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

Citation for published version: Rafehi, H, Szmulewicz, DJ, Bennett, MF, Sobreira, NLM, Pope, K, Smith, KR, Gillies, G, Diakumis, P, Dolzhenko, E, Eberle, MA, Barcina, MG, Breen, DP, Chancellor, AM, Cremer, PD, Delatycki, MB, Fogel, BL, Hackett, A, Halmagyi, GM, Kapetanovic, S, Lang, A, Mossman, S, Mu, W, Patrikios, P, Perlman, SL, Rosemergy, I, Storey, E, Watson, SRD, Wilson, MA, Zee, DS, Valle, D, Amor, DJ, Bahlo, M & Lockhart, PJ 2019, 'Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS' American Journal of Human Genetics. DOI: 10.1016/j.ajhg.2019.05.016

[1]  Jana Vandrovcova,et al.  Biallelic expansion of an intronic repeat in RFC1 is a common cause of late-onset ataxia , 2019, Nature Genetics.

[2]  M. Aoki,et al.  [Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS): a case report]. , 2019, Rinsho shinkeigaku = Clinical neurology.

[3]  Melanie Bahlo,et al.  Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data. , 2018, American journal of human genetics.

[4]  T. Strom,et al.  SACS variants are a relevant cause of autosomal recessive hereditary motor and sensory neuropathy , 2018, Human Genetics.

[5]  H. Houlden,et al.  Spinocerebellar ataxia: an update , 2018, Journal of Neurology.

[6]  Belinda Phipson,et al.  STRetch: detecting and discovering pathogenic short tandem repeat expansions , 2018, Genome Biology.

[7]  Nima Mousavi,et al.  Profiling the genome-wide landscape of tandem repeat expansions , 2018, bioRxiv.

[8]  Melanie Bahlo,et al.  Recent advances in the detection of repeat expansions with short-read next-generation sequencing , 2018, F1000Research.

[9]  T. Requena,et al.  Clinical and Functional Characterization of a Missense ELF2 Variant in a CANVAS Family , 2018, Front. Genet..

[10]  A. Hannan,et al.  Tandem repeats mediating genetic plasticity in health and disease , 2018, Nature Reviews Genetics.

[11]  Koji Abe,et al.  Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy , 2018, Nature Genetics.

[12]  M. Taki,et al.  Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS). , 2017, Auris, nasus, larynx.

[13]  K. Caldecott,et al.  Nonsyndromic cerebellar ataxias associated with disorders of DNA single-strand break repair. , 2018, Handbook of clinical neurology.

[14]  David Heckerman,et al.  Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes , 2017, American journal of human genetics.

[15]  Cleo C. van Diemen,et al.  Exome sequencing and network analysis identifies shared mechanisms underlying spinocerebellar ataxia , 2017, Brain : a journal of neurology.

[16]  D. Szmulewicz.  Combined Central and Peripheral Degenerative Vestibular Disorders: CANVAS, Idiopathic Cerebellar Ataxia with Bilateral Vestibulopathy (CABV) and Other Differential Diagnoses of the CABV Phenotype , 2017, Current Otorhinolaryngology Reports.

[17]  Patrizia Rizzu,et al.  A Pentanucleotide ATTTC Repeat Insertion in the Non-coding Region of DAB1, Mapping to SCA37, Causes Spinocerebellar Ataxia. , 2017, American journal of human genetics.

[18]  Chris Shaw,et al.  Detection of long repeat expansions from PCR-free whole-genome sequence data , 2016, bioRxiv.

[19]  A. Filla,et al.  Clinical application of next generation sequencing in hereditary spinocerebellar ataxia: increasing the diagnostic yield and broadening the ataxia-spasticity spectrum. A retrospective analysis , 2017, neurogenetics.

[20]  S. Lagalwar,et al.  Expansion, mosaicism and interruption: mechanisms of the CAG repeat mutation in spinocerebellar ataxia type 1 , 2016, Cerebellum & Ataxias.

[21]  Brent S. Pedersen,et al.  Vcfanno: fast, flexible annotation of genetic variants , 2016, Genome Biology.

[22]  A. Sharp,et al.  Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans , 2016, Nucleic acids research.

[23]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[24]  Yaniv Erlich,et al.  Abundant contribution of short tandem repeats to gene expression variation in humans , 2015, Nature Genetics.

[25]  E. Storey,et al.  Neurophysiological evidence for generalized sensory neuronopathy in cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome , 2015, Muscle & nerve.

[26]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[27]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[28]  T. Speed,et al.  Dating Rare Mutations from Small Samples with Dense Marker Data , 2014, Genetics.

[29]  E. Storey,et al.  Dorsal root ganglionopathy is responsible for the sensory impairment in CANVAS , 2014, Neurology.

[30]  I. Curthoys,et al.  A Novel Quantitative Bedside Test of Balance Function: The Video Visually Enhanced Vestibulo-ocular Reflex (VVOR) (S19.002) , 2014 .

[31]  Paula Coutinho,et al.  The Global Epidemiology of Hereditary Ataxia and Spastic Paraplegia: A Systematic Review of Prevalence Studies , 2014, Neuroepidemiology.

[32]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[33]  A. Caspi,et al.  Impaired vestibulo-ocular reflex (VOR) in spinocerebellar ataxia type 3 (SCA3): bedside and search coil evaluation. , 2014, Journal of vestibular research : equilibrium & orientation.

[34]  E. Storey,et al.  CANVAS an update: clinical presentation, investigation and management. , 2014, Journal of vestibular research : equilibrium & orientation.

[35]  K. Bushara,et al.  Expansion of the Spinocerebellar Ataxia Type 10 (SCA10) Repeat in a Patient with Sioux Native American Ancestry , 2013, PloS one.

[36]  J. Petersen,et al.  The pivotal sign of CANVAS , 2013, Neurology.

[37]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[38]  Yoon-Hee Cha,et al.  Less Common Neuro-otologic Disorders , 2012, Continuum.

[39]  S. Merchant,et al.  Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome: a histopathologic case report. , 2011, Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology.

[40]  Melanie Bahlo,et al.  Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes , 2011, Genome Biology.

[41]  S. Merchant,et al.  Cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS): a review of the clinical features and video‐oculographic diagnosis , 2011, Annals of the New York Academy of Sciences.

[42]  E. Storey,et al.  Sensory neuropathy as part of the cerebellar ataxia neuropathy vestibular areflexia syndrome , 2011, Neurology.

[43]  C. McMurray.  Mechanisms of trinucleotide repeat instability during human development , 2010, Nature Reviews Genetics.

[44]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[45]  J. Taylor,et al.  Repeat expansion disease: progress and puzzles in disease pathogenesis , 2010, Nature Reviews Genetics.

[46]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[47]  Yuko Saito,et al.  Spinocerebellar ataxia type 31 is associated with "inserted" penta-nucleotide repeats containing (TGGAA)n. , 2009, American journal of human genetics.

[48]  M. Bahlo,et al.  Generating linkage mapping files from Affymetrix SNP chip data , 2009, Bioinform..

[49]  Joseph T. Glessner,et al.  PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. , 2007, Genome research.

[50]  Cynthia Gagnon,et al.  Autosomal recessive spastic ataxia of Charlevoix-Saguenay: upper extremity aptitudes, functional independence and social participation , 2004, International journal of rehabilitation research. Internationale Zeitschrift fur Rehabilitationsforschung. Revue internationale de recherches de readaptation.

[51]  O. Combarros,et al.  GAA expansion size and age at onset of Friedreich’s ataxia , 2003, Neurology.

[52]  Madhusudhan W. Pandit,et al.  Triplet repeats in human genome: distribution and their association with genes and other genomic regions , 2003, Bioinform..

[53]  G. Abecasis,et al.  Merlin—rapid analysis of dense genetic maps using sparse gene flow trees , 2002, Nature Genetics.

[54]  R. Giugliani,et al.  Neurologic findings in Machado-Joseph disease: relation with disease duration, subtypes, and (CAG)n. , 2001, Archives of neurology.

[55]  Z. Kelman,et al.  Studies on the interactions between human replication factor C and human proliferating cell nuclear antigen. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[56]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[57]  A. Bronstein,et al.  Bilateral loss of vestibular function: clinical findings in 53 patients , 1998, Journal of Neurology.

[58]  P. Patel,et al.  Friedreich's Ataxia: Autosomal Recessive Disease Caused by an Intronic GAA Triplet Repeat Expansion , 1996, Science.

[59]  M. Lovett,et al.  A single ataxia telangiectasia gene with a product similar to PI-3 kinase. , 1995, Science.

[60]  A. Harding.  ‘Idiopathic’ late onset cerebellar ataxia A clinical and genetic study of 36 cases , 1981, Journal of the Neurological Sciences.