Cited by 759Genetic Associations and EpidemiologyNutrition, Genetics, and DiseaseDiabetes, Cardiovascular Risks, and Lipoproteins

Genotype score in addition to common risk factors for prediction of type 2 diabetes

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Meigs, James B., Shrader, Peter, Sullivan, Lisa M., McAteer, Jarred B., Fox, Caroline S., Dupuis, Josée, Manning, Alisa K., Florez, Jose C. +3 more·2008·New England Journal of Medicine

Abstract

BACKGROUND: Multiple genetic loci have been convincingly associated with the risk of type 2 diabetes mellitus. We tested the hypothesis that knowledge of these loci allows better prediction of risk than knowledge of common phenotypic risk factors alone. METHODS: We genotyped single-nucleotide polymorphisms (SNPs) at 18 loci associated with diabetes in 2377 participants of the Framingham Offspring Study. We created a genotype score from the number of risk alleles and used logistic regression to generate C statistics indicating the extent to which the genotype score can discriminate the risk of diabetes when used alone and in addition to clinical risk factors. RESULTS: There were 255 new cases of diabetes during 28 years of follow-up. The mean (+/-SD) genotype score was 17.7+/-2.7 among subjects in whom diabetes developed and 17.1+/-2.6 among those in whom diabetes did not develop (P<0.001). The sex-adjusted odds ratio for diabetes was 1.12 per risk allele (95% confidence interval, 1.07 to 1.17). The C statistic was 0.534 without the genotype score and 0.581 with the score (P=0.01). In a model adjusted for sex and self-reported family history of diabetes, the C statistic was 0.595 without the genotype score and 0.615 with the score (P=0.11). In a model adjusted for age, sex, family history, body-mass index, fasting glucose level, systolic blood pressure, high-density lipoprotein cholesterol level, and triglyceride level, the C statistic was 0.900 without the genotype score and 0.901 with the score (P=0.49). The genotype score resulted in the appropriate risk reclassification of, at most, 4% of the subjects. CONCLUSIONS: A genotype score based on 18 risk alleles predicted new cases of diabetes in the community but provided only a slightly better prediction of risk than knowledge of common risk factors alone.

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  • Models to combine multiple markers into a cumulative risk score are often flawed and are usually no better than traditional risk factors such as family history, demographics and non-genetic clinical phenotypes.

    “models to combine multiple markers into a cumulative risk score are often flawed and are usually no better than traditional risk factors such as family history, demographics and non-genetic clinical phenotypes.”

    From Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (2015) · cites this paper as [55]

    The Discussion reports that this 18-allele genotype score did not substantially improve type 2 diabetes prediction beyond common phenotypic risk factors measured in adulthood. It does not establish that cumulative risk-score models are often flawed or usually perform no better across diseases or settings. (LLM, conf=0.88)

    Experimental — accuracy not yet measured
  • The risk alleles in these loci all have relatively small effects and do not significantly enhance our ability to predict the risk of type 2 diabetes.

    “However, the risk alleles in these loci all have relatively small effects and do not significantly enhance our ability to predict the risk of type 2 diabetes (396,397).”

    From Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus (2023) · cites this paper as [397]

    The Discussion reports small individual per-allele effects and says the 18-allele score did not substantially improve prediction beyond common phenotypic risk factors measured in adulthood. The claim omits that condition: the paper also reports modest discriminatory ability when only factors known in youth were considered. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • The risk alleles at these loci have small effects (odds ratios 1.1-1.3) and do not substantially improve type 2 diabetes risk prediction.

    “The risk alleles in these loci all have relatively small effects (odds ratios of 1. 1 to 1.3), however, and do not significantly enhance our ability to predict the risk of type 2 diabetes (274).”
  • Together these genes do not explain much of the genetic basis of type 2 diabetes; genotype risk scores only slightly improve prediction compared to common clinical risk factors.

    “Together these genes do not appear to explain much of the genetic basis of the disease with the use of genotype risk scores only slightly improving prediction of subsequent diabetes compared to common clinical risk factors22,23.”
  • Known diabetes polymorphisms add modestly to risk assessment, being associated with 5% to 37% increases in relative risk.

    “There has been interest in genetic risk prediction, but the known diabetes polymorphisms add modestly to risk assessment27,28. For instance, known polymorphisms are only associated with 5% to 37% increases in the relative risk of diabetes”

    From Metabolite profiles and the risk of developing diabetes (2011) · cites this paper as [27]

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Authors
Meigs, J. B., Shrader, P., Sullivan, L. M., McAteer, J. B., Fox, C. S., Dupuis, J., Manning, A. K., Florez, J. C., Wilson, P. W. F., D'Agostino, R. B., & Cupples, L. A.
Affiliations
  • Massachusetts General Hospital (US)
  • Boston University (US)
  • Broad Institute (US)
  • Brigham and Women's Hospital (US)
Venue
New England Journal of Medicine
Published
2008-11-20
Volume
359
Issue
21
Pages
2208-2219
ISSN
  • 0028-4793 (ISSN-L)
  • 1533-4406
OpenAlex
W2101359494
Cited by
759
References
41
Citations by year
2026: 5 · 2025: 14 · 2024: 13 · 2023: 20 · 2022: 20 · 2021: 26 · 2020: 16 · 2019: 37 · 2018: 37 · 2017: 42 · 2016: 47 · 2015: 41 · 2014: 58 · 2013: 72 · 2012: 85
FWCI
42.93
Type
journal article
Language
en
Open access
Locations
  • New England Journal of Medicine (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health (n01hc25195-41-0-1)
  • National Heart, Lung, and Blood Institute (N01‐HC25195, N01-HC-025195)
  • National Institute of Diabetes and Digestive and Kidney Diseases (K23 DK65978, R01DK078616, K24DK080140, K23DK065978)
  • National Center for Research Resources (1S10 RR163736-01A1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
  • Health Sciences › Medicine › Endocrinology, Diabetes and Metabolism › Diabetes, Cardiovascular Risks, and Lipoproteins
Keywords
type 2 diabetes, genotype score, genetic susceptibility loci, single nucleotide polymorphisms, diabetes risk prediction, Framingham Offspring Study, family history of diabetes, risk alleles
MeSH terms
Adult, Diabetes Mellitus, Type 2, Female, Follow-Up Studies, Gene Frequency, Genotype, Humans, Male, Middle Aged, Phenotype, Risk Factors, Logistic Models, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide

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