Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network.

Common hereditary neurodevelopmental disorders such as autism, bipolar disorder, and schizophrenia are most likely both genetically multifactorial and heterogeneous. Because of these characteristics traditional methods for genetic analysis fail when applied to such diseases. To address the problem we propose a novel probabilistic framework that combines the standard genetic linkage formalism with whole-genome molecular-interaction data to predict pathways or networks of interacting genes that contribute to common heritable disorders. We apply the model to three large genotype-phenotype data sets, identify a small number of significant candidate genes for autism (24), bipolar disorder (21), and schizophrenia (25), and predict a number of gene targets likely to be shared among the disorders.

[1]  Richard Bellman,et al.  Adaptive Control Processes: A Guided Tour , 1961, The Mathematical Gazette.

[2]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[3]  B. Efron The jackknife, the bootstrap, and other resampling plans , 1987 .

[4]  M Speer,et al.  Chromosome‐based method for rapid computer simulation in human genetic linkage analysis , 1993, Genetic epidemiology.

[5]  J. Milne,et al.  An integrative approach , 1995 .

[6]  E. Lander,et al.  Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results , 1995, Nature Genetics.

[7]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[8]  L Kruglyak,et al.  Parametric and nonparametric linkage analysis: a unified multipoint approach. , 1996, American journal of human genetics.

[9]  B. Leventhal,et al.  The serotonin system in autism. , 1996, Current opinion in pediatrics.

[10]  A Benner,et al.  Serotonin transporter (5-HTT) gene variants associated with autism? , 1997, Human molecular genetics.

[11]  N J Cox,et al.  Evidence of linkage between the serotonin transporter and autistic disorder , 1997, Molecular Psychiatry.

[12]  B. Leventhal,et al.  Mutation screening of the UBE3A/E6-AP gene in autistic disorder , 1999, Molecular Psychiatry.

[13]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[14]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[15]  X. Estivill,et al.  Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1. , 2000, Human molecular genetics.

[16]  Y. Benjamini,et al.  THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .

[17]  E. Stordal,et al.  The phospholipase C‐γ1 gene (PLCG1) and lithium‐responsive bipolar disorder: re‐examination of an intronic dinucleotide repeat polymorphism , 2001, Psychiatric genetics.

[18]  R. Ebstein,et al.  Evidence for an association with the serotonin transporter promoter region polymorphism and autism. , 2001, American journal of medical genetics.

[19]  J. Sutcliffe,et al.  Linkage disequilibrium at the Angelman syndrome gene UBE3A in autism families. , 2001, Genomics.

[20]  M. Egan,et al.  Serotonin Transporter Genetic Variation and the Response of the Human Amygdala , 2002, Science.

[21]  Stephen J. Guter,et al.  Transmission disequilibrium mapping at the serotonin transporter gene (SLC6A4) region in autistic disorder , 2002, Molecular Psychiatry.

[22]  [Detection of level and mutation of neurofilament mRNA in Alzheimer's disease]. , 2002, Zhonghua yi xue za zhi.

[23]  E. Bacchelli,et al.  Screening of nine candidate genes for autism on chromosome 2q reveals rare nonsynonymous variants in the cAMP-GEFII gene , 2003, Molecular Psychiatry.

[24]  Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource , 2003 .

[25]  Maladies neurodégénératives et polymorphisme des gènes de l'apolipoprotéine E et de la bléomycine hydrolase , 2003 .

[26]  P. Boutin,et al.  Islet-brain1/C-Jun N-terminal kinase interacting protein-1 (IB1/JIP-1) promoter variant is associated with Alzheimer's disease , 2003, Molecular Psychiatry.

[27]  P. Boutin,et al.  Islet-brain 1/c-Jun N-terminal kinase interacting protein-1 (IB1/JIP-1) promoter variant is associated with Alzheimer's disease , 2003, Molecular Psychiatry.

[28]  A. Arkin,et al.  Motifs, modules and games in bacteria. , 2003, Current opinion in microbiology.

[29]  S. Spence,et al.  A genomewide screen of 345 families for autism-susceptibility loci. , 2003, American journal of human genetics.

[30]  [Apolipoprotein E and bleomycin hydrolase. Polymorphisms: association with neurodegenerative diseases]. , 2003, Annales de biologie clinique.

[31]  T. Gilliam,et al.  Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[32]  C. Gillberg,et al.  Bipolar disorder, schizophrenia, and other psychotic disorders in adults with childhood onset AD/HD and/or autism spectrum disorders , 2004, Journal of Neural Transmission.

[33]  Michael Krauthammer,et al.  GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data , 2004, J. Biomed. Informatics.

[34]  Edwin H Cook,et al.  Autism as a paradigmatic complex genetic disorder. , 2004, Annual review of genomics and human genetics.

[35]  Tomoko Watanabe,et al.  No genetic association between Fyn kinase gene polymorphisms (−93A/G, IVS10+37T/C and Ex12+894T/G) and Japanese sporadic Alzheimer's disease , 2004, Neuroscience Letters.

[36]  J. Bressler,et al.  A mixed epigenetic/genetic model for oligogenic inheritance of autism with a limited role for UBE3A , 2004, American journal of medical genetics. Part A.

[37]  J. Gorman,et al.  Autism or Schizophrenia: A Diagnostic Dilemma in Adults with Intellectual Disabilities , 2004, Journal of psychiatric practice.

[38]  Leo Breiman,et al.  Bagging Predictors , 1996, Machine Learning.

[39]  J. Buxbaum,et al.  Expression of calsenilin in neurons and astrocytes in the Alzheimer's disease brain , 2005, Neuroreport.

[40]  Paul J. Harrison,et al.  Schizophrenia genes, gene expression, and neuropathology: on the matter of their convergence , 2005, Molecular Psychiatry.

[41]  S. Nanko,et al.  Gene expression and association analyses of LIM (PDLIM5) in bipolar disorder and schizophrenia , 2005, Molecular Psychiatry.

[42]  Ryan D. Hernandez,et al.  Natural selection on protein-coding genes in the human genome , 2005, Nature.

[43]  S. Brahmachari,et al.  MLC1 Gene Is Associated with Schizophrenia and Bipolar Disorder in Southern India , 2005, Biological Psychiatry.

[44]  Li Wang,et al.  An integrative approach for causal gene identification and gene regulatory pathway inference , 2006, ISMB.

[45]  N. Craddock,et al.  Genetics of affective (mood) disorders , 2006, European Journal of Human Genetics.

[46]  J. Poirier,et al.  A polymorphism in lipoprotein lipase affects the severity of Alzheimer's disease pathophysiology , 2006, The European journal of neuroscience.

[47]  C. Wijmenga,et al.  Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. , 2006, American journal of human genetics.

[48]  J. Richardson,et al.  MAPK-activated Protein Kinase 2 Deficiency in Microglia Inhibits Pro-inflammatory Mediator Release and Resultant Neurotoxicity , 2006, Journal of Biological Chemistry.

[49]  Bassem A. Hassan,et al.  Gene prioritization through genomic data fusion , 2006, Nature Biotechnology.

[50]  V. McKusick Mendelian Inheritance in Man and Its Online Version, OMIM , 2007, The American Journal of Human Genetics.

[51]  Léon Personnaz,et al.  Enrichment or depletion of a GO category within a class of genes: which test? , 2007, Bioinform..

[52]  Pall I. Olason,et al.  A human phenome-interactome network of protein complexes implicated in genetic disorders , 2007, Nature Biotechnology.

[53]  Tijl De Bie,et al.  Kernel-based data fusion for gene prioritization , 2007, ISMB/ECCB.

[54]  D. Vitkup,et al.  Network properties of genes harboring inherited disease mutations , 2008, Proceedings of the National Academy of Sciences.