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Pipo-Deveza J, Fehlings D, Chitayat D, Yoon G, Sroka H, Tein I. Rationale for dopa-responsive CTNNB1/ß-catenin deficient dystonia. Mov Disord 2018; 33:656-657. [PMID: 29436745 DOI: 10.1002/mds.27320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/23/2017] [Accepted: 01/05/2018] [Indexed: 11/12/2022] Open
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Yoon G, Caldecott KW. Nonsyndromic cerebellar ataxias associated with disorders of DNA single-strand break repair. HANDBOOK OF CLINICAL NEUROLOGY 2018; 155:105-115. [DOI: 10.1016/b978-0-444-64189-2.00007-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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78
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Zhang H, Zheng Y, Yoon G, Zhang Z, Gao T, Joyce B, Zhang W, Schwartz J, Vokonas P, Colicino E, Baccarelli A, Hou L, Liu L. Regularized estimation in sparse high-dimensional multivariate regression, with application to a DNA methylation study. Stat Appl Genet Mol Biol 2017; 16:159-171. [PMID: 28734115 DOI: 10.1515/sagmb-2016-0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this article, we consider variable selection for correlated high dimensional DNA methylation markers as multivariate outcomes. A novel weighted square-root LASSO procedure is proposed to estimate the regression coefficient matrix. A key feature of this method is tuning-insensitivity, which greatly simplifies the computation by obviating cross validation for penalty parameter selection. A precision matrix obtained via the constrained ℓ1 minimization method is used to account for the within-subject correlation among multivariate outcomes. Oracle inequalities of the regularized estimators are derived. The performance of our proposed method is illustrated via extensive simulation studies. We apply our method to study the relation between smoking and high dimensional DNA methylation markers in the Normative Aging Study (NAS).
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Hartley T, Wagner JD, Warman-Chardon J, Tétreault M, Brady L, Baker S, Tarnopolsky M, Bourque PR, Parboosingh JS, Smith C, McInnes B, Innes AM, Bernier F, Curry CJ, Yoon G, Horvath GA, Bareke E, Gillespie M, Majewski J, Bulman DE, Dyment DA, Boycott KM. Whole-exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families. Clin Genet 2017; 93:301-309. [PMID: 28708278 DOI: 10.1111/cge.13101] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 01/02/2023]
Abstract
The inherited peripheral neuropathies (IPNs) are characterized by marked clinical and genetic heterogeneity and include relatively frequent presentations such as Charcot-Marie-Tooth disease and hereditary motor neuropathy, as well as more rare conditions where peripheral neuropathy is associated with additional features. There are over 250 genes known to cause IPN-related disorders but it is estimated that in approximately 50% of affected individuals a molecular diagnosis is not achieved. In this study, we examine the diagnostic utility of whole-exome sequencing (WES) in a cohort of 50 families with 1 or more affected individuals with a molecularly undiagnosed IPN with or without additional features. Pathogenic or likely pathogenic variants in genes known to cause IPN were identified in 24% (12/50) of the families. A further 22% (11/50) of families carried sequence variants in IPN genes in which the significance remains unclear. An additional 12% (6/50) of families had variants in novel IPN candidate genes, 3 of which have been published thus far as novel discoveries (KIF1A, TBCK, and MCM3AP). This study highlights the use of WES in the molecular diagnostic approach of highly heterogeneous disorders, such as IPNs, places it in context of other published neuropathy cohorts, while further highlighting associated benefits for discovery.
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Osuna C, Apps R, Lim SY, Kublin J, Thomas R, Chen E, Yoon G, Han Huang S, Chan D, Truong R, Ren Y, Bachtel N, Ackerman M, Ananworanich J, Barouch D, Michael N, Brad Jones R, Nixon D, Whitney J. CD32 does not mark the HIV-1/SIV latent reservoir. J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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81
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Renaud M, Tranchant C, Martin JVT, Mochel F, Synofzik M, van de Warrenburg B, Pandolfo M, Koenig M, Kolb SA, Anheim M, Alonso I, Azzedine H, Barbot C, Bereau M, Berkovic S, Bernard G, Bindoff LA, Bompaire F, Bonneau D, Bonneau P, Boycott KM, Bras J, Brais B, Brigatti KW, Cameron J, Chamova T, Choquet K, Delague V, Denizeau P, Dotti MT, El‐Euch G, Elmalik SA, Federico A, Fiskerstrand T, Gagnon C, Guerreiro R, Guissart C, Hassin‐Baer S, Heimdal KR, Héron B, Isohanni P, Kalaydijeva L, Kawarai T, Koht JA, Lai S, Piana RL, Lecocq C, Linnankivi T, Lönnqvist T, Lu C, Maas R, Mahlaoui N, Mallaret M, Marelli C, Mariotti C, Mathieu J, Méneret A, Mignarri A, Monin ML, Montaut S, Nanetti L, Nadjar Y, Poujois A, Salih MA, Sousa S, Stanier P, Stoppa‐Lyonnet D, Strauss K, Tallaksen C, Tarnopolsky M, Tinant N, Tournev I, Topaloglu H, Varhaug KN, Woimant F, Wolf NI, Yahalom G, Yoon G, Young M. A recessive ataxia diagnosis algorithm for the next generation sequencing era. Ann Neurol 2017; 82:892-899. [DOI: 10.1002/ana.25084] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 02/06/2023]
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Baskin B, Kalia LV, Banwell BL, Ray PN, Yoon G. Complex genomic rearrangement in SPG11 due to a DNA replication-based mechanism. Mov Disord 2017; 32:1792-1794. [PMID: 29082553 DOI: 10.1002/mds.27188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/10/2017] [Indexed: 01/15/2023] Open
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Abdullah S, Hawkins C, Wilson G, Yoon G, Mertens L, Carter MT, Guerin A. Noncompaction cardiomyopathy in an infant with Walker-Warburg syndrome. Am J Med Genet A 2017; 173:3082-3086. [PMID: 28980384 DOI: 10.1002/ajmg.a.38394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/22/2017] [Accepted: 07/18/2017] [Indexed: 12/30/2022]
Abstract
Walker-Warburg syndrome (WWS) is a rare autosomal recessive, congenital muscular dystrophy that is associated with brain and eye anomalies. Several genes encoding proteins involved in α-dystroglycan glycosylation have been implicated in the aetiology of WWS. We describe a patient with nonclassical features of WWS presenting with heart failure related to noncompaction cardiomyopathy resulting in death at 4 months of age. Muscle biopsy revealed absent α-dystroglycan on immunostaining and genetic testing confirmed the diagnosis with two previously described POMT2 mutations. This is the first reported case of WWS syndrome associated with noncompaction cardiomyopathy.
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McCormick A, Farmer J, Perlman S, Delatycki M, Wilmot G, Matthews K, Yoon G, Hoyle C, Subramony SH, Zesiewicz T, Lynch DR, McCormack SE. Impact of diabetes in the Friedreich ataxia clinical outcome measures study. Ann Clin Transl Neurol 2017; 4:622-631. [PMID: 28904984 PMCID: PMC5590524 DOI: 10.1002/acn3.439] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/12/2017] [Accepted: 06/19/2017] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE Friedreich ataxia (FA) is a progressive neuromuscular disorder caused by GAA triplet repeat expansions or point mutations in the FXN gene. FA is associated with increased risk of diabetes mellitus (DM). This study assessed the age-specific prevalence of FA-associated DM and its impact on neurologic outcomes. RESEARCH DESIGN AND METHODS Participants were 811 individuals with FA from 12 international sites in a prospective natural history study (FA Clinical Outcome Measures Study, FACOMS). Physical function was assessed, using validated instruments. Multivariable regression analyses examined the independent association of DM with outcomes. RESULTS Mean age of participants was 30.1 years (SD 15.3, range: 7-82), 50% were female, and 94% were non-Hispanic white. 9% (42/459) of adults and 3% (10/352) of children had DM. Individuals with FA-associated DM were older (P < 0.001), had longer GAA repeat length on the least affected FXN allele (P = 0.037), and more severe FA (P = 0.0001). Of individuals with DM, 65% (34/52) were taking insulin. Even after accounting statistically for both age and GAA repeat length, DM was independently associated with greater FA symptom burden (P = 0.010), reduced capacity to perform activities of daily living (P = 0.021), and a decrease of 0.33 SDs on a composite performance measure (95% CI: -0.56-0.11, P = 0.004); the relative impact of DM was most apparent in younger individuals. CONCLUSIONS DM-associated FA has an independent adverse impact on well-being in affected individuals, particularly at younger ages. In future, evidence-based approaches for identification and management of FA-related DM may improve both health and function.
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Gonorazky HD, Amburgey K, Yoon G, Vajsar J, Widjaja E, Dowling JJ. Subacute demyelinating peripheral neuropathy as a novel presentation of late infantile metachromatic leukodystrophy. Muscle Nerve 2017; 56:E41-E44. [PMID: 28667691 DOI: 10.1002/mus.25737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/13/2017] [Accepted: 06/25/2017] [Indexed: 01/11/2023]
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Yoon G, Zheng Y, Zhang Z, Zhang H, Gao T, Joyce B, Zhang W, Guan W, Baccarelli AA, Jiang W, Schwartz J, Vokonas PS, Hou L, Liu L. Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome. BMC Bioinformatics 2017; 18:156. [PMID: 28264653 PMCID: PMC5340011 DOI: 10.1186/s12859-017-1568-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 02/24/2017] [Indexed: 01/02/2023] Open
Abstract
Background Metabolic syndrome has become a major public health challenge worldwide. The association between metabolic syndrome and DNA methylation is of great research interest. Results We constructed a binomial model to investigate the association between a metabolic syndrome index and DNA methylation in the Normative Aging Study. We applied the Iterative Sure Independence Screening (ISIS) method with elastic net penalty to DNA methylation levels at 484,548 CpG markers from 659 human subjects, and demonstrated that the screening step in ISIS can significantly improve the performance of the elastic net. Conclusion The proposed method identifies four CpGs which can be mapped to two biologically relevant and functional genes. Identification of significant CpG markers may potentially have practical implications for disease prevention and treatment.
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Wang BX, Grover SA, Kannu P, Yoon G, Laxer RM, Yeh EA, Fish EN. Interferon-Stimulated Gene Expression as a Preferred Biomarker for Disease Activity in Aicardi-Goutières Syndrome. J Interferon Cytokine Res 2017; 37:147-152. [PMID: 28387595 DOI: 10.1089/jir.2016.0117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aicardi-Goutières syndrome (AGS) is an early-onset, genetic disease characterized by recurrent fever, multifocal lesions of the brain, and systemic autoimmunity. We report on 3 AGS patients, 2 siblings with an RNASEH2A gene mutation and 1 patient with a SAMHD1 gene mutation. Serial analysis of peripheral blood from all 3 AGS patients showed consistently elevated expression of the interferon-stimulated genes (ISGs): ISG15, RSAD2, and IFI27, not observed in unaffected family members. Enumeration of circulating white blood cells and platelets and examination of C-reactive protein showed no significant deviation from the normal range for Patient 2 with the RNASEH2A mutation and Patient 3 with the SAMHD1 mutation, even when Patient 2 had magnetic resonance imaging abnormalities and ongoing febrile episodes. Erythrocyte sedimentation rates fluctuated within the normal range for Patient 2, with some elevation, yet, were in the normal range during the second febrile episode when there were accompanying neurological abnormalities. These preliminary data suggest that ISG expression may be a more specific indicator of disease activity in comparison to standard inflammatory markers.
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Gonorazky HD, Marshall CR, Al-Murshed M, Hazrati LN, Thor MG, Hanna MG, Männikkö R, Ray PN, Yoon G. Congenital myopathy with "corona" fibres, selective muscle atrophy, and craniosynostosis associated with novel recessive mutations in SCN4A. Neuromuscul Disord 2017; 27:574-580. [PMID: 28262468 DOI: 10.1016/j.nmd.2017.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/19/2016] [Accepted: 02/03/2017] [Indexed: 12/30/2022]
Abstract
We describe two brothers with lower facial weakness, highly arched palate, scaphocephaly due to synostosis of the sagittal and metopic sutures, axial hypotonia, proximal muscle weakness, and mild scoliosis. The muscle MRI of the younger sibling revealed a selective pattern of atrophy of the gluteus maximus, adductor magnus and soleus muscles. Muscle biopsy of the younger sibling revealed myofibres with internalized nuclei, myofibrillar disarray, and "corona" fibres. Both affected siblings were found to be compound heterozygous for c.3425G>A (p.Arg1142Gln) and c.1123T>C (p.Cys375Arg) mutations in SCN4A on exome sequencing, and the parents were confirmed carriers of one of the mutations. Electrophysiological characterization of the mutations revealed the Cys375Arg confers full and Arg1142Gln mild partial loss-of-function. Loss of function of the Nav1.4 channel leads to a decrement of the action potential and subsequent reduction of muscle contraction. The unusual muscle biopsy features suggest a more complex pathomechanism, and broaden the phenotype associated with SCN4A mutations.
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Hoch N, Hanzlikova H, Rulten SL, Tétreault M, Koumulainen E, Ju L, Hornyak P, Zeng Z, Gittens W, Rey S, Staras K, Mancini GM, McKinnon PJ, Wang ZQ, Wagner J, Yoon G, Caldecott KW. XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Nature 2017; 541:87-91. [PMID: 28002403 PMCID: PMC5218588 DOI: 10.1038/nature20790] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/15/2016] [Indexed: 01/14/2023]
Abstract
XRCC1 is a molecular scaffold protein that assembles multi-protein complexes involved in DNA single-strand break repair. Here we show that biallelic mutations in the human XRCC1 gene are associated with ocular motor apraxia, axonal neuropathy, and progressive cerebellar ataxia. Cells from a patient with mutations in XRCC1 exhibited not only reduced rates of single-strand break repair but also elevated levels of protein ADP-ribosylation. This latter phenotype is recapitulated in a related syndrome caused by mutations in the XRCC1 partner protein PNKP and implicates hyperactivation of poly(ADP-ribose) polymerase/s as a cause of cerebellar ataxia. Indeed, remarkably, genetic deletion of Parp1 rescued normal cerebellar ADP-ribose levels and reduced the loss of cerebellar neurons and ataxia in Xrcc1-defective mice, identifying a molecular mechanism by which endogenous single-strand breaks trigger neuropathology. Collectively, these data establish the importance of XRCC1 protein complexes for normal neurological function and identify PARP1 as a therapeutic target in DNA strand break repair-defective disease.
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Gan-Or Z, Yoon G, Suchowersky O, Dupré N, Rouleau GA. KCNA2 mutations are rare in hereditary spastic paraplegia. Ann Neurol 2016; 81:325-326. [PMID: 28019661 DOI: 10.1002/ana.24855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 10/31/2016] [Indexed: 11/11/2022]
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91
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Chrestian N, Dupré N, Gan-Or Z, Szuto A, Chen S, Venkitachalam A, Brisson JD, Warman-Chardon J, Ahmed S, Ashtiani S, MacDonald H, Mohsin N, Mourabit-Amari K, Provencher P, Boycott KM, Stavropoulos DJ, Dion PA, Ray PN, Suchowersky O, Rouleau GA, Yoon G. Clinical and genetic study of hereditary spastic paraplegia in Canada. NEUROLOGY-GENETICS 2016; 3:e122. [PMID: 27957547 PMCID: PMC5141523 DOI: 10.1212/nxg.0000000000000122] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/20/2016] [Indexed: 11/18/2022]
Abstract
Objective: To describe the clinical, genetic, and epidemiologic features of hereditary spastic paraplegia (HSP) in Canada and to determine which clinical, radiologic, and genetic factors determine functional outcomes for patients with HSP. Methods: We conducted a multicenter observational study of patients who met clinical criteria for the diagnosis of HSP in the provinces of Alberta, Ontario, and Quebec from 2012 to 2015. Characteristics of the participants were analyzed using descriptive statistics. The main outcome measure for a subset of the cohort (n = 48) was the Spastic Paraplegia Rating Scale. We also used the SPATAX-EUROSPA disability stage (disability score) to assess disability (n = 65). Results: A total of 526 patients were identified with HSP across the country, and 150 patients had a confirmed genetic diagnosis. Mutations were identified in 15 different genes; the most common were SPAST (SPG4, 48%), ATL1 (SPG3A, 16%), SPG11 (8%), SPG7 (7%), and KIAA0196 (SPG8, 5%). The diagnosis of SPG4 was associated with older age at symptom onset (p = 0.0017). SPG4 and SPG3A were less associated with learning disabilities compared to other subtypes of HSP, and SPG11 was strongly associated with progressive cognitive deficits (odds ratio 87.75, 95% confidence interval 14.04–548.24, p < 0.0001). SPG3A was associated with better functional outcomes compared to other HSP subtypes (p = 0.04) on multivariate analysis. The strongest predictor of significant disability was abnormal brain MRI (p = 0.014). Conclusions: The most important predictors of disability in our HSP cohort were SPG11 mutations and abnormal brain MRI. Accurate molecular characterization of well-phenotyped cohorts and international collaboration are essential to establish the natural history of these rare neurodegenerative disorders.
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Suh Y, Yoon CH, Kim RK, Lim EJ, Oh YS, Hwang SG, An S, Yoon G, Gye MC, Yi JM, Kim MJ, Lee SJ. Claudin-1 induces epithelial-mesenchymal transition through activation of the c-Abl-ERK signaling pathway in human liver cells. Oncogene 2016; 36:1167-1168. [PMID: 27841864 DOI: 10.1038/onc.2016.294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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93
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Gonorazky H, Marshall C, Hazrati L, Männikkö R, Ray P, Yoon G. Congenital myopathy with selective muscle atrophy, necklace-like fibres/central cores and craniosynostosis associated with recessive mutations in SCN4A. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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94
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Al-Maawali A, Yoon G, Feigenbaum AS, Halliday WC, Clarke JTR, Branson HM, Banwell BL, Chitayat D, Blaser SI. Validation of the finding of hypertrophy of the clava in infantile neuroaxonal dystrophy/PLA2G6 by biometric analysis. Neuroradiology 2016; 58:1035-1042. [PMID: 27516098 DOI: 10.1007/s00234-016-1726-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/07/2016] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Infantile neuroaxonal dystrophy (INAD), an autosomal recessive neurodegenerative disorder due to PLA2G6 mutation, is classified both as a PLA2G6-associated neurodegeneration (PLAN) disorder and as one of the neurodegeneration with brain iron accumulation (NBIA) disorders. Age of onset and clinical presentation in INAD is variable. Typically described imaging features of cerebellar atrophy, cerebellar cortex bright FLAIR signal, and globus pallidus iron deposition are variable or late findings. We characterize clinical and neuroimaging phenotypes in nine children with confirmed PLA2G6 mutations and show a useful imaging feature, clava hypertrophy, which may aid in earlier identification of patients. Measurements of the clava confirm actual enlargement, rather than apparent enlargement due to volume loss of the other brain stem structures. METHODS A retrospective clinical and MRI review was performed. Brain stem measurements were performed and compared with age-matched controls. RESULTS We identified nine patients, all with novel PLA2G6 gene mutations. MRI, available in eight, showed clava hypertrophy, regardless of age or the absence of other more typically described neuroimaging findings. Brain autopsy in our cohort confirmed prominent spheroid bodies in the clava nuclei. CONCLUSION Clava hypertrophy is an important early imaging feature which may aid in indentification of children who would benefit from specific testing for PLA2G6 mutations.
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Shinnick JE, Schadt K, Strawser C, Wilcox N, Perlman SL, Wilmot GR, Gomez CM, Mathews KD, Yoon G, Zesiewicz T, Hoyle C, Subramony SH, Yiu EM, Delatycki MB, Brocht AF, Farmer JM, Lynch DR. Comorbid Medical Conditions in Friedreich Ataxia: Association With Inflammatory Bowel Disease and Growth Hormone Deficiency. J Child Neurol 2016; 31:1161-5. [PMID: 27071470 DOI: 10.1177/0883073816643408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/07/2016] [Indexed: 11/16/2022]
Abstract
Friedreich ataxia is a progressive degenerative disease with neurologic and cardiac involvement. This study characterizes comorbid medical conditions in a large cohort of patients with Friedreich ataxia. Patient diagnoses were collected in a large natural history study of 641 subjects. Prevalence of diagnoses in the cohort with Friedreich ataxia was compared with prevalence in the population without Friedreich ataxia. Ten patients (1.6%) had inflammatory bowel disease, 3.5 times more common in this cohort of individuals with Friedreich ataxia than in the general population. Four subjects were growth hormone deficient, reflecting a prevalence in Friedreich ataxia that is 28 times greater than the general population. The present study identifies specific diagnoses not traditionally associated with Friedreich ataxia that are found at higher frequency in this disease. These associations could represent coincidence, shared genetic background, or potentially interactive disease mechanisms with Friedreich ataxia.
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Patel M, Isaacs CJ, Seyer L, Brigatti K, Gelbard S, Strawser C, Foerster D, Shinnick J, Schadt K, Yiu EM, Delatycki MB, Perlman S, Wilmot GR, Zesiewicz T, Mathews K, Gomez CM, Yoon G, Subramony SH, Brocht A, Farmer J, Lynch DR. Progression of Friedreich ataxia: quantitative characterization over 5 years. Ann Clin Transl Neurol 2016; 3:684-94. [PMID: 27648458 PMCID: PMC5018581 DOI: 10.1002/acn3.332] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE Friedreich ataxia (FRDA) is a progressive neurodegenerative disorder of adults and children. This study analyzed neurological outcomes and changes to identify predictors of progression and generate power calculations for clinical trials. METHODS Eight hundred and twelve subjects in a natural history study were evaluated annually across 12 sites using the Friedreich Ataxia Rating Scale (FARS), 9-Hole Peg Test, Timed 25-Foot Walk, visual acuity tests, self-reported surveys and disability scales. Cross-sectional outcomes were assessed from recent visits, and longitudinal changes were gaged over 5 years from baseline. RESULTS Cross-sectional outcomes correlated with measures of disease severity. Age, genetic severity (guanine-adenine-adenine [GAA] repeat length), and testing site predicted performance. Serial progression was relatively linear using FARS and composite measures of performance, while individual performance outcomes were nonlinear over time. Age strongly predicted change from baseline until removing the effects of baseline FARS scores, when GAA becomes a more important factor. Progression is fastest in younger subjects and subjects with longer GAA repeats. Improved coefficients of variation show that progression results are more reproducible over longer assessment durations. INTERPRETATION While age predicted progression speed in simple analyses and may provide an effective way to stratify cohorts, separating the effects of age and genetic severity is difficult. Controlling for baseline severity, GAA is the major determinant of progression rate in FRDA. Clinical trials will benefit from enrollment of younger subjects, and sample size requirements will shrink with longer assessment periods. These findings should prove useful in devising gene therapy trials in the near future.
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Uddin M, Pellecchia G, Thiruvahindrapuram B, D'Abate L, Merico D, Chan A, Zarrei M, Tammimies K, Walker S, Gazzellone MJ, Nalpathamkalam T, Yuen RKC, Devriendt K, Mathonnet G, Lemyre E, Nizard S, Shago M, Joseph-George AM, Noor A, Carter MT, Yoon G, Kannu P, Tihy F, Thorland EC, Marshall CR, Buchanan JA, Speevak M, Stavropoulos DJ, Scherer SW. Indexing Effects of Copy Number Variation on Genes Involved in Developmental Delay. Sci Rep 2016; 6:28663. [PMID: 27363808 PMCID: PMC4929460 DOI: 10.1038/srep28663] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/06/2016] [Indexed: 01/03/2023] Open
Abstract
A challenge in clinical genomics is to predict whether copy number variation (CNV) affecting a gene or multiple genes will manifest as disease. Increasing recognition of gene dosage effects in neurodevelopmental disorders prompted us to develop a computational approach based on critical-exon (highly expressed in brain, highly conserved) examination for potential etiologic effects. Using a large CNV dataset, our updated analyses revealed significant (P < 1.64 × 10−15) enrichment of critical-exons within rare CNVs in cases compared to controls. Separately, we used a weighted gene co-expression network analysis (WGCNA) to construct an unbiased protein module from prenatal and adult tissues and found it significantly enriched for critical exons in prenatal (P < 1.15 × 10−50, OR = 2.11) and adult (P < 6.03 × 10−18, OR = 1.55) tissues. WGCNA yielded 1,206 proteins for which we prioritized the corresponding genes as likely to have a role in neurodevelopmental disorders. We compared the gene lists obtained from critical-exon and WGCNA analysis and found 438 candidate genes associated with CNVs annotated as pathogenic, or as variants of uncertain significance (VOUS), from among 10,619 developmental delay cases. We identified genes containing CNVs previously considered to be VOUS to be new candidate genes for neurodevelopmental disorders (GIT1, MVB12B and PPP1R9A) demonstrating the utility of this strategy to index the clinical effects of CNVs.
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Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L, Lv J, Baccarelli A, Hou L, Liu L. Estimating and testing high-dimensional mediation effects in epigenetic studies. Bioinformatics 2016; 32:3150-3154. [PMID: 27357171 DOI: 10.1093/bioinformatics/btw351] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/24/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION High-dimensional DNA methylation markers may mediate pathways linking environmental exposures with health outcomes. However, there is a lack of analytical methods to identify significant mediators for high-dimensional mediation analysis. RESULTS Based on sure independent screening and minimax concave penalty techniques, we use a joint significance test for mediation effect. We demonstrate its practical performance using Monte Carlo simulation studies and apply this method to investigate the extent to which DNA methylation markers mediate the causal pathway from smoking to reduced lung function in the Normative Aging Study. We identify 2 CpGs with significant mediation effects. AVAILABILITY AND IMPLEMENTATION R package, source code, and simulation study are available at https://github.com/YinanZheng/HIMA CONTACT: lei.liu@northwestern.edu.
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Gan-Or Z, Bouslam N, Birouk N, Lissouba A, Chambers DB, Vérièpe J, Androschuk A, Laurent SB, Rochefort D, Spiegelman D, Dionne-Laporte A, Szuto A, Liao M, Figlewicz DA, Bouhouche A, Benomar A, Yahyaoui M, Ouazzani R, Yoon G, Dupré N, Suchowersky O, Bolduc FV, Parker JA, Dion PA, Drapeau P, Rouleau GA, Ouled Amar Bencheikh B. Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia. Am J Hum Genet 2016; 98:1271. [PMID: 27259058 DOI: 10.1016/j.ajhg.2016.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Reejhsinghani R, Brown K, Schiller N, Yoon G, Foster E, Gensler L. FRI0434 Prevalence of Structural Cardiac Disease and Diastolic Dysfunction in Axial Spondyloarthritis: A Prospective Case-Control Study. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.3245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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