D N Cooper

Summary

Affiliation: Cardiff University
Country: UK

Publications

  1. ncbi Functional analysis of polymorphic variation within the promoter and 5' untranslated region of the neurofibromatosis type 1 (NF1) gene
    Martin P Horan
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    Am J Med Genet A 131:227-31. 2004
  2. pmc Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16
    Violaine Goidts
    Department of Human Genetics, University of Ulm, 89081 Ulm, Germany
    Genome Res 15:1232-42. 2005
  3. doi The Human Gene Mutation Database (HGMD) and its exploitation in the study of mutational mechanisms
    David N Cooper
    Cardiff University, Cardiff, United Kingdom
    Curr Protoc Bioinformatics . 2006
  4. pmc Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF144XN, UK
    Hum Genomics 4:406-10. 2010
  5. pmc Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
    Hum Genet 132:1077-130. 2013
  6. pmc New clinical and molecular insights on Barth syndrome
    Lorenzo Ferri
    Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence and Paediatric Neurology Unit and Laboratories, Meyer Children s Hospital, Viale Pieraccini n, 24, 50139 Florence, Italy
    Orphanet J Rare Dis 8:27. 2013
  7. pmc Delineation of the clinical phenotype associated with non-mosaic type-2 NF1 deletions: two case reports
    Julia Vogt
    Institute of Human Genetics, University of Ulm, Ulm, Germany
    J Med Case Rep 5:577. 2011
  8. pmc Genetic tests obtainable through pharmacies: the good, the bad, and the ugly
    George P Patrinos
    Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, 26504, Greece
    Hum Genomics 7:17. 2013
  9. pmc Screening in silico predicted remotely acting NF1 gene regulatory elements for mutations in patients with neurofibromatosis type 1
    Stephen E Hamby
    School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
    Hum Genomics 7:18. 2013
  10. pmc An emerging role for microRNAs in NF1 tumorigenesis
    Ashni Sedani
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
    Hum Genomics 6:23. 2012

Detail Information

Publications102 found, 100 shown here

  1. ncbi Functional analysis of polymorphic variation within the promoter and 5' untranslated region of the neurofibromatosis type 1 (NF1) gene
    Martin P Horan
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    Am J Med Genet A 131:227-31. 2004
    ..The del14 variant demonstrated allele-specific protein binding without altered reporter gene expression and the G + 462C allele showed slightly decreased reporter gene expression...
  2. pmc Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16
    Violaine Goidts
    Department of Human Genetics, University of Ulm, 89081 Ulm, Germany
    Genome Res 15:1232-42. 2005
    ..Thus, the most parsimonious interpretation is that the gorilla and chimpanzee homologs exhibit similar but nonidentical derived pericentric inversions, whereas HSA 16 represents the ancestral form among hominoids...
  3. doi The Human Gene Mutation Database (HGMD) and its exploitation in the study of mutational mechanisms
    David N Cooper
    Cardiff University, Cardiff, United Kingdom
    Curr Protoc Bioinformatics . 2006
    ....
  4. pmc Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF144XN, UK
    Hum Genomics 4:406-10. 2010
    ..We therefore estimate that ∼5 per cent of missense/nonsense mutations causing human inherited disease may be attributable to methylation-mediated deamination of 5mC within a CpHpG context...
  5. pmc Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
    Hum Genet 132:1077-130. 2013
    ....
  6. pmc New clinical and molecular insights on Barth syndrome
    Lorenzo Ferri
    Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence and Paediatric Neurology Unit and Laboratories, Meyer Children s Hospital, Viale Pieraccini n, 24, 50139 Florence, Italy
    Orphanet J Rare Dis 8:27. 2013
    ..It is caused by mutations in the TAZ gene encoding tafazzin, a protein involved in the metabolism of cardiolipin, a mitochondrial-specific phospholipid involved in mitochondrial energy production...
  7. pmc Delineation of the clinical phenotype associated with non-mosaic type-2 NF1 deletions: two case reports
    Julia Vogt
    Institute of Human Genetics, University of Ulm, Ulm, Germany
    J Med Case Rep 5:577. 2011
    ..abstract:..
  8. pmc Genetic tests obtainable through pharmacies: the good, the bad, and the ugly
    George P Patrinos
    Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, 26504, Greece
    Hum Genomics 7:17. 2013
    ....
  9. pmc Screening in silico predicted remotely acting NF1 gene regulatory elements for mutations in patients with neurofibromatosis type 1
    Stephen E Hamby
    School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
    Hum Genomics 7:18. 2013
    ....
  10. pmc An emerging role for microRNAs in NF1 tumorigenesis
    Ashni Sedani
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
    Hum Genomics 6:23. 2012
    ....
  11. pmc Genotype-phenotype associations in neurofibromatosis type 1 (NF1): an increased risk of tumor complications in patients with NF1 splice-site mutations?
    Adila Alkindy
    Clinical Genetics Department, Sultan Qaboos University Hospital, Al Khod, Muscat 123, Sultanate of Oman
    Hum Genomics 6:12. 2012
    ..A significant influence of gender was also observed on the number of subcutaneous neurofibromas (females, p = 0.009) and preschool learning difficulties (females, p = 0.022)...
  12. pmc An isolated case of lissencephaly caused by the insertion of a mitochondrial genome-derived DNA sequence into the 5' untranslated region of the PAFAH1B1 (LIS1) gene
    David S Millar
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF144XN, UK
    Hum Genomics 4:384-93. 2010
    ....
  13. pmc 'Sifting the significance from the data' - the impact of high-throughput genomic technologies on human genetics and health care
    Angus J Clarke
    Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, Wales CF14 4XN, UK
    Hum Genomics 6:11. 2012
    ....
  14. pmc Molecular heterogeneity in malignant peripheral nerve sheath tumors associated with neurofibromatosis type 1
    Laura Thomas
    Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
    Hum Genomics 6:18. 2012
    ....
  15. pmc Non-coding RNA ANRIL and the number of plexiform neurofibromas in patients with NF1 microdeletions
    Tanja Mußotter
    Institute of Human Genetics, University of Ulm, Albert Einstein Allee, Ulm, Germany
    BMC Med Genet 13:98. 2012
    ..ANRIL directly binds to the SUZ12 protein, an essential component of polycomb repressive complex 2, and is required for SUZ12 occupancy of the CDKN2A/CDKN2B tumour suppressor genes as well as for their epigenetic silencing...
  16. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
    ....
  17. pmc Molecular genetic analysis of the PLP1 gene in 38 families with PLP1-related disorders: identification and functional characterization of 11 novel PLP1 mutations
    Serena Grossi
    SSD Lab, Diagnosi Pre Postnatale Malattie Metaboliche, IRCCS G, Gaslini, Genova, Italy
    Orphanet J Rare Dis 6:40. 2011
    ..PLP1 mutations range from gene duplications of variable size found in 60-70% of patients to intragenic lesions present in 15-20% of patients...
  18. pmc Is the NIH policy for sharing GWAS data running the risk of being counterproductive?
    Michael Krawczak
    Institut für Medizinische Informatik und Statistik, Christian Albrechts Universitat zu Kiel, Arnold Heller Straße 3, Haus 31, 2105 Kiel, Germany
    Investig Genet 1:3. 2010
    ..Because this policy could adversely affect future transnational scientific collaborations, we explore some of its likely consequences and suggest possible courses of remedial action wherever feasible...
  19. pmc The Human Gene Mutation Database: 2008 update
    Peter D Stenson
    Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
    Genome Med 1:13. 2009
    ..This cooperative agreement covers the exclusive worldwide marketing of the most up-to-date (subscription) version of HGMD, HGMD Professional, to academic, clinical and commercial users...
  20. pmc Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes
    Hui Huang
    Department of Bioinformatics, Genome Therapeutics Corporation, Waltham, MA 02453, USA
    Genome Biol 5:R47. 2004
    ..Here, we investigate whether human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change...
  21. pmc Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution
    Claus Kemkemer
    Institute of Human Genetics, University of Ulm, Ulm, Germany
    BMC Evol Biol 9:84. 2009
    ..Gene synteny analysis (E-painting) not only greatly reduces the complexity of comparative genome sequence analysis but also extends its evolutionary reach...
  22. pmc Exploring the potential relevance of human-specific genes to complex disease
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
    Hum Genomics 5:99-107. 2011
    ....
  23. ncbi Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
    Hum Mutat 31:631-55. 2010
    ....
  24. pmc On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
    Hum Mutat 32:1075-99. 2011
    ..e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease...
  25. ncbi Human growth hormone I gene expression is influenced in a complex haplotype-dependent fashion by polymorphic variation in both the proximal promoter and the locus control region
    David N Cooper
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    J Pediatr Endocrinol Metab 15:1429. 2002
  26. ncbi Inherited factor X deficiency: molecular genetics and pathophysiology
    D N Cooper
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    Thromb Haemost 78:161-72. 1997
  27. doi Chromosomal distribution of disease genes in the human genome
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
    Genet Test Mol Biomarkers 14:441-6. 2010
    ....
  28. ncbi Human gene mutation in pathology and evolution
    D N Cooper
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    J Inherit Metab Dis 25:157-82. 2002
    ....
  29. pmc The human gene mutation database
    D N Cooper
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF4 4XN, UK
    Nucleic Acids Res 26:285-7. 1998
    ..Being both comprehensive and fully integrated into the existing bioinformatics structures relevant to human genetics, HGMD has established itself as the central core database of inherited human gene mutations...
  30. ncbi Proposed guidelines for papers describing DNA polymorphism-disease associations
    David N Cooper
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    Hum Genet 110:207-8. 2002
    ..Guidelines are therefore proposed that are intended to promote the publication of scientifically meaningful disease association studies through the introduction of sensible methodological standards...
  31. ncbi Molecular analysis of the genotype-phenotype relationship in factor VII deficiency
    D S Millar
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, UK
    Hum Genet 107:327-42. 2000
    ..This suggests that the presence of these alleles may have served to increase the likelihood of pathological F7 gene lesions coming to clinical attention...
  32. ncbi Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends
    Nadia Chuzhanova
    Department of Computer Science, Cardiff University, Cardiff, UK
    Hum Mutat 22:245-51. 2003
    ..These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions...
  33. ncbi Long-read sequence analysis of the MECP2 gene in Rett syndrome patients: correlation of disease severity with mutation type and location
    J P Cheadle
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, CF14 4XN, UK
    Hum Mol Genet 9:1119-29. 2000
    ..0023), and milder disease was associated with late as compared with early truncating mutations ( P = 0.0190)...
  34. ncbi Molecular genetic analysis of severe protein C deficiency
    D S Millar
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, UK
    Hum Genet 106:646-53. 2000
    ....
  35. pmc Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes
    M Krawczak
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff CF4 4XN, United Kingdom
    Am J Hum Genet 63:474-88. 1998
    ....
  36. ncbi Evolution of the proximal promoter region of the mammalian growth hormone gene
    M Krawczak
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park Cardiff CF4 4XN, UK
    Gene 237:143-51. 1999
    ....
  37. ncbi Molecular analysis of the genotype-phenotype relationship in factor X deficiency
    D S Millar
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, UK
    Hum Genet 106:249-57. 2000
    ..By contrast, no such relationship could be discerned between laboratory phenotype and polymorphism genotype...
  38. ncbi Human gene mutation database-a biomedical information and research resource
    M Krawczak
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, UK
    Hum Mutat 15:45-51. 2000
    ....
  39. ncbi Changes in primary DNA sequence complexity influence the phenotypic consequences of mutations in human gene regulatory regions
    M Krawczak
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    Hum Genet 107:362-5. 2000
    ..These findings suggest that the maintenance of a defined level of DNA sequence complexity, or at least the avoidance of an increase in sequence complexity, is a critical prerequisite for the function of gene regulatory regions...
  40. ncbi Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs
    Shaun S Abeysinghe
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    Hum Mutat 22:229-44. 2003
    ..Our results are therefore consistent with a role for homologous unequal recombination in deletion mutagenesis and a role for nonhomologous recombination in the generation of translocations...
  41. ncbi Novel mutations of the growth hormone 1 (GH1) gene disclosed by modulation of the clinical selection criteria for individuals with short stature
    David S Millar
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    Hum Mutat 21:424-40. 2003
    ....
  42. pmc Estimating the efficacy and efficiency of cascade genetic screening
    M Krawczak
    Institute of Medical Genetics and Department of Psychological Medicine, University of Wales College of Medicine, Cardiff CF14 4XN, United Kingdom
    Am J Hum Genet 69:361-70. 2001
    ..This notwithstanding, once screening has become cost-effective at the population level, it can be expected that cascade screening would only transiently represent an economically viable option...
  43. ncbi Human growth hormone 1 (GH1) gene expression: complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region
    Martin Horan
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    Hum Mutat 21:408-23. 2003
    ..The genetic basis of inter-individual differences in GH1 gene expression thus appears to be extremely complex...
  44. ncbi Evaluation of denaturing high performance liquid chromatography (DHPLC) for the mutational analysis of the neurofibromatosis type 1 ( NF1) gene
    S S Han
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    Hum Genet 109:487-97. 2001
    ..This represents the highest rate of mutation detection so far reported for the NF1 gene with a single screening technique and genomic DNA as a target...
  45. doi Growth hormone (GH1) gene variation and the growth hormone receptor (GHR) exon 3 deletion polymorphism in a West-African population
    David S Millar
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
    Mol Cell Endocrinol 296:18-25. 2008
    ....
  46. ncbi Characterization of the somatic mutational spectrum of the neurofibromatosis type 1 (NF1) gene in neurofibromatosis patients with benign and malignant tumors
    Meena Upadhyaya
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    Hum Mutat 23:134-46. 2004
    ..These findings are consistent with the view that NF1 tumorigenesis is a complex multistep process involving a variety of different types of genetic defect at multiple loci...
  47. ncbi Gross Rearrangement Breakpoint Database (GRaBD)
    Shaun S Abeysinghe
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, United Kingdom
    Hum Mutat 23:219-21. 2004
    ....
  48. ncbi A novel dysfunctional growth hormone variant (Ile179Met) exhibits a decreased ability to activate the extracellular signal-regulated kinase pathway
    Mark D Lewis
    Section of Endocrinology, Department of Medicine, University of Wales College of Medicine, Heath Park, Cardiff, CF14 4XN, United Kingdom
    J Clin Endocrinol Metab 89:1068-75. 2004
    ..Although differential effects on the activation of distinct signaling pathways by a mutant receptor agonist are unprecedented, these findings also suggest that the ERK pathway could play a role in mediating the action of GH...
  49. pmc Characterisation of a functional intronic polymorphism in the human growth hormone (GH1) gene
    David S Millar
    Institute of Medical Genetics, Cardiff University, Heath Park, UK
    Hum Genomics 4:289-301. 2010
    ....
  50. ncbi Three different pathological lesions in the NF1 gene originating de novo in a family with neurofibromatosis type 1
    Meena Upadhyaya
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    Hum Genet 112:12-7. 2003
    ....
  51. ncbi Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease
    Bent N Terp
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, UK
    Hum Mutat 20:98-109. 2002
    ..However, since the proteins examined here were unrelated, and our findings consistent, it may nevertheless prove possible to extrapolate to other proteins whose dysfunction underlies inherited disease...
  52. ncbi Molecular diagnosis of facioscapulohumeral muscular dystrophy
    Meena Upadhyaya
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    Expert Rev Mol Diagn 2:160-71. 2002
    ..Indeed, the identification of the FSHD gene itself should potentiate major improvements in diagnostic testing...
  53. ncbi Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity
    Nadia A Chuzhanova
    Department of Computer Science, Cardiff University, Cardiff, UK
    Hum Mutat 21:28-44. 2003
    ....
  54. ncbi Early onset seizures and Rett-like features associated with mutations in CDKL5
    Julie C Evans
    Department of Medical Genetics, Cardiff University, Heath Park, Cardiff, UK
    Eur J Hum Genet 13:1113-20. 2005
    ..Combining our three new cases with the previously published cases, 13/14 patients with CDKL5 mutations presented with seizures before the age of 3 months...
  55. ncbi Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity
    Edward V Ball
    Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
    Hum Mutat 26:205-13. 2005
    ..Thus, microinsertions and microdeletions exhibit strong similarities in terms of the characteristics of their flanking DNA sequences, implying that they are generated by very similar underlying mechanisms...
  56. ncbi Promoter shuffling has occurred during the evolution of the vertebrate growth hormone gene
    N A Chuzhanova
    Department of Computer Science, University of Wales, CF24 3XF, Cardiff, UK
    Gene 254:9-18. 2000
    ..Although some of these changes may have had no influence on promoter function, others could have served to alter either the level of gene expression or the responsiveness of the promoter to external stimuli...
  57. ncbi Human Gene Mutation Database (HGMD): 2003 update
    Peter D Stenson
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, UK
    Hum Mutat 21:577-81. 2003
    ..Although HGMD has recently entered into a licensing agreement with Celera Genomics (Rockville, MD), mutation data will continue to be made freely available via the Internet...
  58. ncbi Genetic variation at the growth hormone (GH1) and growth hormone receptor (GHR) loci as a risk factor for hypertension and stroke
    Martin Horan
    Institute of Medical Genetics, Cardiff University, Heath Park, CF14 4XN, Cardiff, UK
    Hum Genet 119:527-40. 2006
    ..Although the underlying mechanisms are still unclear, our findings are consistent with a complex relationship between height, hypertension, GH1 promoter haplotype, GHR polymorphism and the risk of stroke...
  59. ncbi Gonosomal mosaicism for a nonsense mutation (R1947X) in the NF1 gene in segmental neurofibromatosis type 1
    Claudia Consoli
    Institute of Medical Genetics, Cardiff University, Cardiff, UK
    J Invest Dermatol 125:463-6. 2005
    ..These findings confirm that gonosomal mosaicism can occur in SNF1, with consequent important implications for genetic counselling...
  60. ncbi Mutational and functional analysis of the neurofibromatosis type 1 (NF1) gene
    M Upadhyaya
    Institute of Medical Genetics, Heath Park, Cardiff, UK
    Hum Genet 99:88-92. 1997
    ..The mutations reported in this study therefore provide further material for the functional analysis of neurofibromin as well as an insight into the mutational spectrum of the NF1 GRD...
  61. pmc In silico functional profiling of human disease-associated and polymorphic amino acid substitutions
    Matthew Mort
    Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
    Hum Mutat 31:335-46. 2010
    ..Our Web tool, designed to potentiate the functional profiling of novel AAS, has been made available at http://profile.mutdb.org/...
  62. doi A meta-analysis of nonsense mutations causing human genetic disease
    Matthew Mort
    Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
    Hum Mutat 29:1037-47. 2008
    ..56 x 10(-9)) than among nonobserved (potential) nonsense mutations, implying that nonsense mutations that elicit NMD are more likely to come to clinical attention...
  63. ncbi In silico discrimination of single nucleotide polymorphisms and pathological mutations in human gene promoter regions by means of local DNA sequence context and regularity
    Imtiaz A Khan
    Biostatistics and Bioinformatics Unit, Cardiff University, Cardiff, CF14 4XN, UK
    In Silico Biol 6:23-34. 2006
    ..This may reflect the internal axial symmetry that frequently characterizes transcription factor binding sites...
  64. ncbi Detection of NF1 mutations utilizing the protein truncation test (PTT)
    Meena Upadhyaya
    Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
    Methods Mol Biol 217:315-27. 2003
  65. ncbi Molecular reconstruction and homology modelling of the catalytic domain of the common ancestor of the haemostatic vitamin-K-dependent serine proteinases
    M Krawczak
    Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, UK
    Hum Genet 98:351-70. 1996
    ..Studies of the functional architecture of this model provide new insights into the evolution of protein-binding specificity in this family of proteins...
  66. ncbi Utilization of a cryptic noncanonical donor splice site in the KRT14 gene causes a mild form of epidermolysis bullosa simplex
    S Han
    Department of Dermatology and Institute of Medical Genetics, Cardiff University, Welsh School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
    Br J Dermatol 155:201-3. 2006
  67. ncbi Neurofibromatosis type 1: a common familial cancer syndrome
    Meena Upadhyaya
    Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
    Methods Mol Med 92:285-310. 2004
  68. ncbi Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage
    Jian Min Chen
    INSERM Institut National de la Santé et de la Recherche Médicale U613 Génétique Moléculaire et Génétique Epidémiologique, Universite de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France
    Hum Mutat 25:207-21. 2005
    ..Finally, evidence for another novel mechanism of human genetic disease, involving the possible capture of DNA oligonucleotides, is presented in the context of a 26-bp insertion into the ERCC6 gene...
  69. ncbi Structural divergence between the human and chimpanzee genomes
    Hildegard Kehrer-Sawatzki
    Department of Human Genetics, University of Ulm, Ulm, Germany
    Hum Genet 120:759-78. 2007
    ....
  70. ncbi A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease
    Jian Min Chen
    INSERM U613 Génétique moléculaire et génétique épidémiologique, Établissement Français du sang Bretagne, Universite de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, 29220, France
    Hum Genet 117:411-27. 2005
    ..Finally, the identification of independent retrotranspositional events that have integrated at the same genomic locations provides new insight into the L1-mediated insertional process in humans...
  71. pmc Breakpoints of gross deletions coincide with non-B DNA conformations
    Albino Bacolla
    Institute of Biosciences and Technology, Center for Genome Research, Texas A and M University System Health Science Center, Texas Medical Center, 2121 Holcombe Boulevard, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 101:14162-7. 2004
    ..In 11 deletions analyzed, breakpoints were explicable by non-B DNA structure formation. We conclude that alternative DNA conformations trigger genomic rearrangements through recombination-repair activities...
  72. ncbi Human genetic disease caused by de novo mitochondrial-nuclear DNA transfer
    Clesson Turner
    Uniformed Services University of the Health Sciences and Walter Reed Army Medical Center, Washington, DC 20814, USA
    Hum Genet 112:303-9. 2003
    ..Thus, for the time being, it must be considered as an intriguing coincidence. Nevertheless, these data serve to demonstrate that de novo mitochondrial-nuclear transfer of nucleic acid is a novel mechanism of human inherited disease...
  73. ncbi Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms
    Marie Pierre Audrezet
    INSERM U613, Génétique Moléculaire et Génétique Epidémiologique, Centre Hospitalier Universitaire, Brest, France
    Hum Mutat 23:343-57. 2004
    ..The insertion of this ultra-short LINE-1 element (dubbed a "hyphen element") may constitute a novel type of mutation associated with human genetic disease...
  74. ncbi Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms
    Claude Ferec
    INSERM, U613 Génétique Moléculaire et Génétique Epidémiologique, Brest, France
    Eur J Hum Genet 14:567-76. 2006
    ....
  75. ncbi Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions
    Jian Min Chen
    Institut National de la Santé et de la Recherche Médicale U613, Établissement Français du sang Bretagne, Universite de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France
    Hum Mutat 26:362-73. 2005
    ..This study therefore lends broad support to our postulate that intrachromosomal SRStrans can account for a variety of complex gene rearrangements that involve inversions...
  76. ncbi Origin of the prevalent SFTPB indel g.1549C > GAA (121ins2) mutation causing surfactant protein B (SP-B) deficiency
    Mohammed Tredano
    Service de Biochimie and Biologie Moléculaire, Hopital d Enfants Armand Trousseau, AP HP, Paris, France
    Am J Med Genet A 140:62-9. 2006
    ..Taken together, these data are consistent with the view that an indel mutation occurred on a relatively common SFTPB haplotype and now accounts for the majority of (and possibly all) extant 121ins2 chromosomes...
  77. pmc Long homopurine*homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region
    Albino Bacolla
    Institute of Biosciences and Technology, Center for Genome Research, Texas A and M University System Health Science Center, Texas Medical Center, 2121 West Holcombe Blvd, Houston, TX 77030, USA
    Nucleic Acids Res 34:2663-75. 2006
    ..These results support a role for long R*Y tracts in promoting recombination and genome diversity during evolution through destabilization of chromosomal DNA, thereby inducing repair and mutation...
  78. ncbi Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing
    Michael Krawczak
    Institut für Medizinische Informatik und Statistik, Christian Albrechts Universitat, Kiel, Germany
    Hum Mutat 28:150-8. 2007
    ..6% of disease-causing missense substitutions in human genes are likely to affect the mRNA splicing phenotype. Taken together, our results are consistent with correct donor splice-site recognition being a key step in exon recognition...
  79. ncbi Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons
    Hildegard Kehrer-Sawatzki
    Department of Human Genetics, University of Ulm, Ulm, Germany
    Hum Mutat 28:99-130. 2007
    ..Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome...
  80. ncbi Co-inheritance of a novel deletion of the entire SPINK1 gene with a CFTR missense mutation (L997F) in a family with chronic pancreatitis
    Emmanuelle Masson
    INSERM, U613, 29220 Brest, France
    Mol Genet Metab 92:168-75. 2007
    ..Given that the SPINK1 deletion constitutes a clear-cut disease-causing factor, it may be that the CFTR missense mutation acts as a disease modifier in the context of this particular family...
  81. ncbi Gene conversion: mechanisms, evolution and human disease
    Jian Min Chen
    INSERM, U613, 29220 Brest, France
    Nat Rev Genet 8:762-75. 2007
    ....
  82. doi Molecular mechanisms of chromosomal rearrangement during primate evolution
    Hildegard Kehrer-Sawatzki
    Institute of Human Genetics, University of Ulm, Ulm, Germany
    Chromosome Res 16:41-56. 2008
    ....
  83. doi Copy number variations in the NF1 gene region are infrequent and do not predispose to recurrent type-1 deletions
    Katharina Steinmann
    Institute of Human Genetics, University of Ulm, Ulm, Germany
    Eur J Hum Genet 16:572-80. 2008
    ..This duplication could have occurred concomitantly with the deletion as part of a complex rearrangement or may alternatively have preceded the deletion...
  84. pmc Type 2 NF1 deletions are highly unusual by virtue of the absence of nonallelic homologous recombination hotspots and an apparent preference for female mitotic recombination
    Katharina Steinmann
    Institute of Human Genetics, University of Ulm, Ulm, Germany
    Am J Hum Genet 81:1201-20. 2007
    ..Although an influence of chromatin structure was strongly suspected, no sex-specific differences in the methylation pattern exhibited by the SUZ12 gene were apparent that could explain the higher rate of mitotic recombination in females...
  85. ncbi A legal framework for biobanking: the German experience
    Jurgen Simon
    Institut fur Rechtswissenschaften, Universitat Luneburg, Luneburg, Germany
    Eur J Hum Genet 15:528-32. 2007
    ..Here, we provide a brief summary of the major results of this project...
  86. ncbi A novel Alu-mediated 61-kb deletion of the von Willebrand factor (VWF) gene whose breakpoints co-locate with putative matrix attachment regions
    Fei Xie
    Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University, China
    Blood Cells Mol Dis 36:385-91. 2006
    ..To date, only 11 examples of gross deletions have been reported for the VWF gene and the underlying mutational mechanisms remain unclear. A Chinese patient with type 3 VWD was studied to elucidate the underlying mechanism of mutagenesis...
  87. ncbi Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  88. ncbi A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes I: general principles and overview
    Jian Min Chen
    INSERM, U613, 29220, Brest, France
    Hum Genet 120:1-21. 2006
    ....
  89. ncbi Complex gene rearrangements caused by serial replication slippage
    Jian Min Chen
    INSERM U613 Génétique moléculaire et génétique épidémiologique, Établissement Français du sang Bretagne, Universite de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France
    Hum Mutat 26:125-34. 2005
    ..Our postulate that serial replication slippage may account for a variety of complex gene rearrangements has therefore received broad support from the study of the above diverse series of mutations...
  90. ncbi Characterization of the human lineage-specific pericentric inversion that distinguishes human chromosome 1 from the homologous chromosomes of the great apes
    Justyna M Szamalek
    Department of Human Genetics, University of Ulm, Albert Einstein Allee 11, 89081 Ulm, Germany
    Hum Genet 120:126-38. 2006
    ....
  91. ncbi Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization
    Violaine Goidts
    Department of Human Genetics, University of Ulm, Albert Einstein Allee, 11, 89081 Ulm, Germany
    Hum Genet 119:185-98. 2006
    ..The association of human-specific copy number gains with chromosomal breakpoints emphasizes their potential importance in mediating karyotypic evolution as well as in promoting human genomic diversity...
  92. ncbi A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3' UTR variants
    Jian Min Chen
    INSERM, U613, 29220, Brest, France
    Hum Genet 120:301-33. 2006
    ..This not only led us to identify further patterns of secondary structural change but also several potential novel cis-regulatory motifs within the 3' UTRs studied...
  93. ncbi Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome
    Violaine Goidts
    Department of Human Genetics, University of Ulm, Albert Einstein Allee 11, 89081, Ulm, Germany
    Hum Genet 120:270-84. 2006
    ....
  94. ncbi A rare complex DNA rearrangement in the murine Steel gene results in exon duplication and a lethal phenotype
    Saurabh Chandra
    Division of Experimental Hematology, Cincinnati Children s Hospital, Medical Center, 3333 Burnet Ave, Cincinnati, OH 45229, USA
    Blood 102:3548-55. 2003
    ..The KitlSl-20J mutation is a unique KitlSl allele and represents an unusual mechanism of mutation...
  95. ncbi Breakpoint analysis of the pericentric inversion distinguishing human chromosome 4 from the homologous chromosome in the chimpanzee (Pan troglodytes)
    Hildegard Kehrer-Sawatzki
    Department of Human Genetics, University of Ulm, Ulm, Germany
    Hum Mutat 25:45-55. 2005
    ..These findings imply that genomic architecture, and specifically high-copy repetitive elements, may have made a significant contribution to hominoid karyotype evolution, predisposing specific genomic regions to rearrangements...
  96. pmc Diversity of cystathionine beta-synthase haplotypes bearing the most common homocystinuria mutation c.833T>C: a possible role for gene conversion
    Petr Vyletal
    Center for Applied Genomics, Institute of Inherited Metabolic Disorders, Charles University 1st Faculty of Medicine, Prague, Czech Republic
    Hum Mutat 28:255-64. 2007
    ..833C; -] chromosomes may have originated by recurrent gene conversion employing the common nonpathogenic c.[833C; 844_845ins68] chromosomes as templates...
  97. ncbi Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  98. ncbi Detection of two Alu insertions in the CFTR gene
    Jian Min Chen
    INSERM, U613, 29220 Brest, France
    J Cyst Fibros 7:37-43. 2008
    ..This study represents an attempt to identify such mutational events...