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

Bhavesh Borate¹, Andreas D. Baxevanis¹

¹Bethesda, Maryland

Publication Name:

Current Protocols in Bioinformatics

Unit Number:

Unit 1.2

DOI:

10.1002/0471250953.bi0102s27

Online Posting Date:

September, 2009

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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 and clinical aspects of genetic disorders. Curr. Protoc. Bioinform. 27:1.2.1-1.2.13. © 2009 by John Wiley & Sons, Inc.

Keywords: OMIM; human genetic disorders; human genetic inheritance; molecular genetics; clinical trials

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Introduction
Basic Protocol: Searching OMIM Over the Internet
Alternate Protocol: Downloading OMIM
Guidelines for Understanding Results
Commentary
Literature Cited
Figures
Tables

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Figures

Figure 1.2.1

Search result from a complex OMIM query, using both Boolean operators and search term qualifiers. The query here was issued as SNCA [GENE] AND PARKINSON [DIS].

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Figure 1.2.2

The detailed view resulting from the query issued in Figure 1.2.1. Details on the various sections of the detailed view, as well as on alternative views, can be found in the text.

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Figure 1.2.3

The OMIM Gene Map, beginning at the position of the alpha-synuclein gene (SNCA) at chromosomal location 4q21. The contents of the various columns are described fully within the main text.

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Figure 1.2.4

The LinkOut page for the alpha-synuclein gene. This page provides a jumping-off point to numerous, related Web resources not located within OMIM itself. A description of each of these Web sites can be found in the main text.

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Figure 1.2.5

The Mouse Genome Informatics Web page for the mouse ortholog of the human alpha-synuclein gene. Links are provided to additional mouse resources in the different sections.

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Figure 1.2.6

Known allelic variants in the SNCA gene. Four of the variants cause Parkinson's Disease, while one causes Dementia with Lewy Body, a condition with clinical features closely overlapping that of Parkinson's Disease.

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Literature Cited

Literature Cited
	Baxevanis, A.D. and Ouellette, B.F. (eds.) 2005. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd edition. John Wiley & Sons, Hoboken, New Jersey.
	Hamosh, A., Scott, A.F., Amberger, J., Bocchini, C., Valle, D., and McKusick, V.A. 2002. Online Mendelian Inheritance in Man (OMIM): A knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 30:52-55.
	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.
Internet Resources
	http://www.ncbi.nlm.nih.gov/
The NCBI Web site, which offers easy access to OMIM.
	ftp://ftp.ncbi.nih.gov/repository/OMIM
The FTP site for downloading OMIM for local use.
	http://www.ncbi.nlm.nih.gov/Omim/omimfaq.html
Frequently asked questions (FAQ) about OMIM.