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Conconi A, Chiappella A, Orsucci L, Gaidano G, Ferreri AJ, Balzarotti M, Tucci A, Botto B, Moccia A, Vanazzi A, Merli F, Tani M, Esposito F, Bonomini L, Vitolo U, Zucca E. INTENSIFIED (INTRAVENOUS AND INTRATHECAL) CNS PROPHYLAXIS IN PRIMARY TESTICULAR DIFFUSE LARGE B‐CELL LYMPHOMA: 5‐YEAR RESULTS OF THE IELSG30 TRIAL. Hematol Oncol 2021. [DOI: 10.1002/hon.48_2879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Tucci A, Musuraca G, Cavallo F, Zilioli VR, Zanni M, Pelliccia S, Mannina D, Michieli M, Vallisa D, Tani M, Merli F, Re F, Marcheselli L, Campostrini G, Pagani C, Grimaldi D, Liardo EV, Re A, Cox MC, Rossi G. AUTOLOGOUS TRANSPLANT IN ELDERLY PATIENTS WITH R/R AGGRESSIVE LYMPHOMA SELECTED BY SIMPLIFIED CGA: THE RECANZ PROSPECTIVE PHASE 2 STUDY BY THE FONDAZIONE ITALIANA LINFOMI. Hematol Oncol 2021. [DOI: 10.1002/hon.99_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Cattaneo C, Cancelli V, Pagani C, Ogna A, Tucci A, Rossi G, Quaresima V, Sotttini A, Dobbs K, Notarangelo LD, Cohen JI, Burbelo PD. IMPAIRED HUMORAL RESPONSE IN LYMPHOMA PATIENTS SURVIVING THE ACUTE PHASE OF COVID‐19. Hematol Oncol 2021. [PMCID: PMC8427060 DOI: 10.1002/hon.196_2880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Tucci A, Merli F, Fabbri A, Mancuso S, Sartori R, Storti S, Luminari S, Mammi C, Marcheselli L, Arcari A, Cavallo F, Zilioli VR, Bottelli C, Re A, Gini G, Cox MC, Puccini B, Pagani C, Balzarotti M, Spina M, Rossi G. DIFFUSE LARGE B CELL LYMPHOMA (DLBCL) IN LATE‐OCTOGENARIAN (LO) PATIENTS: A SUBSTUDY OF THE “ELDERLY PROJECT” BY THE FONDAZIONE ITALIANA LINFOMI (FIL). Hematol Oncol 2021. [DOI: 10.1002/hon.95_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ferreri AJ, Tarantino V, Cabras G, Ferrara F, Zinzani PL, Arcaini L, Castellino A, Tucci A, Cocito F, Davies A, Salvador Chalup MM, Cwynarski K, Nogueira FL, Petrucci L, Muzi C, Onofrillo D, Ferrario A, Ramakrishnan P, Scalzulli PR, Tani M, Tisi MC, Papageorgiou SG, Calimeri T, Angelillo P, Foppoli M, Dimou M, Ponzoni M, Iannitto E, Vassilakopoulos TP. PROGNOSTIC FACTORS, MANAGEMENT AND OUTCOME OF AN INTERNATIONAL SERIES OF 41 PATIENTS WITH PRIMARY MEDIASTINAL LARGE B‐CELL LYMPHOMA (PMLBCL) AND CENTRAL NERVOUS SYSTEM (CNS) INVOLVEMENT. Hematol Oncol 2021. [DOI: 10.1002/hon.66_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bonfiglio F, Bruscaggin A, Guidetti F, Terzi di Bergamo L, Faderl M, Spina V, Condoluci A, Bonomini L, Forestieri G, Koch R, Piffaretti D, Pini K, Pirosa MC, Cittone MG, Arribas A, Lucioni M, Ghilardi G, Wu W, Arcaini L, Baptista MJ, Bastidas G, Bea S, Boldorini R, Broccoli A, Canzonieri V, Cascione L, Ceriani L, Cogliatti S, Derenzini E, Devizzi L, Dietrich S, Elia AR, Facchetti F, Gaidano G, Garcia JF, Gerber B, Ghia P, Silva MG, Gritti G, Guidetti A, Hitz F, Inghirami G, Ladetto M, Lopez‐Guillermo A, Lucchini E, Maiorana A, Marasca R, Matutes E, Meignin V, Merli M, Moccia A, Mollejo M, Montalban C, Novak U, Oscier DG, Passamonti F, Piazza F, Pizzolitto S, Sabattini E, Salles G, Santambrogio E, Scarfó L, Stathis A, Stüssi G, Geyer JT, Tapia G, Thieblemont C, Tousseyn T, Tucci A, Visco C, Vitolo U, Zenz T, Zinzani PL, Khiabanian H, Calcinotto A, Bertoni F, Bhagat G, Campo E, Leval L, Dirnhofer S, Pileri SA, Piris MÁ, Traverse‐Glehen A, Tzankov A, Paulli M, Ponzoni M, Mazzucchelli L, Cavalli F, Zucca E, Rossi D. GENETIC AND PHENOTYPIC ATTRIBUTES OF SPLENIC MARGINAL ZONE LYMPHOMA. Hematol Oncol 2021. [DOI: 10.1002/hon.43_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Luminari S, Galimberti S, Versari A, Tucci A, Boccomini C, Farina L, Zaja F, Marcheselli L, Ferrero S, Arcaini L, Pulsoni A, Musuraca G, Califano C, Merli M, Bari A, Conconi A, Giudice ID, Re F, Stefani PM, Usai SV, Perrone T, Gini G, Falini B, Gattei V, Manni M, Ladetto M, Mannina D, Federico M. RESPONSE ADAPTED POST INDUCTION THERAPY IN FOLLICULAR LYMPHOMA: UPDATED RESULTS OF THE FOLL12 TRIAL BY THE FONDAZIONE ITALIANA LINFOMI (FIL). Hematol Oncol 2021. [DOI: 10.1002/hon.80_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zilioli VR, Albano D, Arcari A, Merli F, Coppola A, Besutti G, Marcheselli L, Gramegna D, Muzi C, Manicone M, Camalori M, Ciammella P, Colloca G, Tucci A. SARCOPENIA IS AN INDEPENDENT PROGNOSTIC FACTOR IN ELDERLY MALE PATIENTS WITH CLASSICAL HODGKIN LYMPHOMA: RESULTS FROM A MULTICENTER EXPERIENCE. Hematol Oncol 2021. [DOI: 10.1002/hon.116_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Merli F, Tucci A, Arcari A, Rigacci L, Cavallo F, Cabras G, Alvarez I, Fabbri A, Re A, Ferrero S, Puccini B, Usai SV, Ferrari A, Cencini E, Pennese E, Zilioli VR, Marino D, Balzarotti M, Cox MC, Zanni M, Rocco A, Lleshi A, Botto B, Hohaus S, Merli M, Sartori R, Gini G, Nassi L, Musuraca G, Tani M, Bottelli C, Kovalchuk S, Re F, Flenghi L, Molinari A, Tarantini G, Chimienti E, Marcheselli L, Mammi C, Luminari S, Spina M. THE ELDERLY PROGNOSTIC INDEX (EPI) PREDICTS EARLY MORTALITY IN OLDER PATIENTS WITH DLBCL. A SUBSTUDY OF THE ELDERLY PROJECT BY THE FONDAZIONE ITALIANA LINFOMI (FIL). Hematol Oncol 2021. [DOI: 10.1002/hon.85_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Martelli M, Zucca E, Botto B, Kryachok I, Ceriani L, Balzarotti M, Tucci A, Cabras MG, Zilioli VR, Rusconi C, Angrilli F, Arcaini L, Iwanicka AD, Ferreri A, Merli F, Zhao W, Hodgson D, Ionescu C, Fosså A, Cwynarski K, Mikhaeel G, Jerkeman M, Janikova A, Hüttmann A, Ciccone G, Metser U, Barrington S, Malkowski B, Versari A, Esposito F, Cozens K, Ielmini N, Ricardi R, Cavalli F, Johnson P, Davies A. IMPACT OF DIFFERENT INDUCTION REGIMENS ON THE OUTCOME OF PRIMARY MEDIASTINAL B CELL LYMPHOMA IN THE PROSPECTIVE IELSG 37 TRIAL. Hematol Oncol 2021. [DOI: 10.1002/hon.49_2879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mencacci NE, Brockmann MM, Dai J, Pajusalu S, Atasu B, Campos J, Pino G, Gonzalez-Latapi P, Patzke C, Schwake M, Tucci A, Pittman A, Simon-Sanchez J, Carvill GL, Balint B, Wiethoff S, Warner TT, Papandreou A, Soo A, Rein R, Kadastik-Eerme L, Puusepp S, Reinson K, Tomberg T, Hanagasi H, Gasser T, Bhatia KP, Kurian MA, Lohmann E, Õunap K, Rosenmund C, Südhof TC, Wood NW, Krainc D, Acuna C. Biallelic variants in TSPOAP1, encoding the active-zone protein RIMBP1, cause autosomal recessive dystonia. J Clin Invest 2021; 131:140625. [PMID: 33539324 DOI: 10.1172/jci140625] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
Dystonia is a debilitating hyperkinetic movement disorder, which can be transmitted as a monogenic trait. Here, we describe homozygous frameshift, nonsense, and missense variants in TSPOAP1, which encodes the active-zone RIM-binding protein 1 (RIMBP1), as a genetic cause of autosomal recessive dystonia in 7 subjects from 3 unrelated families. Subjects carrying loss-of-function variants presented with juvenile-onset progressive generalized dystonia, associated with intellectual disability and cerebellar atrophy. Conversely, subjects carrying a pathogenic missense variant (p.Gly1808Ser) presented with isolated adult-onset focal dystonia. In mice, complete loss of RIMBP1, known to reduce neurotransmission, led to motor abnormalities reminiscent of dystonia, decreased Purkinje cell dendritic arborization, and reduced numbers of cerebellar synapses. In vitro analysis of the p.Gly1808Ser variant showed larger spike-evoked calcium transients and enhanced neurotransmission, suggesting that RIMBP1-linked dystonia can be caused by either reduced or enhanced rates of spike-evoked release in relevant neural networks. Our findings establish a direct link between dysfunction of the presynaptic active zone and dystonia and highlight the critical role played by well-balanced neurotransmission in motor control and disease pathogenesis.
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Pagnamenta AT, Kaiyrzhanov R, Zou Y, Da'as SI, Maroofian R, Donkervoort S, Dominik N, Lauffer M, Ferla MP, Orioli A, Giess A, Tucci A, Beetz C, Sedghi M, Ansari B, Barresi R, Basiri K, Cortese A, Elgar G, Fernandez-Garcia MA, Yip J, Foley AR, Gutowski N, Jungbluth H, Lassche S, Lavin T, Marcelis C, Marks P, Marini-Bettolo C, Medne L, Moslemi AR, Sarkozy A, Reilly MM, Muntoni F, Millan F, Muraresku CC, Need AC, Nemeth AH, Neuhaus SB, Norwood F, O'Donnell M, O'Driscoll M, Rankin J, Yum SW, Zolkipli-Cunningham Z, Brusius I, Wunderlich G, Karakaya M, Wirth B, Fakhro KA, Tajsharghi H, Bönnemann CG, Taylor JC, Houlden H. An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy. Brain 2021; 144:584-600. [PMID: 33559681 PMCID: PMC8263055 DOI: 10.1093/brain/awaa420] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 01/26/2023] Open
Abstract
The extracellular matrix comprises a network of macromolecules such as collagens, proteoglycans and glycoproteins. VWA1 (von Willebrand factor A domain containing 1) encodes a component of the extracellular matrix that interacts with perlecan/collagen VI, appears to be involved in stabilizing extracellular matrix structures, and demonstrates high expression levels in tibial nerve. Vwa1-deficient mice manifest with abnormal peripheral nerve structure/function; however, VWA1 variants have not previously been associated with human disease. By interrogating the genome sequences of 74 180 individuals from the 100K Genomes Project in combination with international gene-matching efforts and targeted sequencing, we identified 17 individuals from 15 families with an autosomal-recessive, non-length dependent, hereditary motor neuropathy and rare biallelic variants in VWA1. A single disease-associated allele p.(G25Rfs*74), a 10-bp repeat expansion, was observed in 14/15 families and was homozygous in 10/15. Given an allele frequency in European populations approaching 1/1000, the seven unrelated homozygote individuals ascertained from the 100K Genomes Project represents a substantial enrichment above expected. Haplotype analysis identified a shared 220 kb region suggesting that this founder mutation arose >7000 years ago. A wide age-range of patients (6-83 years) helped delineate the clinical phenotype over time. The commonest disease presentation in the cohort was an early-onset (mean 2.0 ± 1.4 years) non-length-dependent axonal hereditary motor neuropathy, confirmed on electrophysiology, which will have to be differentiated from other predominantly or pure motor neuropathies and neuronopathies. Because of slow disease progression, ambulation was largely preserved. Neurophysiology, muscle histopathology, and muscle MRI findings typically revealed clear neurogenic changes with single isolated cases displaying additional myopathic process. We speculate that a few findings of myopathic changes might be secondary to chronic denervation rather than indicating an additional myopathic disease process. Duplex reverse transcription polymerase chain reaction and immunoblotting using patient fibroblasts revealed that the founder allele results in partial nonsense mediated decay and an absence of detectable protein. CRISPR and morpholino vwa1 modelling in zebrafish demonstrated reductions in motor neuron axonal growth, synaptic formation in the skeletal muscles and locomotive behaviour. In summary, we estimate that biallelic variants in VWA1 may be responsible for up to 1% of unexplained hereditary motor neuropathy cases in Europeans. The detailed clinical characterization provided here will facilitate targeted testing on suitable patient cohorts. This novel disease gene may have previously evaded detection because of high GC content, consequential low coverage and computational difficulties associated with robustly detecting repeat-expansions. Reviewing previously unsolved exomes using lower QC filters may generate further diagnoses.
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Dewan R, Chia R, Ding J, Hickman RA, Stein TD, Abramzon Y, Ahmed S, Sabir MS, Portley MK, Tucci A, Ibáñez K, Shankaracharya FNU, Keagle P, Rossi G, Caroppo P, Tagliavini F, Waldo ML, Johansson PM, Nilsson CF, Rowe JB, Benussi L, Binetti G, Ghidoni R, Jabbari E, Viollet C, Glass JD, Singleton AB, Silani V, Ross OA, Ryten M, Torkamani A, Tanaka T, Ferrucci L, Resnick SM, Pickering-Brown S, Brady CB, Kowal N, Hardy JA, Van Deerlin V, Vonsattel JP, Harms MB, Morris HR, Ferrari R, Landers JE, Chiò A, Gibbs JR, Dalgard CL, Scholz SW, Traynor BJ. Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. Neuron 2021; 109:448-460.e4. [PMID: 33242422 PMCID: PMC7864894 DOI: 10.1016/j.neuron.2020.11.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/02/2020] [Accepted: 11/04/2020] [Indexed: 02/01/2023]
Abstract
We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40-64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington's disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered.
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Alghisi A, Borghetti P, Maddalo M, Roccaro A, Tucci A, Magrini S, Casto AL, Bonù M, Tomasini D, Baiguini A, Peretto G, Buglione M, Triggiani L. PO-0917: Radiotherapy-based approach for the treatment of solitary plasmacytoma. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00934-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Steel D, Zech M, Zhao C, Barwick KES, Burke D, Demailly D, Kumar KR, Zorzi G, Nardocci N, Kaiyrzhanov R, Wagner M, Iuso A, Berutti R, Škorvánek M, Necpál J, Davis R, Wiethoff S, Mankad K, Sudhakar S, Ferrini A, Sharma S, Kamsteeg EJ, Tijssen MA, Verschuuren C, van Egmond ME, Flowers JM, McEntagart M, Tucci A, Coubes P, Bustos BI, Gonzalez-Latapi P, Tisch S, Darveniza P, Gorman KM, Peall KJ, Bötzel K, Koch JC, Kmieć T, Plecko B, Boesch S, Haslinger B, Jech R, Garavaglia B, Wood N, Houlden H, Gissen P, Lubbe SJ, Sue CM, Cif L, Mencacci NE, Anderson G, Kurian MA, Winkelmann J. Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities. Ann Neurol 2020; 88:867-877. [PMID: 32808683 DOI: 10.1002/ana.25879] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/31/2020] [Accepted: 08/09/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVES The majority of people with suspected genetic dystonia remain undiagnosed after maximal investigation, implying that a number of causative genes have not yet been recognized. We aimed to investigate this paucity of diagnoses. METHODS We undertook weighted burden analysis of whole-exome sequencing (WES) data from 138 individuals with unresolved generalized dystonia of suspected genetic etiology, followed by additional case-finding from international databases, first for the gene implicated by the burden analysis (VPS16), and then for other functionally related genes. Electron microscopy was performed on patient-derived cells. RESULTS Analysis revealed a significant burden for VPS16 (Fisher's exact test p value, 6.9 × 109 ). VPS16 encodes a subunit of the homotypic fusion and vacuole protein sorting (HOPS) complex, which plays a key role in autophagosome-lysosome fusion. A total of 18 individuals harboring heterozygous loss-of-function VPS16 variants, and one with a microdeletion, were identified. These individuals experienced early onset progressive dystonia with predominant cervical, bulbar, orofacial, and upper limb involvement. Some patients had a more complex phenotype with additional neuropsychiatric and/or developmental comorbidities. We also identified biallelic loss-of-function variants in VPS41, another HOPS-complex encoding gene, in an individual with infantile-onset generalized dystonia. Electron microscopy of patient-derived lymphocytes and fibroblasts from both patients with VPS16 and VPS41 showed vacuolar abnormalities suggestive of impaired lysosomal function. INTERPRETATION Our study strongly supports a role for HOPS complex dysfunction in the pathogenesis of dystonia, although variants in different subunits display different phenotypic and inheritance characteristics. ANN NEUROL 2020;88:867-877.
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Chen Z, Yan Yau W, Jaunmuktane Z, Tucci A, Sivakumar P, Gagliano Taliun SA, Turner C, Efthymiou S, Ibáñez K, Sullivan R, Bibi F, Athanasiou‐Fragkouli A, Bourinaris T, Zhang D, Revesz T, Lashley T, DeTure M, Dickson DW, Josephs KA, Gelpi E, Kovacs GG, Halliday G, Rowe DB, Blair I, Tienari PJ, Suomalainen A, Fox NC, Wood NW, Lees AJ, Haltia MJ, Hardy J, Ryten M, Vandrovcova J, Houlden H. Neuronal intranuclear inclusion disease is genetically heterogeneous. Ann Clin Transl Neurol 2020; 7:1716-1725. [PMID: 32777174 PMCID: PMC7480908 DOI: 10.1002/acn3.51151] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/15/2020] [Indexed: 02/04/2023] Open
Abstract
Neuronal intranuclear inclusion disease (NIID) is a clinically heterogeneous neurodegenerative condition characterized by pathological intranuclear eosinophilic inclusions. A CGG repeat expansion in NOTCH2NLC was recently identified to be associated with NIID in patients of Japanese descent. We screened pathologically confirmed European NIID, cases of neurodegenerative disease with intranuclear inclusions and applied in silico-based screening using whole-genome sequencing data from 20 536 participants in the 100 000 Genomes Project. We identified a single European case harbouring the pathogenic repeat expansion with a distinct haplotype structure. Thus, we propose new diagnostic criteria as European NIID represents a distinct disease entity from East Asian cases.
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Dolzhenko E, Deshpande V, Schlesinger F, Krusche P, Petrovski R, Chen S, Emig-Agius D, Gross A, Narzisi G, Bowman B, Scheffler K, van Vugt JJFA, French C, Sanchis-Juan A, Ibáñez K, Tucci A, Lajoie BR, Veldink JH, Raymond FL, Taft RJ, Bentley DR, Eberle MA. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. Bioinformatics 2020; 35:4754-4756. [PMID: 31134279 PMCID: PMC6853681 DOI: 10.1093/bioinformatics/btz431] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/26/2019] [Accepted: 05/23/2019] [Indexed: 12/16/2022] Open
Abstract
SUMMARY We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. AVAILABILITY AND IMPLEMENTATION ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Tolchin D, Yeager JP, Prasad P, Dorrani N, Russi AS, Martinez-Agosto JA, Haseeb A, Angelozzi M, Santen G, Ruivenkamp C, Mercimek-Andrews S, Depienne C, Kuechler A, Mikat B, Ludecke HJ, Bilan F, Le Guyader G, Gilbert-Dussardier B, Keren B, Heide S, Haye D, Van Esch H, Keldermans L, Ortiz D, Lancaster E, Krantz ID, Krock BL, Pechter KB, Arkader A, Medne L, DeChene ET, Calpena E, Melistaccio G, Wilkie AO, Suri M, Foulds N, Begtrup A, Henderson LB, Forster C, Reed P, McDonald MT, McConkie-Rosell A, Thevenon J, Le Tanno P, Coutton C, Tsai AC, Stewart S, Maver A, Gorazd R, Pichon O, Nizon M, Cogné B, Isidor B, Martin-Coignard D, Stoeva R, Lefebvre V, Le Caignec C, Ambrose J, Bleda M, Boardman-Pretty F, Boissiere J, Boustred C, Caulfield M, Chan G, Craig C, Daugherty L, de Burca A, Devereau A, Elgar G, Foulger R, Fowler T, Furió-Tarí P, Hackett J, Halai D, Holman J, Hubbard T, Kasperaviciute D, Kayikci M, Lahnstein L, Lawson K, Leigh S, Leong I, Lopez F, Maleady-Crowe F, Mason J, McDonagh E, Moutsianas L, Mueller M, Need A, Odhams C, Patch C, Perez-Gil D, Polychronopoulos D, Pullinger J, Rahim T, Rendon A, Rogers T, Ryten M, Savage K, Scott R, Siddiq A, Sieghart A, Smedley D, Smith K, Sosinsky A, Spooner W, Stevens H, Stuckey A, Thomas E, Thompson S, Tregidgo C, Tucci A, Walsh E, Watters S, Welland M, Williams E, Witkowska K, Wood S, Zarowiecki M. De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas. Am J Hum Genet 2020; 106:830-845. [PMID: 32442410 DOI: 10.1016/j.ajhg.2020.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.
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Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E, Thomas E, Scott RH, Baple E, Tucci A, Brittain H, de Burca A, Ibañez K, Kasperaviciute D, Smedley D, Caulfield M, Rendon A, McDonagh EM. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat Genet 2020; 51:1560-1565. [PMID: 31676867 DOI: 10.1038/s41588-019-0528-2] [Citation(s) in RCA: 226] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E, Thomas E, Scott RH, Baple E, Tucci A, Brittain H, de Burca A, Ibañez K, Kasperaviciute D, Smedley D, Caulfield M, Rendon A, McDonagh EM. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat Genet 2019. [PMID: 31676867 DOI: 10.1038/s41588‐019‐0528‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Dolzhenko E, Deshpande V, Schlesinger F, Krusche P, Petrovski R, Chen S, Emig-Agius D, Gross A, Narzisi G, Bowman B, Scheffler K, van Vugt JJFA, French C, Sanchis-Juan A, Ibáñez K, Tucci A, Lajoie BR, Veldink JH, Raymond FL, Taft RJ, Bentley DR, Eberle MA. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. BIOINFORMATICS (OXFORD, ENGLAND) 2019; 35:4754-4756. [PMID: 31134279 DOI: 10.1101/361162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/26/2019] [Accepted: 05/23/2019] [Indexed: 05/25/2023]
Abstract
SUMMARY We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. AVAILABILITY AND IMPLEMENTATION ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Rosati G, Cordio S, Reggiardo G, Aprile G, Butera A, Avallone A, Tucci A, Novello G, Blanco G, Caputo G, Bilancia D, Bordonaro R. Oxaliplatin-based chemotherapy in patients aged at least 75 years with metastatic colorectal cancer: a post-hoc subgroup analysis if three phase II studies. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz155.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Spina M, Merli F, Puccini B, Cavallo F, Cabras M, Fabbri A, Angrilli F, Zilioli V, Marino D, Balzarotti M, Ladetto M, Cox M, Petrucci L, Arcari A, Gini G, Chiappella A, Hohaus S, Musuraca G, Merli M, Sartori R, Nassi L, Tani M, Re F, Flenghi L, Molinari A, Kovalchuk S, Bottelli C, Ferrero S, Dessì D, Cencini E, Pennese E, Marcheselli L, Mammi C, Luminari S, Tucci A. THE ELDERLY PROJECT BY THE FONDAZIONE ITALIANA LINFOMI: A PROSPECTIVE COMPREHENSIVE GERIATRIC ASSESSMENT (CGA) OF 1353 ELDERLY PATIENTS WITH DIFFUSE LARGE B-CELL LYMPHOMA. Hematol Oncol 2019. [DOI: 10.1002/hon.58_2630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Balzarotti M, Ricardi U, Spina M, Monagheddu C, Tucci A, Cavallo F, Zanni M, Arcari A, Rusconi C, Sartori R, Merli F, Re F, Vitolo U, Dessi D, Melis L, Gaidano G, Chiti A, Deidda M, Santoro A, Ciccone G, Chauvie S, Cabras M. PET-DRIVEN RADIOTHERAPY IN PATIENTS WITH LOW RISK DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL): THE DLCL10 MULTICENTER PHASE 2 TRIAL BY FONDAZIONE ITALIANA LINFOMI (FIL). Hematol Oncol 2019. [DOI: 10.1002/hon.62_2630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Federico M, Mannina D, Versari A, Ferrero S, Marcheselli L, Boccomini C, Dondi A, Tucci A, Guerra L, Galimberti S, Cavallo F, Olivieri J, Corradini P, Arcaini L, Chauvie S, Del Giudice I, Rusconi C, Pinto A, Molinari A, Pulsoni A, Merli M, Kovalchuk S, Nassi L, Bolis S, Gattei V, Manni M, Pileri S, Brugiatelli M, Luminari S. RESPONSE ORIENTED MAINTENANCE THERAPY IN ADVANCED FOLLICULAR LYMPHOMA. RESULTS OF THE INTERIM ANALYSIS OF THE FOLL12 TRIAL CONDUCTED BY THE FONDAZIONE ITALIANA LINFOMI. Hematol Oncol 2019. [DOI: 10.1002/hon.110_2629] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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