Searching Online Mendelian Inheritance in Man (OMIM) for Information on Genetic Loci Involved in Human Disease

Andreas D. Baxevanis1

1 null, Bethesda, Maryland
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 9.13
DOI:  10.1002/0471142905.hg0913s73
Online Posting Date:  April, 2012
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of information on human genes and genetic disorders, with a particular emphasis on the interplay between observed phenotypes and underlying genotypes. This unit focuses on the basic methodology for formulating OMIM searches and illustrates the types of information that can be retrieved from OMIM, including descriptions of clinical manifestations resulting from genetic abnormalities. This unit also provides information on additional relevant medical and molecular biology databases. A basic knowledge of OMIM should be part of the armamentarium of physicians and scientists with an interest in research on the clinical aspects of genetic disorders. Curr. Protoc. Hum. Genet. 73:9.13.1‐9.13.10. © 2012 by John Wiley & Sons, Inc.

Keywords: OMIM; human genetic disorders; human genetic inheritance; molecular genetics; mammalian orthology

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol: Searching OMIM
  • Alternate Protocol: Downloading OMIM
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

  •  FigureFigure 9.13.1 Search results from the OMIM query, returning all OMIM entries that pertain to the deleted in colorectal carcinoma (DCC) gene. The first entry in the list is the main entry discussing DCC.
    View Image
  •  FigureFigure 9.13.2 The detailed view of the DCC entry in OMIM. Details on the various sections of this view can be found in the main text.
    View Image
  •  FigureFigure 9.13.3 The OMIM Gene Map, centered on the position of the DCC gene at chromosomal location 18q21.2. The contents of the various columns are described in Guidelines for Understanding Results.
    View Image
  •  FigureFigure 9.13.4 A tabular view of all known allelic variants in the DCC gene, leading to a variety of clinical outcomes. Here, five allelic variants are shown: one for somatic colorectal cancer, one for somatic esophageal carcinoma, and three for congenital mirror movements. For each, the actual mutation (either at the nucleotide or protein level) is given in the third column.
    View Image
  •  FigureFigure 9.13.5 A detailed description of each of the known allelic variants in the DCC gene. The text in this part of the OMIM entry deals specifically with each of these allelic variants, providing information on how these mutations were found, implications of these mutations for basic cellular processes, and information on the ultimate clinical outcome in individuals carrying these mutations.
    View Image
  •  FigureFigure 9.13.6 The Mouse Genome Informatics Web page for the mouse ortholog of the human DCC gene. Mapping information, homology to other mammalian genes, information on mouse alleles and their phenotypes, and similar information of interest can be found on this site.
    View Image

Videos

Literature Cited

Literature Cited
    Amberger, J., Bocchini, C.A., Scott, A.F., and Hamosh, A. 2009. McKusick's Online Inheritance in Man (OMIM). Nucleic Acids Res. 37:D793‐D796.
    Amberger, J., Bocchini, C.A., and Hamosh, A. 2011. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM). Hum. Mutat. 32:564‐567.
    Aoki, K.F. and Kanehisa, M. 2005. Using the KEGG database resource. Curr. Protoc. Bioinform. 11:1.12.1‐1.12.54.
    Fernández‐Suárez, X.M. and Schuster, M.K. 2010. Using the Ensembl genome server to browse genomic sequence data. Curr. Protoc. Bioinform. 30:1.15.1–1.15.48.
    Gong, L., Owen, R.P., Gor, W., Altman, R.B., and Klein, T.E. 2008. PharmGKB: An integrated resource of pharmacogenomic data and knowledge. Curr. Protoc. Bioinform. 23:14.7.1‐14.7.17.
    Karolchik, D., Hinrichs, A.S., and Kent, W.J. 2009. The UCSC genome browser. Curr. Protoc. Bioinform. 28:1.4.1‐1.4.26.
    McKusick, V.A. 1998. Online Mendelian Inheritance in Man: A Catalog of Human Genes and Genetic Disorders, 12th edition. Johns Hopkins University Press, Baltimore, Maryland.
    Ramachandran, S., Ruef, B., Pich, C. and Sprague, J. 2010. Exploring zebrafish genomic, functional and phenotypic data using ZFIN. Curr. Protoc. Bioinform. 31:1.18.1‐1.18.44.
    Shaw, D. R. 2009. Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype. Curr. Protoc. Bioinform. 25:1.7.1‐1.7.14.
    Stein, L.D. 2004. Using the reactome database. Curr. Protoc. Bioinform. 7:8.7.1‐8.7.16.
    Wolfsberg, T.G. 2010. Using the NCBI Map Viewer to browse genomic sequence data. Curr. Protoc. Bioinform. 29:1.5.1‐1.5.25.
 Internet Resources
    http://omim.org

The OMIM Web site.

    http://omim.org/help/faq

Frequently asked questions (FAQ) about OMIM.

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library