Evidence map›Paper›PMID 31230722›Full record

ArticleAmerican journal of human genetics2019

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 and 23 more

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In one paragraph

Article in American journal of human genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
139citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

139 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
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79 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

33 authors.

Haloom RafehiPopulation 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.
David J SzmulewiczCerebellar 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.
Mark F BennettPopulation 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.
Nara L M SobreiraMcKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Kate PopeBruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia.
Katherine R SmithPopulation Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.
Greta GilliesBruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia.
Peter DiakumisUniversity of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia.
Egor DolzhenkoIllumina Inc, 5200 Illumina Way, San Diego, CA 92122, USA.
Michael A EberleIllumina Inc, 5200 Illumina Way, San Diego, CA 92122, USA.
María García BarcinaGenetic Unit, Basurto University Hospital, OSI Bilbao-Basurto, avenida Montevideo 18, 48013 Bilbao, Spain.
David P BreenCentre 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.
Andrew M ChancellorDepartment of Neurology, Tauranga Hospital, Private Bag, Cameron Road, Tauranga 3171, New Zealand.
Phillip D CremerUniversity of Sydney, Camperdown, NSW 2006, Australia; Royal North Shore Hospital, Pacific Hwy, St Leonards, NSW 2065, Australia.
Martin B DelatyckiBruce 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.
Brent L FogelDepartments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
Anna HackettHunter Genetics, Hunter New England Health Service, Waratah, Newcastle, NSW 2300, Australia; University of Newcastle, Newcastle, NSW 2300, Australia.
G Michael HalmagyiNeurology Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia.
Solange KapetanovicServicio de Neurología, Hospital de Basurto, Avenida de Montevideo 18, 48013 Bilbao, Bizkaia, Spain.
Anthony LangEdmond 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.
Stuart MossmanDepartment of Neurology, Wellington Hospital, Wellington 6021, New Zealand.
Weiyi MuMcKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Peter PatrikiosSunshine Neurology, Maroochydore, QLD 4558, Australia.
Susan L PerlmanDepartment of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
Ian RosemergyDepartment of Neurology, Wellington Hospital, Newtown, Wellington 6021, New Zealand.
Elsdon StoreyDepartment of Neuroscience, Central Clinical School, Monash University, Alfred Hospital Campus, Commercial Road, Melbourne, VIC 3004, Australia.
Shaun R D WatsonInstitute of Neurological Sciences, Prince of Wales Hospital, Randwick, NSW 2031, Australia.
Michael A WilsonBruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia.
David S ZeeDepartment of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA.
David ValleMcKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
David J AmorBruce 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.
Melanie BahloPopulation 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.
Paul J LockhartBruce 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.

Funding

Baylor-Johns Hopkins Center for Mendelian GeneticsU54HG006542 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 2012 to 2015
$15.6M
Predoctoral Training Program in Human GeneticsT32GM007814 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 1985 to 2021
$10.6M
Sleep and Circadian Dysfunction, Brain and Neurobehavioral Development in AutismP50HD103538 · NICHD · HUGO W. MOSER RES INST KENNEDY KRIEGER · PI S. Ali Fatemi, Bradley L Schlaggar · 2020 to 2026
$9.9M
Rare and Novel Genetic Variation in the Pathogenesis of Cerebellar AtaxiaR01NS082094 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FOGEL, BRENT LINDEN · 2013 to 2017
$1.7M
NHGRI NIH HHS U54 HG006542NICHD NIH HHS P50 HD103538NIGMS NIH HHS T32 GM007814NINDS NIH HHS R01 NS082094Wellcome Trust
6 · The paper itself

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)

Indexed as

IntronsMicrosatellite RepeatsAlgorithmsCerebellar AtaxiaCohort StudiesComputational BiologyFamilyFemaleGenomicsHumansMaleMiddle AgedPolyneuropathiesReplication Protein CSensation DisordersSyndromeReplication Protein CRFC1 protein, humanataxiaCANVASrepeat expansionsshort tandem repeatswhole-genome sequencing

Identifiers

PMID31230722
PMCPMC6612533

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.