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3. The enrichment of breakpoints in late-replicating chromatin provides novel insights into chromoanagenesis mechanisms

Author

Chatron, N., Giannuzzi, G., Rollat-Farnier, P., Diguet, F., Porcu, E., Yammine, T., Uguen, K., Bellil, Z., Zillhardt, J. Lauer, Sorlin, A., Ader, F., Afenjar, A., Andrieux, J., Bardel, Claire, Calpena, E., Chantot-Bastaraud, S., Callier, P., Chelloug, N., Chopin, E., Cordier, M., Dubourg, C., Faivre, L., Girard, F., Heide, S., Herenger, Y., Jaillard, S., Keren, B., Knight, S. J. L., Lespinasse, J., Lohmann, L., Marle, N., Maroofian, R., Masurel-Paulet, Alice, Mathieu-Dramard, M., Metay, C., Pagnamenta, A. T., Portnoi, M., Prieur, F., Rio, M., Siffroi, J., Valence, S., Taylor, J. C., Wilkie, A. O. M., Edery, P., Reymond, A., Sanlaville, D., Schluth-Bolard, C., Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospices Civils de Lyon, Departement de Neurologie (HCL), Université de Lausanne = University of Lausanne (UNIL), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire de Diagnostic Génétique [CHU Strasbourg], Université de Strasbourg (UNISTRA)-CHU Strasbourg, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Assistance publique-Hôpitaux de Paris - Espace éthique (AP-HP Espace éthique), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Trousseau [APHP], Service de neurophysiologie clinique (CHRU Lille), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), The Weatherall Institute of Molecular Medicine, University of Oxford, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), CHU Pontchaillou [Rennes], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Strasbourg, The Wellcome Trust Centre for Human Genetics [Oxford], Centre Hospitalier Métropole Savoie [Chambéry], Laboratoire CERBA [Saint Ouen l'Aumône], University College of London [London] (UCL), CHU Amiens-Picardie, CHU Henri Mondor [Créteil], Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), CHU Necker - Enfants Malades [AP-HP], Université Paris 1 Panthéon-Sorbonne (UP1), Chard-Hutchinson, Xavier, Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service d'Hépato-Gastro-Entérologie [CHU Pitié-Salpêtrière], CHU Henri Mondor, Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Centre de recherche en neurosciences de Lyon (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne (UNIL), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Oxford [Oxford], Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020
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4. Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome

Author

van Bon, B W M, Mefford, H C, Menten, B, Koolen, D A, Sharp, A J, Nillesen, W M, Innis, J W, de Ravel, T J L, Mercer, C L, Fichera, M, Stewart, H, Connell, L E, Õunap, K, Lachlan, K, Castle, B, Van der Aa, N, van Ravenswaaij, C, Nobrega, M A, Serra-Juhé, C, Simonic, I, de Leeuw, N, Pfundt, R, Bongers, E M, Baker, C, Finnemore, P, Huang, S, Maloney, V K, Crolla, J A, van Kalmthout, M, Elia, M, Vandeweyer, G, Fryns, J P, Janssens, S, Foulds, N, Reitano, S, Smith, K, Parkel, S, Loeys, B, Woods, C G, Oostra, A, Speleman, F, Pereira, A C, Kurg, A, Willatt, L, Knight, S J L, Vermeesch, J R, Romano, C, Barber, J C, Mortier, G, Pérez-Jurado, L A, Kooy, F, Brunner, H G, Eichler, E E, Kleefstra, T, and de Vries, B B A

Published
2009
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6. Clinical and molecular delineation of the 17q21.31 microdeletion syndrome

Author

Koolen, D A, Sharp, A J, Hurst, J A, Firth, H V, Knight, S J L, Goldenberg, A, Saugier-Veber, P, Pfundt, R, Vissers, L E L M, Destrée, A, Grisart, B, Rooms, L, Van der Aa, N, Field, M, Hackett, A, Bell, K, Nowaczyk, M J M, Mancini, G M S, Poddighe, P J, Schwartz, C E, Rossi, E, De Gregori, M, Antonacci-Fulton, L L, II, McLellan M D, Garrett, J M, Wiechert, M A, Miner, T L, Crosby, S, Ciccone, R, Willatt, L, Rauch, A, Zenker, M, Aradhya, S, Manning, M A, Strom, T M, Wagenstaller, J, Krepischi-Santos, A C, Vianna-Morgante, A M, Rosenberg, C, Price, S M, Stewart, H, Shaw-Smith, C, Brunner, H G, Wilkie, A O M, Veltman, J A, Zuffardi, O, Eichler, E E, and de Vries, B B A

Published
2008
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9. FRAXE and mental retardation

Author

Mulley, J. C., Yu, S., Loesch, D. Z., Hay, D. A., Donnelly, A., Gedeon, A. K., Carbonell, P., Lopez, I., Glover, G., Gabarron, I., Yu, P. W. L., Baker, E., Haan, E. A., Hockey, A., Knight, S. J. L., Davies, K. E., Richards, R. I., and Sutherland, G. R.

Published
1995

10. Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups.

Author

Burns, A, Alsolami, R, Becq, J, Stamatopoulos, Basile, Timbs, Adele, Bruce, D.W, Robbe, P, Vavoulis, Dimitris D.V., Clifford, R, Cabes, Maite, Dreau, Hélène, Taylor, J Andrew, Knight, S J L, Mansson, R, Bentley, David, Beekman, Robert, Martín-Subero, J I, Campo, E, Houlston, R S, Ridout, K E, Schuh, A C, Burns, A, Alsolami, R, Becq, J, Stamatopoulos, Basile, Timbs, Adele, Bruce, D.W, Robbe, P, Vavoulis, Dimitris D.V., Clifford, R, Cabes, Maite, Dreau, Hélène, Taylor, J Andrew, Knight, S J L, Mansson, R, Bentley, David, Beekman, Robert, Martín-Subero, J I, Campo, E, Houlston, R S, Ridout, K E, and Schuh, A C

Abstract

This corrects the article DOI: 10.1038/leu.2017.177., info:eu-repo/semantics/published

Published
2017

11. Assignment of Emery-Dreifuss muscular dystrophy to the distal region of Xq28: the results of a collaborative study

Author

Gian Giacomo Consalez, Thomas, N. S. T., Stayton, C. L., Knight, S. J. L., Johnson, M., Hopkins, L. C., Harper, P. S., Elsas, L. J., and Warren, S. T.

Subjects
congenital, hereditary, and neonatal diseases and abnormalities
Abstract

Emery-Dreifuss muscular dystrophy (EDMD) is an X-linked humeroperoneal dystrophy associated with cardiomyopathy that is distinct from the Duchenne and Becker forms of X-linked muscular dystrophy. Linkage analysis has assigned EDMD to the terminal region of the human X chromosome long arm. We report here further linkage analysis in two multigenerational EDMD families using seven Xq28 marker loci. Cumulative lod scores suggest that EDMD is approximately 2 cM from DXS52 (lod = 15.67) and very close to the factor VIII (F8C) and the red/green color pigment (R/GCP) loci, with respective lod scores of 9.62 and 10.77, without a single recombinant. Several recombinations between EDMD and three proximal Xq28 markers suggest that the EDMD gene is located in distal Xq28. Multipoint linkage analysis indicates that the odds are 2,000:1 that EDMD lies distal to DXS305. These data substantially refine the ability to perform accurate carrier detection, prenatal diagnosis, and the presymptomatic diagnosis of at-risk males for EDMD by linkage analysis. The positioning of the EDMD locus close to the loci for F8C and R/GCP will assist in future efforts to identify and isolate the disease gene.

Published
2016

12. A study of FRAXE in mentally retarded individuals referred for fragile X syndrome (FRAXA) testing in the United Kingdom

Author

Knight, S. J. L., Ritchie, R. J., Lisa Chakrabarti, Cross, G., Taylor, G. R., Mueller, R. F., Hurst, J., Paterson, J., Yates, J. R. W., Dow, D. J., and Davies, K. E.

Subjects
congenital, hereditary, and neonatal diseases and abnormalities
Abstract

The folate-sensitive fragile site FRAXE is located in proximal Xq28 of the human X chromosome and lies approximately 600 kb distal to the fragile X syndrome (FRAXA) fragile site at Xq27.3. The cytogenetic expression of FRAXE is thought to be associated with mental handicap, but this is usually mild compared to that of the more common fragile X syndrome that is associated with the expression of the FRAXA fragile site. The exact incidence of FRAXE mental retardation is uncertain. We describe here the results of a U.K. survey designed to assess the frequency of FRAXE in a population of individuals referred for fragile X syndrome testing and found to be negative for expansion events at the FRAXA locus. No FRAXE expansion events were found in 362 cytogenetically negative males studied, and one expansion event was identified in a sample of 534 males for whom cytogenetic analyses were either unrecorded or not performed. Further FRAXE expansion events were detected in two related females known to be cytogenetically positive for a fragile site in Xq27.3-28. To gain insight into the FRAXE phenotype, the clinical details of the identified FRAXE male plus three other FRAXE individuals identified through previous referrals for fragile X syndrome testing are presented. For the population studied, we conclude that FRAXE mental retardation is a relatively rare but significant form of mental retardation for which genetic diagnosis would be appropriate.

Published
2016

13. Erratum: Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups

Author

Burns, A, primary, Alsolami, R, additional, Becq, J, additional, Stamatopoulos, B, additional, Timbs, A, additional, Bruce, D, additional, Robbe, P, additional, Vavoulis, D, additional, Clifford, R, additional, Cabes, M, additional, Dreau, H, additional, Taylor, J, additional, Knight, S J L, additional, Mansson, R, additional, Bentley, D, additional, Beekman, R, additional, Martín-Subero, J I, additional, Campo, E, additional, Houlston, R S, additional, Ridout, K E, additional, and Schuh, A, additional

Published
2017
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14. Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmut and IgHVunmut subgroups

Author

Burns, A, primary, Alsolami, R, additional, Becq, J, additional, Stamatopoulos, B, additional, Timbs, A, additional, Bruce, D, additional, Robbe, P, additional, Vavoulis, D, additional, Clifford, R, additional, Cabes, M, additional, Dreau, H, additional, Taylor, J, additional, Knight, S J L, additional, Mansson, R, additional, Bentley, D, additional, Beekman, R, additional, Martín-Subero, J I, additional, Campo, E, additional, Houlston, R S, additional, Ridout, K E, additional, and Schuh, A, additional

Published
2017
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16. Clinical studies on submicroscopic subtelomeric rearrangements: a checklist

Author

Vries, B B A de, White, S M., Knight, S J L, Regan, R, Homfray, T, Young, I D., Super, M, McKeown, C, Splitt, M, Quarrell, O W J, Trainer, A H., Niermeijer, M F., Malcolm, S, Flint, J, Hurst, J A., and Winter, R M.

Subjects
Mental retardation -- Causes of -- Physiological aspects, Chromosome deletion -- Physiological aspects, Health
Abstract

Abstract Background--Submicroscopic subtelomeric chromosome defects have been found in 7.4% of children with moderate to severe mental retardation and in 0.5% of children with mild retardation. Effective clinical preselection is [...]

Published
2001

17. Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmutand IgHVunmutsubgroups

Author

Burns, A, Alsolami, R, Becq, J, Stamatopoulos, B, Timbs, A, Bruce, D, Robbe, P, Vavoulis, D, Clifford, R, Cabes, M, Dreau, H, Taylor, J, Knight, S J L, Mansson, R, Bentley, D, Beekman, R, Martín-Subero, J I, Campo, E, Houlston, R S, Ridout, K E, and Schuh, A

Abstract

Chronic lymphocytic leukaemia (CLL) consists of two biologically and clinically distinct subtypes defined by the abundance of somatic hypermutation (SHM) affecting the Ig variable heavy-chain locus (IgHV). The molecular mechanisms underlying these subtypes are incompletely understood. Here, we present a comprehensive whole-genome sequencing analysis of somatically acquired genetic events from 46 CLL patients, including a systematic comparison of coding and non-coding single-nucleotide variants, copy number variants and structural variants, regions of kataegis and mutation signatures between IgHVmutand IgHVunmutsubtypes. We demonstrate that one-quarter of non-coding mutations in regions of kataegis outside the Ig loci are located in genes relevant to CLL. We show that non-coding mutations in ATM may negatively impact on ATM expression and find non-coding and regulatory region mutations in TCL1A, and in IgHVunmutCLL in IKZF3, SAMHD1,PAX5 and BIRC3. Finally, we show that IgHVunmutCLL is dominated by coding mutations in driver genes and an aging signature, whereas IgHVmutCLL has a high incidence of promoter and enhancer mutations caused by aberrant activation-induced cytidine deaminase activity. Taken together, our data support the hypothesis that differences in clinical outcome and biological characteristics between the two subgroups might reflect differences in mutation distribution, incidence and distinct underlying mutagenic mechanisms.

Published
2018
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18. Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant

Author

UCL, Hannes, F. D., Sharp, A. J., Mefford, H. C., de Ravel, Thomy, Ruivenkamp, C. A., Breuning, M. H., Fryns, J-P, Devriendt, Koenraad, Van Buggenhout, Griet, Vogels, A., Stewart, H., Hennekam, R. C., Cooper, G. M., Regan, R., Knight, S. J. L., Eichler, E. E., Vermeesch, J. R., UCL, Hannes, F. D., Sharp, A. J., Mefford, H. C., de Ravel, Thomy, Ruivenkamp, C. A., Breuning, M. H., Fryns, J-P, Devriendt, Koenraad, Van Buggenhout, Griet, Vogels, A., Stewart, H., Hennekam, R. C., Cooper, G. M., Regan, R., Knight, S. J. L., Eichler, E. E., and Vermeesch, J. R.

Abstract

Background: Genomic disorders are often caused by non-allelic homologous recombination between segmental duplications. Chromosome 16 is especially rich in a chromosome-specific low copy repeat, termed LCR16. Methods and Results: A bacterial artificial chromosome (BAC) array comparative genome hybridisation (CGH) screen of 1027 patients with mental retardation and/or multiple congenital anomalies (MR/MCA) was performed. The BAC array CGH screen identified five patients with deletions and five with apparently reciprocal duplications of 16p13 covering 1.65 Mb, including 15 RefSeq genes. In addition, three atypical rearrangements overlapping or flanking this region were found. Fine mapping by high-resolution oligonucleotide arrays suggests that these deletions and duplications result from non-allelic homologous recombination (NAHR) between distinct LCR16 subunits with >99% sequence identity. Deletions and duplications were either de novo or inherited from unaffected parents. To determine whether these imbalances are associated with the MR/MCA phenotype or whether they might be benign variants, a population of 2014 normal controls was screened. The absence of deletions in the control population showed that 16p13.11 deletions are significantly associated with MR/MCA (p = 0.0048). Despite phenotypic variability, common features were identified: three patients with deletions presented with MR, microcephaly and epilepsy (two of these had also short stature), and two other deletion carriers ascertained prenatally presented with cleft lip and midline defects. In contrast to its previous association with autism, the duplication seems to be a common variant in the population (5/1682, 0.29%). Conclusion: These findings indicate that deletions inherited from clinically normal parents are likely to be causal for the patients' phenotype whereas the role of duplications (de novo or inherited) in the phenotype remains uncertain. This difference in knowledge regarding the clinical rele

Published
2009

19. A de novo frameshift in HNRNPK causing a Kabuki-like syndrome with nodular heterotopia.

Author

Lange, L., Pagnamenta, A. T., Lise, S., Clasper, S., Stewart, H., Akha, E. S., Quaghebeur, G., Knight, S. J. L., Keays, D. A., Taylor, J. C., and Kini, U.

Subjects
FRAMESHIFT mutation, PROTEIN genetics, NUCLEOPROTEINS, KABUKI syndrome, MULTIPLE human abnormalities, CARRIER proteins
Abstract

Kabuki syndrome is a heterogeneous condition characterized by distinctive facial features, intellectual disability, growth retardation, skeletal abnormalities and a range of organ malformations. Although at least two major causative genes have been identified, these do not explain all cases. Here we describe a patient with a complex Kabuki-like syndrome that included nodular heterotopia, in whom testing for several single-gene disorders had proved negative. Exome sequencing uncovered a de novo c.931_932insTT variant in HNRNPK (heterogeneous nuclear ribonucleoprotein K). Although this variant was identified in March 2012, its clinical relevance could only be confirmed following the August 2015 publication of two cases with HNRNPK mutations and an overlapping phenotype that included intellectual disability, distinctive facial dysmorphism and skeletal/connective tissue abnormalities. Whilst we had attempted (unsuccessfully) to identify additional cases through existing collaborators, the two published cases were 'matched' using GeneMatcher, a web-based tool for connecting researchers and clinicians working on identical genes. Our report therefore exemplifies the importance of such online tools in clinical genetics research and the benefits of periodically reviewing cases with variants of unproven significance. Our study also suggests that loss of function variants in HNRNPK should be considered as a molecular basis for patients with Kabuki-like syndrome. [ABSTRACT FROM AUTHOR]

Published
2016
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20. Expansion and methylation status at FRAXE can be detected on EcoRI blots used for FRAXA diagnosis: analysis of four FRAXE families with mild mental retardation in males

Author

Biancalana, V., Taine, L., Bouix, J. -C, Finck, S., Chauvin, A., Verneuil, H., Knight, S. J. L., Stoll, C., Didier Lacombe, and Mandel, J. -L

Subjects
Adult, Male, congenital, hereditary, and neonatal diseases and abnormalities, Adolescent, Chromosome Fragile Sites, Chromosome Fragility, Infant, Newborn, Infant, Nuclear Proteins, Proteins, RNA-Binding Proteins, Nerve Tissue Proteins, Deoxyribonuclease EcoRI, Pedigree, Blotting, Southern, Fragile X Mental Retardation Protein, Child, Preschool, Fragile X Syndrome, Intellectual Disability, Trans-Activators, Humans, Female, Child, Deoxyribonucleases, Type II Site-Specific, Research Article
Abstract

The original test for the analysis of the CCG expansion at the FRAXE locus involves Southern blot analysis of HindIII digests. We show that, by using a different probe, the FRAXE mutation can be detected easily on the same EcoRI or EagI+EcoRI blots as are used for detection of FRAXA. Unexpectedly, we found that both the expansion and methylation status can be determined on a single EcoRI digest, because of the presence of a methylation-sensitive EcoRI site very close to the CCG repeat. We thus detected in a series of mentally retarded individuals previously tested for FRAXA expansion a FRAXE proband who led to the identification of a large sibship (7 of 10 children carrying a mutation). We also show that two fragile X families without FRAXA mutation that previously have been described by Oberlé et al. have the FRAXE expansion. In another family also ascertained initially by cytogenetic finding of a fragile X site, we performed the combined cytogenetic and molecular prenatal diagnosis of a mutated male fetus. All nine males (>3 years old) in whom we found a methylated mutation had mild mental retardation. Our results suggest that the threshold of repeat length for abnormal methylation and fragile-site expression may be smaller at FRAXE than at FRAXA.

Published
1996

21. Quantification of subclonal distributions of recurrent genomic aberrations in paired pre-treatment and relapse samples from patients with B-cell chronic lymphocytic leukemia

Author

Knight, S J L, primary, Yau, C, additional, Clifford, R, additional, Timbs, A T, additional, Sadighi Akha, E, additional, Dréau, H M, additional, Burns, A, additional, Ciria, C, additional, Oscier, D G, additional, Pettitt, A R, additional, Dutton, S, additional, Holmes, C C, additional, Taylor, J, additional, Cazier, J-B, additional, and Schuh, A, additional

Published
2012
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22. Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant

Author

Hannes, F D, primary, Sharp, A J, additional, Mefford, H C, additional, de Ravel, T, additional, Ruivenkamp, C A, additional, Breuning, M H, additional, Fryns, J-P, additional, Devriendt, K, additional, Van Buggenhout, G, additional, Vogels, A, additional, Stewart, H, additional, Hennekam, R C, additional, Cooper, G M, additional, Regan, R, additional, Knight, S J L, additional, Eichler, E E, additional, and Vermeesch, J R, additional

Published
2008
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27. Idiopathic learning disability and genome imbalance.

Author

Knight, S. J. L. and Regan, R.

Subjects
*LEARNING disabilities, *CHROMOSOME abnormalities, *GENETIC polymorphisms, *COGNITION disorders, *GENOTYPE-environment interaction, *PHENOTYPES
Abstract

Learning disability (LD) is a very common, lifelong and disabling condition, affecting about 3% of the population. Despite this, it is only over the past 10–15 years that major progress has been made towards understanding the origins of LD. In particular, genetics driven advances in technology have led to the unequivocal demonstration of the importance of genome imbalance in the aetiology of idiopathic LD (ILD). In this review we provide an overview of these advances, discussing technologies such as multi-telomere FISH and array CGH that have already emerged as well as new approaches that show diagnostic potential for the future. The advances to date have highlighted new considerations such as copy number polymorphisms (CNPs) that can complicate the interpretation of genome imbalance and its relevance to ILD. More importantly though, they have provided a remarkable ∼15–20% improvement in diagnostic capability as well as facilitating genotype/phenotype correlations and providing new avenues for the identification and understanding of genes involved in neurocognitive function. Copyright © 2006 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Published
2006
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28. Trinucleotide repeat amplification and hypermethylation of a CpG island in FRAXE mental retardation.

Author

Knight, S. J. L. and Flannery, A. V.

Subjects
*CHROMOSOMES, *MOLECULAR biology
Abstract

Presents the cloning of the FRAXE site to elucidate the mechanism of chromosome fragility and determine whether the expression of FRAXE leads to disruption of gene expression causing mental retardation. Amplifications of a GCC repeat adjacent to a CpG island in Xq28 of human X chromosome; FRAXA locus; Comparison with fragile X syndrome.

Published
1993
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29. Correction: Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmutand IgHVunmutsubgroups

Author

Burns, A, Alsolami, R, Becq, J, Stamatopoulos, B, Timbs, A, Bruce, D, Robbe, P, Vavoulis, D, Clifford, R, Cabes, M, Dreau, H, Taylor, J, Knight, S J L, Mansson, R, Bentley, D, Beekman, R, Martín-Subero, J I, Campo, E, Houlston, R S, Ridout, K E, and Schuh, A

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2019
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30. Erratum: Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHVmutand IgHVunmutsubgroups

Author

Burns, A, Alsolami, R, Becq, J, Stamatopoulos, B, Timbs, A, Bruce, D, Robbe, P, Vavoulis, D, Clifford, R, Cabes, M, Dreau, H, Taylor, J, Knight, S J L, Mansson, R, Bentley, D, Beekman, R, Martín-Subero, J I, Campo, E, Houlston, R S, Ridout, K E, and Schuh, A

Abstract

Correction to: Leukemia (2018) 32, 332–342; doi: 10.1038/leu.2017.177; published online 27 June 2017 Since the publication of this article, the authors have identified an omission in their paper, namely that two contributing authors were not included in the author list: B Stamatopoulos1, R Clifford2

Published
2018
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31. SW-ARRAY: a dynamic programming solution for the identification of copy number changes in genomic DNA using array comparative genome hybridisation data.

Author

Price, Tom, Regan, R., Mall, R., Hedman, A., Honey, B., Daniels, R. J., Smith, L., Greenfield, A., Tiganescu, A., Buckle, V., Ayyub, H., Ragoussis, J., Higgs, D. R., Flint, J., and Knight, S. J. L.

Subjects
GENOMICS
Abstract

Presents an abstract of the article "SW-ARRAY: A Dynamic Programming Solution for the Identification of Copy Number Changes in Genomic DNA Using Array Comparative Genome Hybridization Data," by Tom Price, R. Regan, R. Mott, A. Hedman, B. Honey, R. J. Daniels, L. Smith, A. Greenfield, A. Tiganescu, V. Buckle, H. Ayyub, J. Ragoussis, D. R. Higgins, J. Flint and S. J. L. Knight.

Published
2005

32. Whole Genome Microarrays for the Detection of Cryptic Genomic Imbalances in Idiopathic Learning Disability.

Author

Regan, Regina, Smith, K., Crocker, M., Hedman, A., Honey, B., Hurst, J., Taylor, J., Flint, J., and Knight, S. J. L.

Subjects
COGNITION disorders
Abstract

Presents an abstract of the article " Whole Genome Microarrays for the Detection of Cryptic Genomic Imbalances in Idiopathic Learning Disability," by Regina Regan, K. Smith, M. Crocker, A. Hedman, B. Honey, J. Hurst, J. Taylor, J. Flint, and S. J. L. Knight.

Published
2005

33. Characterization of a recurrent 15q24 microdeletion syndrome

Author

Stefania Gimelli, Raoul C.M. Hennekam, Regina Regan, Antonietta Coppola, Giorgio Gimelli, Joris A. Veltman, Orsetta Zuffardi, Nine V A M Knoers, Samantha J. L. Knight, Bert B.A. de Vries, Andrew J. Sharp, Evan E. Eichler, Peggy S. Eis, Pasquale Striano, Han G. Brunner, Sue Price, Rebecca R. Selzer, Sharp, A. J., Selzer, R. R., Veltman, J. A., Gimelli, S., Gimelli, G., Striano, P., Coppola, A., Regan, R., Price, S. M., Knoers, N. V., Eis, P. S., Brunner, H. G., Hennekam, R. C., Knight, S. J. L., de Vries, B. B. A., Zuffardi, O., Eichler, E. E., Amsterdam Neuroscience, Amsterdam Public Health, and Paediatric Genetics

Subjects
Adult, Male, Microcephaly, Health aging / healthy living [IGMD 5], Genetics and epigenetic pathways of disease [NCMLS 6], Adolescent, DNA Mutational Analysis, Molecular Sequence Data, Membrane transport and intracellular motility [NCMLS 5], Biology, Chromosomes, Genomic disorders and inherited multi-system disorders [IGMD 3], Translational research [ONCOL 3], medicine, Humans, Abnormalities, Multiple, genetics, Hypertelorism, Molecular Biology, Genetics (clinical), Segmental duplication, Renal disorder [IGMD 9], Molecular diagnosis, prognosis and monitoring [UMCN 1.2], Oligonucleotide Array Sequence Analysis, Genetics, Chromosomes, Human, Pair 15, Base Sequence, Sotos syndrome, Breakpoint, Pair 15, Chromosome, Chromosome Breakage, General Medicine, Anatomy, Syndrome, medicine.disease, Abnormalities, Multiple, genetics, Adolescent, Adult, Base Sequence, Chromosome Breakage, Chromosome Deletion, Chromosomes, Human, genetics, DNA Mutational Analysis, Humans, Male, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Syndrome, Chromosome breakage, medicine.symptom, Chromosome Deletion, Haploinsufficiency, Functional Neurogenomics [DCN 2]
Abstract

Contains fulltext : 53175.pdf (Publisher’s version ) (Closed access) We describe multiple individuals with mental retardation and overlapping de novo submicroscopic deletions of 15q24 (1.7-3.9 Mb in size). High-resolution analysis showed that in three patients both proximal and distal breakpoints co-localized to highly identical segmental duplications (>51 kb in length, > 94% identity), suggesting non-allelic homologous recombination as the likely mechanism of origin. Sequencing studies in a fourth individual provided base pair resolution and showed that both breakpoints in this case were located in unique sequence. Despite the differences in the size and location of the deletions, all four individuals share several major features (growth retardation, microcephaly, digital abnormalities, hypospadias and loose connective tissue) and resemble one another facially (high anterior hair line, broad medial eyebrows, hypertelorism, downslanted palpebral fissures, broad nasal base, long smooth philtrum and full lower lip), indicating that this represents a novel syndrome caused by haploinsufficiency of one or more dosage-sensitive genes in the minimal deletion region. Our results define microdeletion of 15q24 as a novel recurrent genomic disorder.

Published
2007

34. Whole-genome sequencing of chronic lymphocytic leukaemia reveals distinct differences in the mutational landscape between IgHV mut and IgHV unmut subgroups.

Author

Burns A, Alsolami R, Becq J, Stamatopoulos B, Timbs A, Bruce D, Robbe P, Vavoulis D, Clifford R, Cabes M, Dreau H, Taylor J, Knight SJL, Mansson R, Bentley D, Beekman R, Martín-Subero JI, Campo E, Houlston RS, Ridout KE, and Schuh A

Abstract

This corrects the article DOI: 10.1038/leu.2017.177.

Published
2018
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35. Sixteen New Cases Contributing to the Characterization of Patients with Distal 22q11.2 Microduplications.

Author

Wincent J, Bruno DL, van Bon BW, Bremer A, Stewart H, Bongers EM, Ockeloen CW, Willemsen MH, Keays DD, Baird G, Newbury DF, Kleefstra T, Marcelis C, Kini U, Stark Z, Savarirayan R, Sheffield LJ, Zuffardi O, Slater HR, de Vries BB, Knight SJ, Anderlid BM, and Schoumans J

Abstract

The chromosome region 22q11.2 has long been recognized to be susceptible to genomic rearrangement. More recently, this genomic instability has been shown to extend distally (involving LCR22E-H) to the commonly deleted/duplicated region. To date, 21 index cases with 'distal' 22q11.2 duplications have been reported. We report on the clinical and molecular characterization of 16 individuals with distal 22q11.2 duplications identified by DNA microarray analysis. Two of the individuals have been partly described previously. The clinical phenotype varied among the patients in this study, although the majority displayed various degrees of developmental delay and speech disturbances. Other clinical features included behavioral problems, hypotonia, and dysmorphic facial features. Notably, none of the patients was diagnosed with a congenital heart defect. We found a high degree of inherited duplications. Additional copy number changes of unclear clinical significance were identified in 5 of our patients, and it is possible that these may contribute to the phenotypic expression in these patients as has been suggested recently in a 2-hit 'digenic' model for 16p12.1 deletions. The varied phenotypic expression and incomplete penetrance observed for distal 22q11.2 duplications makes it exceedingly difficult to ascribe pathogenicity for these duplications. Given the observed enrichment of the duplication in patient samples versus healthy controls, it is likely that distal 22q11.2 duplications represent a susceptibility/risk locus for speech and mild developmental delay.

Published
2010
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