Selected HuGENet Bibliography

This page contains citations and links for selected publications related to HuGENet.

Guidelines

• Evaluation of the Endorsement of the STrengthening the REporting of Genetic Association Studies (STREGA) Statement on the Reporting Quality of Published Genetic Association Studies.
  Nedovic D, Panic N, Pastorino R, Ricciardi W, Boccia S. J Epidemiol. 2016 Jun 25.
• Editorial: Updated guidance on Human Genome Epidemiology (HuGE) reviews and meta-analyses of genetic associations
  Marta Gwinn, John P. Ioannidis, Julian Little and Muin J. Khoury Am. J. Epidemiol. (2014) Aug 26
• Recommendations and proposed guidelines for assessing the cumulative evidence on joint effects of genes and environments on cancer occurrence in humans.
  Boffetta P, Winn DM, Ioannidis JP, Thomas DC, Little J, Davey Smith G, Cogliano VJ, Hecht SS, Seminara D, Vineis P, Khoury MJ.
  International Journal of Epidemiology 2012;41(3):686-704.
• Strengthening the Reporting of Genetic Risk Prediction Studies: The GRIPS Statement
  Janssens ACJW, Ioannidis JPA, van Duijn CM, Little J, Khoury MJ, et al.
  PLoS Medicine 2011;8(3):e1000420.
• STrengthening the REporting of Genetic Association Studies (STREGA): An Extension of the STROBE Statement
  Little J, Higgins JPT, Ioannidis JPA, Moher D, Gagnon, F, von Elm E, et al.
  Annals of Internal Medicine. 2009;150(3):206-215.
• The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop.
  Khoury MJ, McBride CM, Schully SD, Ioannidis JP, Feero WG, Janssens AC, et al.; Centers for Disease Control and Prevention.
  Genetics in Medicine 2009;11(8):559-67.
• Assessment of cumulative evidence on genetic associations: interim guidelines
  Ioannidis JP, Boffetta P, Little J, O’Brien TR, Uitterlinden AG, Vineis P, et al.
  International Journal of Epidemiology 2008;37(1):120-32.
• Reporting, appraising, and integrating data on genotype prevalence and gene-disease associations
  Little J, Bradley L, Bray MS, Clyne M, Dorman J, Ellsworth, DL, et al.
  American Journal of Epidemiology 2002;156(4):300-10.

Methods and Analysis

Knowledge synthesis

• Comprehensive research synopsis and systematic meta-analyses in Parkinson’s disease genetics: The PDGene database.
  Lill CM, Roehr JT, McQueen MB, Kavvoura FK, Bagade S, Schjeide BM, et al.
  PLoS Genetics 2012;8(3):e1002548.

• Estimating the contribution of genetic variants to difference in incidence of disease between population groups.
  Moonesinghe R, Ioannidis JP, Flanders WD, Yang Q, Truman BI, Khoury MJ.
  European Journal of Human Genetics 2012;20(8):831-6.

• Assessing causal relationships in genomics: From Bradford-Hill criteria to complex gene-environment interactions and directed acyclic graphs.
  Geneletti S, Gallo V, Porta M, Khoury MJ, Vineis P.
  Emerging Themes in Epidemiology 2011;8(1):5.

• Combining molecular and genetic data from different sources.
  Ntzani EE, Khoury MJ, Ioannidis JP.
  IARC Scientific Publications 2011;(163):323-36.

• Synopsis of preterm birth genetic association studies: the preterm birth genetics knowledge base (PTBGene).
  Dolan SM, Hollegaard MV, Merialdi M, Betran AP, Allen T, Abelow C, et al.
  Public Health Genomics 2010;13(7-8):514-23.

• A Hardy-Weinberg equilibrium test for analyzing population genetic surveys with complex sample designs.
  Moonesinghe R, Yesupriya A, Chang MH, Dowling NF, Khoury MJ, Scott AJ; CDC/NCI NHANES III Genomics Working Group.
  American Journal of Epidemiology 2010;171(8):932-41.

• Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation and human diseases.
  Khoury MJ, Bertram L, Boffetta P, Butterworth AS, Chanock SJ, Dolan SM,, et al.
  American Journal of Epidemiology 2009;170(3):269-79.

• Trends in pharmacogenomic epidemiology: 2001-2007.
  Guessous I, Gwinn M, Yu W, Yeh J, Clyne M, Khoury MJ.
  Public Health Genomics 2009;12(3):142-8.

• An empirical comparison of meta-analyses of published gene-disease associations versus consortium analyses.
  Janssens AC, González-Zuloeta Ladd AM, López-Léon S, Ioannidis JP, Oostra BA, Khoury MJ, van Duijn CM.
  Genetics in Medicine 2009;11(3):153-62.

• Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.
  Burton PR, Hansell AL, Fortier I, Manolio TA, Khoury MJ, Little J, Elliott P.
  International Journal of Epidemiology 2009;38(1):263-73.

• Evaluation of the potential excess of statistically significant findings in published genetic association studies: application to Alzheimer’s disease.
  Kavvoura FK, McQueen MB, Khoury MJ, Tanzi RE, Bertram L, Ioannidis JP.
  American Journal of Epidemiology 2008;168(8):855-65.

• Required sample size and nonreplicability thresholds for heterogeneous genetic associations
  Moonesinghe R, Khoury MJ, Liu T, Ioannidis JP.
  Proceedings of the National Academy of Sciences U S A. 2008;105:617-22.

• Sample size requirements to detect the effect of a group of genetic variants in case-control studies.
  Moonesinghe R, Yang Q, Khoury MJ.
  Emerging Themes in Epidemiology 2008;5:24.

• Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database.
  Allen NC, Bagade S, McQueen MB, Ioannidis JP, Kavvoura FK, Khoury MJ, Tanzi RE, Bertram L.
  Nature Genetics 2008;40(7):827-34.

• Reporting of human genome epidemiology (HuGE) association studies: an empirical assessment.
  Yesupriya A, Evangelou E, Kavvoura FK, Patsopoulos NA, Clyne M, Walsh MC, Lin BK, Yu W, Gwinn M, Ioannidis JP, Khoury MJ.
  BMC Medical Research Methodology 2008;8:31.

• Meta-analysis in genome-wide association datasets: strategies and application in Parkinson disease
  Evangelou E, Maraganore DM, Ioannidis JP.
  PLoS ONE 2007;2(2):e196.
• Turning the pump handle: evolving methods for integrating the evidence on gene-disease association
  Higgins J, Little J, Ioannidis JP, Bray MS, Manolio TA, Smeeth L, et al.
  American Journal of Epidemiology 2007;166(8):863-66.
• On the synthesis and interpretation of consistent but weak gene–disease associations in the era of genome-wide association studies
  Khoury MJ, Little J, Gwinn M, Ioannidis JP.
  International Journal of Epidemiology 2007;36(2):439-45.
• Most published research findings are false–but a little replication goes a long way
  Moonesinghe R, Khoury MJ, Janssens AC.
  PLoS Medicine 2007;4(2):e28.
• Genetic epidemiological studies of preterm birth: guidelines for research
  Pennell CE, Jacobsson B, Williams SM, Buus RM, Muglia LJ, Dolan SM, et al.
  American Journal of Obstetrics and Gynecology 2007;196(2):107-18.
• Tools for assessing quality and susceptibility to bias in observational studies in epidemiology: a systematic review and annotated bibliography
  Sanderson S, Tatt ID, Higgins JP.
  International Journal of Epidemiology 2007;36(3):666-76.
• Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases
  Ioannidis JP, Trikalinos TA, Khoury MJ.
  American Journal of Epidemiology 2006;164(7):609-14

Clinical validity

• Predictive genetic testing for the identification of high-risk groups: a simulation study on the impact of predictive ability.
  Mihaescu R, Moonesinghe R, Khoury MJ, Janssens AC.
  Genome Medicine 2011;3(7):51.
• Discriminative accuracy of genomic profiling comparing multiplicative and additive risk models.
  Moonesinghe R, Khoury MJ, Liu T, Janssens AC.
  European Journal of Human Genetics 2011;19(2):180-5.
• The emergence of translational epidemiology: from scientific discovery to population health impact.
  Khoury MJ, Gwinn M, Ioannidis JP.
  American Journal of Epidemiology 2010;172(5):517-24.
• Application of support vector machine modeling for prediction of common diseases: the case of diabetes and pre-diabetes.
  Yu W, Liu T, Valdez R, Gwinn M, Khoury MJ.
  BMC Medical Informatics & Decision Making 2010;10:16.
• Evaluation of the discriminative accuracy of genomic profiling in the prediction of common complex diseases.
  Moonesinghe R, Liu T, Khoury MJ.
  European Journal of Human Genetics 2010;18(4):485-9.
• Using lifetime risk estimates in personal genomic profiles: estimation of uncertainty.
  Yang Q, Flanders WD, Moonesinghe R, Ioannidis JP, Guessous I, Khoury MJ.
  American Journal of Human Genetics 2009;85(6):786-800.
• A critical appraisal of the scientific basis of commercial genomic profiles used to assess health risks and personalize health interventions
  Janssens AC, Gwinn M, Bradley LA, Oostra BA, van Duijn CM, Khoury MJ.
  American Journal of Human Genetics 2008;82(3):593-9.
• The impact of genotype frequencies on the clinical validity of genomic profiling for predicting common chronic diseases
  Janssens AC, Moonesinghe R, Yang Q, Steyerberg EW, van Duijn CM, Khoury MJ.
  Genetics in Medicine 2007;9(8):528-35.
• Quantifying the health benefits of genetic tests: the importance of a population perspective
  Khoury MJ, Jones K, Grosse SD.
  Genetics in Medicine 2006; 8(3):191-5
• Improving the prediction of complex diseases by testing for multiple disease-susceptibility genes
  Yang Q, Khoury MJ, Botto L, Friedman JM, Flanders WD.
  American Journal of Human Genetics 2003;72(3):636-49.
• Genetic test evaluation: information needs of clinicians, policy-makers and the public
  Burke W, Atkins D, Gwinn M, Guttmacher A, Haddow J, Lau J, et al.
  American Journal of Epidemiology2002; 156(4):311-8.

HuGE Navigator

• GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies.
  Yu W, Yesupriya A, Wulf A, Hindorff LA, Dowling N, Khoury MJ, Gwinn M.
  European Journal of Human Genetics 2011;19(10):1095-9.

• Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations.
  Yu W, Clyne M, Khoury MJ, Gwinn M.
  Bioinformatics 2010;26(1):145-6.
• The need for genetic variant naming standards in published abstracts of human genetic association studies.
  Yu W, Ned R, Wulf A, Liu T, Khoury MJ, Gwinn M.
  BMC Research Notes 2009;2:56.
• Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.
  Yu W, Wulf A, Liu T, Khoury MJ, Gwinn M.
  BMC Bioinformatics 2008;9:528.
• HuGE Watch: tracking trends and patterns of published studies of genetic association and human genome epidemiology in near-real time.
  Yu W, Wulf A, Yesupriya A, Clyne M, Khoury MJ, Gwinn M.
  European Journal of Human Genetics 2008;16(9):1155-8.
• GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.
  Yu W, Clyne M, Dolan SM, Yesupriya A, Wulf A, Liu T, Khoury MJ, Gwinn M.
  BMC Bioinformatics 2008 Apr 22;9:205.
• A navigator for human genome epidemiology.
  Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ.
  Nature Genetics 2008;40(2):124-5.
• An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology.
  Yu W, Yesupriya A, Wulf A, Qu J, Khoury MJ, Gwinn M.
  BMC Bioinformatics 2007;8:436.
• An automatic method to generate domain-specific investigator networks using PubMed abstracts.
  Yu W, Yesupriya A, Wulf A, Qu J, Gwinn M, Khoury MJ.
  BMC Medical Informatics & Decision Making 2007;7:17.
• Online genetic databases informing human genome epidemiology
  Frodsham AJ, Higgins JP.
  BMC Medical Research Methodology 2007 Jul 4;7:31.
• Tracking the epidemiology of human genes in the literature: the HuGE Published Literature database.
  Lin BK, Clyne M, Walsh M, Gomez O, Yu W, Gwinn M, Khoury MJ.
  American Journal of Epidemiology 2006;164(1):1-4.

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Commentary

• A population approach to precision medicine.
  Khoury MJ, Gwinn ML, Glasgow RE, Kramer BS.
  American Journal of Preventive Medicine 2012;42(6):639-45.
• Knowledge integration at the center of genomic medicine.
  Khoury MJ, Gwinn M, Dotson WD, Schully SD.
  Genetics in Medicine 2012 May 3. doi: 10.1038/gim.2012.43.
• Improving validation practices in “omics” research.
  Ioannidis JP, Khoury MJ.
  Science 2011;334(6060):1230-2.
• Genetic epidemiology with a capital E, ten years after.
  Khoury MJ, Gwinn M, Clyne M, Yu W.
  Genetic Epidemiology 2011 Dec;35(8):845-52.
• Assessment of improved prediction beyond traditional risk factors: when does a difference make a difference?
  Janssens AC, Khoury MJ.
  Circulation: Cardiovascular Genetics 2010;3(1):3-5.
• Invited commentary: genes, environment, and hybrid vigor.
  Gwinn M, Guessous I, Khoury MJ.
  American Journal of Epidemiology 2009;170(6):703-7.
• Genome-wide association studies in pharmacogenomics: untapped potential for translation.
  Guessous I, Gwinn M, Khoury MJ.
  Genome Medicine 2009;1(4):46.
• Building a knowledge base on genetic variation and cancer risk through field synopses.
  Yesupriya A, Gwinn M, Khoury MJ.
  Journal of the National Cancer Institute 2009;101(1):4-5.
• Invited commentary: from genome-wide association studies to gene-environment-wide interaction studies–challenges and opportunities.
  Khoury MJ, Wacholder S.
  American Journal of Epidemiology 2009;169(2):227-30; discussion 234-5.
• Intention to analyze in pharmacogenomics studies.
  Gwinn M, Guessous I, Khoury M.
  Cancer Epidemiology Biomarkers & Prevention 2008;17(3):740; author reply 740-1.
• The continued need to synthesize the results of genetic associations across multiple studies.
  Yesupriya A, Yu W, Clyne M, Gwinn M, Khoury MJ.
  Genetics in Medicine 2008;10(8):633-5.
• The path from genome-based research to population health: development of an international public health genomics network
  Burke, W, Khoury, MJ, Stewart, A, Zimmern, RL, for the Bellagio Group.
  Genetics in Medicine 2006; 8(7):451-58
• Predictive value of testing for multiple genetic variants in multifactorial diseases: implications for the discourse on ethical, legal and social issues [PDF 327 KB]
  Janssens AC, Khoury MJ.
  Italian Journal of Public Health 2007;4(3):35-41.
• Reporting of systematic reviews: the challenge of genetic association studies
  Khoury MJ, Little J, Higgins J, Ioannidis JP, Gwinn M.
  PLoS Medicine 2007;4(3):e78.
• The emergence of networks in human genome epidemiology: challenges and opportunities
  Seminara D, Khoury MJ, O’Brien TR, Manolio T, Gwinn ML, Little J, et al
  Epidemiology 2007;18(1):1-8.
• Commentary: grading the credibility of molecular evidence for complex diseases
  Ioannidis JP.
  International Journal of Epidemiology 2006 Jun;35(3):572-8
• Genomics, epidemiology and common complex diseases: let’s not throw out the baby with the bathwater!
  Khoury MJ, Gwinn M.
  International Journal of Epidemiology 2006; 35(5):1363-1364
• Getting ready for the future: integration of genomics into public health research, policy and practice in Europe and globally
  Brand A, Schroder P, Brand H, Zimmern R.
  Community Genetics 2006; 9(1):67-71
• Expanded publishing model for genetic association studies
  Gwinn M, Khoury MJ.
  Cancer Epidemiology Biomarkers & Prevention 2006;15(1):185
• Genomics and public health in the United States: signposts on the translation highway
  Gwinn M, Khoury MJ
  Community Genetics 2006; 9(1):21-6
• A road map for efficient and reliable human genome epidemiology
  Ioannidis JP, Gwinn M, Little J, Higgins J, Bernstein JL, Boffetta P,
  Nature Genetics 2006;38:305.
• Do we need genomic research for the prevention of common diseases with environmental causes?
  Khoury MJ, Davis R, Gwinn M, Lindegren ML, Yoon P.
  American Journal of Epidemiology 2006; 161(9):799-805
• A network of investigator networks in human genome epidemiology
  Ioannidis JP, Bernstein J, Boffetta P, Danesh J, Dolan S, Hartge P, et al.
  American Journal of Epidemiology 2005; 162(4):302-304
• The epidemiologic approach to pharmacogenomics
  Little J, Sharp L, Khoury MJ, Bradley L, Gwinn M.
  American Journal of Pharmacogenomics 2005; 5(1):1-20
• The emergence of epidemiology in the genomics age
  Khoury MJ, Millikan R, Little J, Gwinn M.
  International Journal of Epidemiology 2004; 33(5):936-944
• Commentary: mendelian randomisation: a new spin or real progress?
  Little J, Khoury MJ.
  Lancet 2003;362(9388):930-1
• The human genome project is now complete. How do we develop a handle for the pump?
  Little J, Khoury MJ, Bradley L, Clyne M, Gwinn M, Lin B, et al.,
  American Journal of Epidemiology 2003; 157:667-673
• The case for a global human genome epidemiology initiative
  Khoury MJ.
  Nature Genetics 2004;36(10):1027-8
• Commentary: epidemiology and the continuum from genetic research to genetic testing
  Khoury MJ.
  American Journal of Epidemiology 2002; 156:297-299.
• The Human Genome Epidemiology Network (HuGENet)
  Khoury MJ, Dorman JS.
  American Journal of Epidemiology 1998; 198:4

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Books

• Human Genome Epidemiology (2nd ed.): Building the evidence for using genetic information to improve health and prevent disease.
  Khoury MJ, Bedrosian S, Gwinn M, Little J, Ioannidis JP (eds). Oxford University Press, New York, 2010.
• Human genome epidemiology: a scientific foundation for using genetic information to improve health and prevent disease
  Khoury MJ, Little J, Burke W (eds). Oxford University Press, New York, 2004.

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