Clinical genetic strategies for early onset neurodegenerative diseases

[1]  R. Luthra,et al.  Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges , 2015, Cancers.

[2]  D. Serie,et al.  Late-onset Alzheimer disease risk variants mark brain regulatory loci , 2015, Neurology: Genetics.

[3]  S. An,et al.  Role of apolipoprotein E in neurodegenerative diseases , 2015, Neuropsychiatric disease and treatment.

[4]  S. An,et al.  Gene panels and primers for next generation sequencing studies on neurodegenerative disorders , 2015, Molecular & Cellular Toxicology.

[5]  M. Pericak-Vance,et al.  F-box/LRR-repeat protein 7 is genetically associated with Alzheimer’s disease , 2015, Annals of clinical and translational neurology.

[6]  Marjolein Kriek,et al.  Next‐Generation Diagnostics: Gene Panel, Exome, or Whole Genome? , 2015, Human mutation.

[7]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[8]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[9]  K. Lunetta,et al.  Two rare AKAP9 variants are associated with Alzheimer's disease in African Americans , 2014, Alzheimer's & Dementia.

[10]  C. Thermes,et al.  Ten years of next-generation sequencing technology. , 2014, Trends in genetics : TIG.

[11]  Caspar Zialor.  DNA sequencing with chain terminating inhibitors , 2014 .

[12]  J. Skinner,et al.  Application of Massively Parallel Sequencing in the Clinical Diagnostic Testing of Inherited Cardiac Conditions , 2014 .

[13]  E. Diamandis,et al.  Whole genome sequencing as a diagnostic test: challenges and opportunities. , 2014, Clinical chemistry.

[14]  Marco Biasini,et al.  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information , 2014, Nucleic Acids Res..

[15]  Erick R. Scott,et al.  Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease , 2013, Nature.

[16]  Mustafa Tekin,et al.  The promise of whole-exome sequencing in medical genetics , 2013, Journal of Human Genetics.

[17]  Nick C Fox,et al.  Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease , 2013, Nature Genetics.

[18]  Christopher H Wade,et al.  Growing up in the genomic era: implications of whole-genome sequencing for children, families, and pediatric practice. , 2013, Annual review of genomics and human genetics.

[19]  Thomas W. Mühleisen,et al.  Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease , 2013, Nature Genetics.

[20]  A. Hofman,et al.  Variant of TREM2 associated with the risk of Alzheimer's disease. , 2013, The New England journal of medicine.

[21]  Anushya Muruganujan,et al.  PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees , 2012, Nucleic Acids Res..

[22]  J. Miller,et al.  Predicting the Functional Effect of Amino Acid Substitutions and Indels , 2012, PloS one.

[23]  Jian Peng,et al.  Template-based protein structure modeling using the RaptorX web server , 2012, Nature Protocols.

[24]  Joaquín Dopazo,et al.  SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants , 2011, Nucleic Acids Res..

[25]  C. Kimchi-Sarfaty,et al.  Understanding the contribution of synonymous mutations to human disease , 2011, Nature Reviews Genetics.

[26]  C. Duyckaerts,et al.  Neuropathology of Alzheimer's Disease and its Variants , 2011 .

[27]  K. Yaffe,et al.  The projected effect of risk factor reduction on Alzheimer's disease prevalence , 2011, The Lancet Neurology.

[28]  C. Sander,et al.  Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.

[29]  P. Sham,et al.  Evaluating the heritability explained by known susceptibility variants: a survey of ten complex diseases , 2011, Genetic epidemiology.

[30]  Nick C Fox,et al.  Common variants in ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer’s disease , 2011, Nature Genetics.

[31]  D. G. Clark,et al.  Common variants in MS4A4/MS4A6E, CD2uAP, CD33, and EPHA1 are associated with late-onset Alzheimer’s disease , 2011, Nature Genetics.

[32]  Duan Ma,et al.  Detection of RASA1 mutations in patients with sporadic Sturge–Weber syndrome , 2011, Child's Nervous System.

[33]  A. Butte,et al.  Non-Synonymous and Synonymous Coding SNPs Show Similar Likelihood and Effect Size of Human Disease Association , 2010, PloS one.

[34]  Nick C Fox,et al.  The diagnosis of young-onset dementia , 2010, The Lancet Neurology.

[35]  Sudha Seshadri,et al.  Genome-wide analysis of genetic loci associated with Alzheimer disease. , 2010, JAMA.

[36]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[37]  K. Elliott,et al.  Potential late-onset Alzheimer's disease-associated mutations in the ADAM10 gene attenuate {alpha}-secretase activity. , 2009, Human molecular genetics.

[38]  L. Kiemeney,et al.  Corrigendum: Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer , 2009, Nature Genetics.

[39]  L. Defebvre,et al.  A genetic variation in the ADORA2A gene modifies age at onset in Huntington's disease , 2009, Neurobiology of Disease.

[40]  E. Capriotti,et al.  Functional annotations improve the predictive score of human disease‐related mutations in proteins , 2009, Human mutation.

[41]  M. Itokawa,et al.  A two-stage case–control association study of PADI2 with schizophrenia , 2009, Journal of Human Genetics.

[42]  Yun Liu,et al.  LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures , 2009, Bioinform..

[43]  L. Hurst,et al.  The price of silent mutations. , 2009, Scientific American.

[44]  C. Béroud,et al.  Human Splicing Finder: an online bioinformatics tool to predict splicing signals , 2009, Nucleic acids research.

[45]  R Parasuraman,et al.  Synergistic effects of genetic variation in nicotinic and muscarinic receptors on visual attention but not working memory , 2009, Proceedings of the National Academy of Sciences.

[46]  Jennifer Williamson,et al.  Genetic Aspects of Alzheimer Disease , 2009, The neurologist.

[47]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[48]  S. Tavtigian,et al.  In silico analysis of missense substitutions using sequence‐alignment based methods , 2008, Human mutation.

[49]  K. Hsiao,et al.  Simultaneous assessment of the effects of exonic mutations on RNA splicing and protein functions. , 2008, Biochemical and biophysical research communications.

[50]  J. Brockmöller,et al.  Common genetic variations in human brain-specific tryptophan hydroxylase-2 and response to antidepressant treatment , 2008, Pharmacogenetics and genomics.

[51]  M. Gratacós,et al.  Association Study of 10 Genes Encoding Neurotrophic Factors and Their Receptors in Adult and Child Attention-Deficit/Hyperactivity Disorder , 2008, Biological Psychiatry.

[52]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[53]  Song-Yu Yang,et al.  HSD17B10: a gene involved in cognitive function through metabolism of isoleucine and neuroactive steroids. , 2007, Molecular genetics and metabolism.

[54]  A. Misra,et al.  SNP genotyping: technologies and biomedical applications. , 2007, Annual review of biomedical engineering.

[55]  Lise Getoor,et al.  SplicePort—An interactive splice-site analysis tool , 2007, Nucleic Acids Res..

[56]  B. Rost,et al.  SNAP: predict effect of non-synonymous polymorphisms on function , 2007, Nucleic acids research.

[57]  Rebecca F. Halperin,et al.  A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease. , 2007, The Journal of clinical psychiatry.

[58]  M. Gill,et al.  Evidence for novel susceptibility genes for late-onset Alzheimer's disease from a genome-wide association study of putative functional variants. , 2007, Human molecular genetics.

[59]  Bruce L. Miller,et al.  Appendix B: Practice parameter: Diagnosis of dementia (an evidence-based review): Report of the quality standards subcommittee of the American academy neurology , 2007 .

[60]  K. Lunetta,et al.  The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease , 2007, Nature Genetics.

[61]  K. Shokat,et al.  Human Catechol-O-Methyltransferase Haplotypes Modulate Protein Expression by Altering mRNA Secondary Structure , 2006, Science.

[62]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[63]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.

[64]  W. Parson,et al.  Direct molecular haplotyping of multiple polymorphisms within exon 4 of the human catechol-O-methyltransferase gene by liquid chromatography–electrospray ionization time-of-flight mass spectrometry , 2006, Analytical and bioanalytical chemistry.

[65]  Mark Diekhans,et al.  Regions of extreme synonymous codon selection in mammalian genes , 2006, Nucleic acids research.

[66]  L. Fratiglioni,et al.  Role of genes and environments for explaining Alzheimer disease. , 2006, Archives of general psychiatry.

[67]  Mark I McCarthy,et al.  What makes a good genetic association study? , 2005, The Lancet.

[68]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[69]  Ravi Sachidanandam,et al.  GObar: A Gene Ontology based analysis and visualization tool for gene sets , 2005, BMC Bioinformatics.

[70]  E. Eichler,et al.  Segmental duplications and copy-number variation in the human genome. , 2005, American journal of human genetics.

[71]  A. Sidow,et al.  Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. , 2005, Genome research.

[72]  Piero Fariselli,et al.  I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure , 2005, Nucleic Acids Res..

[73]  Mi Zhou,et al.  nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms , 2005, Nucleic Acids Res..

[74]  E. Eichler,et al.  Fine-scale structural variation of the human genome , 2005, Nature Genetics.

[75]  S. Leal,et al.  Complex phenotypes and complex genetics: An introduction to genetic studies of complex traits , 2005, Current atherosclerosis reports.

[76]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[77]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[78]  Gil Ast,et al.  Comparative analysis detects dependencies among the 5' splice-site positions. , 2004, RNA.

[79]  Ting Chen,et al.  Mapping gene ontology to proteins based on protein-protein interaction data , 2004, Bioinform..

[80]  W. Kozubski,et al.  Genetic study of familial cases of Alzheimer's disease. , 2004, Acta biochimica Polonica.

[81]  Joaquín Dopazo,et al.  FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes , 2004, Bioinform..

[82]  Michael Dean,et al.  Approaches to identify genes for complex human diseases: Lessons from Mendelian disorders , 2003, Human mutation.

[83]  D. Bennett,et al.  Alzheimer disease in the US population: prevalence estimates using the 2000 census. , 2003, Archives of neurology.

[84]  S. Henikoff,et al.  Accounting for human polymorphisms predicted to affect protein function. , 2002, Genome research.

[85]  J. Stephens,et al.  Haplotype Variation and Linkage Disequilibrium in 313 Human Genes , 2001, Science.

[86]  L. Feuk,et al.  SNP association studies in Alzheimer's disease highlight problems for complex disease analysis. , 2001, Trends in genetics : TIG.

[87]  B. Miller,et al.  CME Practice parameter : Diagnosis of dementia ( an evidence-based review ) Report of the Quality Standards Subcommittee of the American Academy of Neurology , 2001 .

[88]  S. Henikoff,et al.  Predicting deleterious amino acid substitutions. , 2001, Genome research.

[89]  C. Mathew.  Science, medicine, and the future: Postgenomic technologies: hunting the genes for common disorders. , 2001, BMJ.

[90]  D. Selkoe.  Alzheimer's disease: genes, proteins, and therapy. , 2001, Physiological reviews.

[91]  D. Nickerson,et al.  Variation is the spice of life , 2001, Nature Genetics.

[92]  S. Salzberg,et al.  GeneSplicer: a new computational method for splice site prediction. , 2001, Nucleic acids research.

[93]  L. Cardon,et al.  Association study designs for complex diseases , 2001, Nature Reviews Genetics.

[94]  M Ronaghi,et al.  Improved performance of pyrosequencing using single-stranded DNA-binding protein. , 2000, Analytical biochemistry.

[95]  N. Schork,et al.  Single nucleotide polymorphisms and the future of genetic epidemiology , 2000, Clinical genetics.

[96]  H. Allawi,et al.  Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[97]  Bruce P. Neri,et al.  Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes , 1999, Nature Biotechnology.

[98]  J. Meyer,et al.  Multiple threshold model for the onset of Alzheimer's disease in the NAS-NRC twin panel. , 1998, American journal of medical genetics.

[99]  J. Haines,et al.  Effects of Age, Sex, and Ethnicity on the Association Between Apolipoprotein E Genotype and Alzheimer Disease: A Meta-analysis , 1997 .

[100]  David Haussler,et al.  Improved splice site detection in Genie , 1997, RECOMB '97.

[101]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[102]  J. Rommens,et al.  Familial Alzheimer's disease in kindreds with missense mutations in a gene on chromosome 1 related to the Alzheimer's disease type 3 gene , 1995, Nature.

[103]  G. Schellenberg,et al.  Candidate gene for the chromosome 1 familial Alzheimer's disease locus , 1995, Science.

[104]  D. Pollen,et al.  Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease , 1995, Nature.

[105]  A. L. Bergem.  Heredity in dementia of the Alzheimer type , 1994, Clinical genetics.

[106]  A. M. Saunders,et al.  Protective effect of apolipoprotein E type 2 allele for late onset Alzheimer disease , 1994, Nature Genetics.

[107]  M. Pericak-Vance,et al.  Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[108]  J. Haines,et al.  Assessment of amyloid beta-protein precursor gene mutations in a large set of familial and sporadic Alzheimer disease cases. , 1992, American journal of human genetics.

[109]  E. Otomo,et al.  Apolipoprotein E immunoreactivity in cerebral amyloid deposits and neurofibrillary tangles in Alzheimer's disease and kuru plaque amyloid in Creutzfeldt-Jakob disease , 1991, Brain Research.

[110]  R. Wartell,et al.  Detecting base pair substitutions in DNA fragments by temperature-gradient gel electrophoresis. , 1990, Nucleic acids research.

[111]  T. Sekiya,et al.  Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[112]  U Landegren,et al.  A ligase-mediated gene detection technique. , 1988, Science.

[113]  P. Nyrén,et al.  Enzymatic method for continuous monitoring of DNA polymerase activity. , 1987, Analytical biochemistry.

[114]  Marvin B. Shapiro,et al.  RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. , 1987, Nucleic acids research.

[115]  D. Riesner,et al.  Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. , 1987, Biophysical chemistry.

[116]  D. Botstein,et al.  Construction of a genetic linkage map in man using restriction fragment length polymorphisms. , 1980, American journal of human genetics.

[117]  Paul D Thomas,et al.  The Gene Ontology and the Meaning of Biological Function. , 2017, Methods in molecular biology.

[118]  Mark W. Loguea,et al.  Two rare AKAP 9 variants are associated with Alzheimer ’ s disease in African Americans , 2014 .

[119]  M. Arfan Ikram,et al.  Variant of TREM 2 Associated with the Risk of Alzheimer ’ s Disease , 2012 .

[120]  J. Plotkin,et al.  Synonymous but not the same: the causes and consequences of codon bias , 2011, Nature Reviews Genetics.

[121]  D. G. Clark,et al.  Common variants at MS 4 A 4 / MS 4 A 6 E , CD 2 AP , CD 33 and EPHA 1 are associated with late-onset Alzheimer ’ s disease , 2011 .

[122]  Nick C Fox,et al.  Common variants at ABCA 7 , MS 4 A 6 A / MS 4 A 4 E , EPHA 1 , CD 33 and CD 2 AP are associated with Alzheimer ’ s disease , 2011 .

[123]  R. Swerdlow,et al.  Polymorphic variation in cytochrome oxidase subunit genes. , 2010, Journal of Alzheimer's disease : JAD.

[124]  D. Perl.  Neuropathology of Alzheimer's disease. , 2010, The Mount Sinai journal of medicine, New York.

[125]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[126]  Nick C Fox,et al.  Letter abstract - Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's Disease , 2009 .

[127]  R. Storb,et al.  Restriction fragment length polymorphism of the major histocompatibility complex of the dog , 2004, Immunogenetics.

[128]  F. Christians,et al.  High-density genechip oligonucleotide probe arrays. , 2002, Advances in biochemical engineering/biotechnology.

[129]  Mostafa Ronaghi.  Pyrosequencing Sheds Light on DNA Sequencing , 2001 .

[130]  C. Mathew.  DNA diagnostics: goals and challenges. , 1999, British medical bulletin.

[131]  J. Haines,et al.  Apolipoprotein E4 allele and Alzheimer disease: Examination of Allelic association and effect on age at onset in both early‐and late‐onset cases , 1995, Genetic epidemiology.

[132]  M. Pericak-Vance,et al.  Linkage studies in familial Alzheimer's disease. , 1989 .

[133]  Lippincott-Schwartz,et al.  Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .