, Greta Gillies⁵, Peter Diakumis⁷, Egor Dolzhenko⁸, Michael A Eberle⁸, María García Barcina⁹, David P Breen¹⁰, Andrew M Chancellor¹¹, Phillip D Cremer¹², Martin B Delatycki¹³, Brent L Fogel¹⁴, Anna Hackett¹⁵, G Michael Halmagyi¹⁶, Solange Kapetanovic¹⁷, Anthony Lang¹⁸, Stuart Mossman¹⁹, Weiyi Mu⁴, Peter Patrikios²⁰, Susan L Perlman²¹, Ian Rosemergy²², Elsdon Storey²³, Shaun R D Watson²⁴, Michael A Wilson⁵, David S Zee²⁵, David Valle⁴, David J Amor¹³, Melanie Bahlo¹, Paul J Lockhart²⁶

Affiliations

¹ Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia.
² Cerebellar Ataxia Clinic, Neuroscience Department, Alfred Health, Melbourne, VIC 3004, Australia; Balance Disorders and Ataxia Service, Royal Victorian Eye & Ear Hospital, East Melbourne, VIC 3002, Australia.
³ Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia; Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, 245 Burgundy Street, Heidelberg, VIC 3084, Australia.
⁴ McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁵ Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia.
⁶ Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.
⁷ University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia.
⁸ Illumina Inc, 5200 Illumina Way, San Diego, CA 92122, USA.
⁹ Genetic Unit, Basurto University Hospital, OSI Bilbao-Basurto, avenida Montevideo 18, 48013 Bilbao, Spain.
¹⁰ Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, Scotland.
¹¹ Department of Neurology, Tauranga Hospital, Private Bag, Cameron Road, Tauranga 3171, New Zealand.
¹² University of Sydney, Camperdown, NSW 2006, Australia; Royal North Shore Hospital, Pacific Hwy, St Leonards, NSW 2065, Australia.
¹³ Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia.
¹⁴ Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
¹⁵ Hunter Genetics, Hunter New England Health Service, Waratah, Newcastle, NSW 2300, Australia; University of Newcastle, Newcastle, NSW 2300, Australia.
¹⁶ Neurology Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia.
¹⁷ Servicio de Neurología, Hospital de Basurto, Avenida de Montevideo 18, 48013 Bilbao, Bizkaia, Spain.
¹⁸ Edmond J. Safra Program in Parkinson disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada; Department of Medicine, Division of Neurology, University Health Network and the University of Toronto, Toronto, ON M5T 2S8, Canada.
¹⁹ Department of Neurology, Wellington Hospital, Wellington 6021, New Zealand.
²⁰ Sunshine Neurology, Maroochydore, QLD 4558, Australia.
²¹ Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
²² Department of Neurology, Wellington Hospital, Newtown, Wellington 6021, New Zealand.
²³ Department of Neuroscience, Central Clinical School, Monash University, Alfred Hospital Campus, Commercial Road, Melbourne, VIC 3004, Australia.
²⁴ Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, NSW 2031, Australia.
²⁵ Department of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA.
²⁶ Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia. Electronic address: paul.lockhart@mcri.edu.au.

Abstract

Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole-genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)_exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)₁₁ short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS-affected families and identified a core ancestral haplotype, estimated to have arisen in Europe more than twenty-five thousand years ago. WGS of the four RFC1-negative CANVAS-affected families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type, and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.

Keywords: CANVAS; ataxia; repeat expansions; short tandem repeats; whole-genome sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Cerebellar Ataxia / etiology*
Cerebellar Ataxia / pathology
Cohort Studies
Computational Biology / methods*
Family
Female
Genomics
Humans
Introns*
Male
Microsatellite Repeats*
Middle Aged
Polyneuropathies / etiology*
Polyneuropathies / pathology
Replication Protein C / genetics*
Sensation Disorders / etiology*
Sensation Disorders / pathology
Syndrome
Vestibular Diseases / etiology*
Vestibular Diseases / pathology
Whole Genome Sequencing

Substances

RFC1 protein, human
Replication Protein C

Abstract

Publication types

MeSH terms

Substances

Grants and funding