Centers for Disease Control and Prevention
Centers for Disease Control and Prevention		 Centers for Disease Control and Prevention CDC Home Search CDC CDC Health Topics A-Z    
Office of Genomics and Disease Prevention  
Office of Genomics and Disease Prevention


Beta version. Contact us with comments

A genotype has been defined as ‘the genetic identity of an individual that does not show as outward characteristics’ (1). Within human populations, genotype prevalence, or the proportion of individuals in a defined population possessing specific gene variants at one or more loci, may vary considerably.

The Office of Genomics and Disease Prevention has established an online repository for human genotype prevalence data from selected studies. The database includes a description of the study population, references to the published report or the researcher’s contact information, and genotype frequency data that are stratified by geographic area, and in some instances, race and gender. The database presents genotype frequencies in preference to allele frequencies because a) genotypes have been proposed for researchers who either report or appraise studies of prevalence and gene-disease associations, b) specific genotypes, not alleles, are often associated with disease risk, and c) genotype frequency data can be used to calculate allele frequency (2).

On This Page: Go to the search page
Data sources

The database currently includes genotype prevalence data for 13 genes. Data sources include information abstracted from 13 HuGE Reviews (3-15). Future updates to the database will include updated prevalence data for genotypes in the database and data for additional genotypes.

Data elements

Study Location (Reference #): Geographic region where study was conducted, as defined by the authors or contributing researcher.
Gender: M-male; F-female; NS-not specified in abstract or paper or data presented was not stratified by gender.
Race/Ethnicity: Race or ethnicity of study subjects, as defined by the researcher. NS- not specified in abstract or paper.
# Subjects Studied: Number of subjects that were genotyped in study, as defined by the authors or contributing researcher.
Study population: Description of the study population abstracted from published reports or provided by the researcher.
Reference or Contact: Published reference or contact information for researcher contributing genotype frequency data.
Genotype analyzed and proportion in the population studied: Each column heading represents a specific genotype. Whenever possible, gene variant nomenclature follows the Human Genome Variation Society recommendations (16). Frequencies for each genotype can be displayed as percentages, 95% confidence intervals, or counts. A value of ‘-1’ indicates the genotype was not assessed in the study.

Viewing genotype prevalence tables
  1. As you scroll down the page, the table header will roll down accordingly.
  2. Click on a column heading to sort data within that column. The ‘^’ symbol appearing next to the column heading indicates the data has been sorted in ascending order. A ‘V’‘ symbol indicates the data has been sorted in descending order. If no symbol appears next to the column heading, the data has not been sorted.
  3. You may choose to view prevalence frequencies (shown as percentages), corresponding 95% confidence intervals, or counts. Click on the appropriate check box in the upper right hand corner above the table to change your view.

Viewing the references and documentation for each genotype prevalence table

  1. Read a brief description of each study population or view the complete reference or contact information for every record in the data window titled ‘Study Population | Reference or Contact’ (found at the bottom of the table). Using the reference # presented in the prevalence table, scroll down to find the appropriate record. Links to PubMed abstracts are provided for published studies.
  2. Column headings are repeated at the bottom of the web page. Read additional comments about each column heading or find links to external web sites to learn more about each gene variant by clicking on the column heading of your choice.
Data limitations

Users should review individual studies for details and be aware of the following issues when viewing the data (2):

  • studies referenced may derive their frequency data from convenience samples or highly-selected populations (e.g. blood donors, community samples) and thus may not be population-based.
  • study methods from published and unpublished reports, including genotyping procedure or selection of subjects, will vary.
  • genotype results may be derived from polymerase chain reaction methods or inferred on the basis of a phenotypic test.
  • whenever possible, gene variant nomenclature follows Human Genome Variation Society recommendations; otherwise, nomenclature for genotypes are defined by the author of the study or the researcher contributing unpublished data.
  • study location and race/ethnicity, if available, are defined by the author of the study or the researcher contributing unpublished data.
  • the database may not include all relevant studies for a given gene.

Submitting unpublished data

OGDP welcomes researchers who wish to submit unpublished genotype prevalence data for inclusion into the database. For more information, please e-mail genetics@cdc.gov. Indicate in the subject heading of your e-mail, 'Submitting genotype prevalence data.'

Technical Comments

This application is best viewed in Microsoft Internet Explorer 5 or higher. If viewed in Netscape, some functionality will be lost. Furthermore, this application is best viewed with a monitor display setting of 1024 x 768 pixels or higher.
Questions or Comments
OGDP welcomes feedback on the genotype prevalence database. Please E-mail comments or questions to genetics@cdc.gov. Indicate in the subject heading of your email, 'Genotype prevalence db.'
Links to other prevalence databases

Disclaimer

Links to non-federal organizations found within GDPInfo are provided solely as a service to our users. These links do not constitute an endorsement of these organizations or their programs by CDC or the federal government, and none should be inferred. The CDC is not responsible for the content of the individual organization web pages found at these links.

References
  1. Talking glossary of genetic terms.
    Bethesda, MD: National Human Genome Research Institute, 2003.
  2. Reporting, Appraising, and Integrating Data On Genotype Prevalence and Gene-Disease Associations
    Little J, Bradley L, Bray M, et al. Am J Epidemiol. 2002; 156(4): 300-10
  3. Pooled analysis and meta-analysis of glutathione S-transferase M1 and bladder cancer: a HuGE review.
    Engel LS, Taioli E, Pfeiffer R, Garcia-Closas M, et al. Am J Epidemiol. 2002 Jul 15;156(2):95-109.
  4. Glutathione S-transferase polymorphisms and risk of ovarian cancer: a HuGE review.
    Coughlin SS, Hall IJ. Genet Med. 2002 Jul-Aug;4(4):250-7.
  5. GSTM1, GSTT1, and the risk of squamous cell carcinoma of the head and neck: a mini-HuGE review.
    Geisler SA, Olshan AF. Am J Epidemiol. 2001 Jul 15;154(2):95-105.
  6. Apolipoprotein E polymorphism and cardiovascular disease: a HuGE review.
    Eichner JE, Dunn ST, Perveen G, Thompson DM, Stewart KE, Stroehla BC. Am J Epidemiol. 2002 Mar 15;155(6):487-95.
  7. HFE gene and hereditary hemochromatosis: a HuGE review.
    Hanson EH, Imperatore G, Burke W. Am J Epidemiol. 2001 Aug 1;154(3):193-206
  8. 5,10-Methylenetetrahydrofolate reductase gene variants and congenital anomalies: a HuGE review.
    Botto LD, Yang Q. Am J Epidemiol. 2000 May 1;151(9):862-77.
  9. 5,10-Methylenetetrahydrofolate Reductase Polymorphisms and Leukemia Risk
    Robien K, Ulrich CM. Am J Epidemiol. 2003 April; 157(7): 571-82
  10. Glutathione S-transferase polymorphisms and colorectal cancer: a HuGE review
    Cotton SC, Sharp L, Little J, Brockton N.   Am J Epidemiol. 2000 Jan 1;151(1):7-32
  11. Delta-aminolevulinic acid dehydratase genotype and lead toxicity: a HuGE review
    Kelada SN, Shelton E, Kaufmann RB, Khoury MJ.    Am J Epidemiol. 2001 Jul 1;154(1):1-13.
  12. NAD(P)H:quinone oxidoreductase (NQO1) polymorphism, exposure to benzene, and predisposition to disease: a HuGE review
    Nebert DW, Roe AL, Vandale SE, Bingham E, Oakley GG.  Genet Med. 2002 Mar-Apr;4(2):62-70
  13. Pooled Analysis of Alcohol Dehydrogenase Genotypes and Head and Neck Cancer: A HuGE Review
    Brennan P, Lewis S, Hashibe M, Bell DA, et alAm J Epidemiol Jan 2004; 159(1):1-16
  14. Meta-Analysis of the Association of the Cathepsin D Ala224Val Gene Polymorphism with the Risk of Alzheimers Disease A HuGE Gene-Disease Association Review
    Ntais C, Polycarpou A, Ioannidis JP. Am J Epidemiol Mar 2004; 159(6):527-536
  15. GJB2 (connexin 26) variants and nonsyndromic sensorineural hearing loss: A HuGE review
    Kenneson A, Van Naarden Braun K, Boyle CAGenet Med Aug 2002; 4(4): 258-74
  16. Human Genome Variation Society Nomenclature for the description of sequence variations
    (May 1, 2003). [Cited December 5, 2003].
Last Updated October 12, 2004