lunes, 8 de julio de 2013

Variations in predicted risks in personal genome testing for common complex diseases : Genetics in Medicine : Nature Publishing Group

Variations in predicted risks in personal genome testing for common complex diseases : Genetics in Medicine : Nature Publishing Group

Variations in predicted risks in personal genome testing for common complex diseases

Genetics in Medicine
(2013)
doi:10.1038/gim.2013.80
Received
Accepted
Published online

Abstract

Purpose:

The promise of personalized genomics for common complex diseases depends, in part, on the ability to predict genetic risks on the basis of single nucleotide polymorphisms. We examined and compared the methods of three companies (23andMe, deCODEme, and Navigenics) that have offered direct-to-consumer personal genome testing.

Methods:

We simulated genotype data for 100,000 individuals on the basis of published genotype frequencies and predicted disease risks using the methods of the companies. Predictive ability for six diseases was assessed by the AUC.

Results:

AUC values differed among the diseases and among the companies. The highest values of the AUC were observed for age-related macular degeneration, celiac disease, and Crohn disease. The largest difference among the companies was found for celiac disease: the AUC was 0.73 for 23andMe and 0.82 for deCODEme. Predicted risks differed substantially among the companies as a result of differences in the sets of single nucleotide polymorphisms selected and the average population risks selected by the companies, and in the formulas used for the calculation of risks.

Conclusion:

Future efforts to design predictive models for the genomics of common complex diseases may benefit from understanding the strengths and limitations of the predictive algorithms designed by these early companies.
Genet Med advance online publication 27 June 2013
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Keywords:

direct-to-consumer; genetic testing; genomics; personal genome testing; risk prediction

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Author information

Affiliations

  1. Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands

    • Rachel R.J. Kalf,
    • Raluca Mihaescu,
    • Suman Kundu &
    • A. Cecile J.W. Janssens

  2. Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands

    • Peter de Knijff

  3. Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA

    • Robert C. Green

  4. Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA

    • A. Cecile J.W. Janssens

Corresponding author

Correspondence to:

Supplementary information

Word documents


  1. Supplementary Figure S1 (526 KB)


  2. Supplementary Figure S2 (620 KB)


  3. Supplementary Table S1 (201 KB)


  4. Supplementary Materials and Methods (60 KB)

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