Dataset Information

Genome-based prediction of common diseases: methodological considerations for future research.

ABSTRACT: The translation of emerging genomic knowledge into public health and clinical care is one of the major challenges for the coming decades. At the moment, genome-based prediction of common diseases, such as type 2 diabetes, coronary heart disease and cancer, is still not informative. Our understanding of the genetic basis of multifactorial diseases is improving, but the currently identified susceptibility variants contribute only marginally to the development of disease. At the same time, an increasing number of companies are offering personalized lifestyle and health recommendations on the basis of individual genetic profiles. This discrepancy between the limited predictive value and the commercial availability of genetic profiles highlights the need for a critical appraisal of the usefulness of genome-based applications in clinical and public health care. Anticipating the discovery of a large number of genetic variants in the near future, we need to prepare a framework for the design and analysis of studies aiming to evaluate the clinical validity and utility of genetic tests. In this article, we review recent studies on the predictive value of genetic profiling from a methodological perspective and address issues around the choice of the study population, the construction of genetic profiles, the measurement of the predictive value, calibration and validation of prediction models, and assessment of clinical utility. Careful consideration of these issues will contribute to the knowledge base that is needed to identify useful genome-based applications for implementation in clinical and public health practice.

SUBMITTER: Janssens AC

PROVIDER: S-EPMC2664953 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Genome-based prediction of common diseases: methodological considerations for future research.

Janssens A Cecile Jw AC van Duijn Cornelia M CM

Genome medicine 20090218 2

The translation of emerging genomic knowledge into public health and clinical care is one of the major challenges for the coming decades. At the moment, genome-based prediction of common diseases, such as type 2 diabetes, coronary heart disease and cancer, is still not informative. Our understanding of the genetic basis of multifactorial diseases is improving, but the currently identified susceptibility variants contribute only marginally to the development of disease. At the same time, an incre ...[more]

PMID: 19341491

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Project description:BackgroundPneumonitis is one of the most common adverse events induced by the use of immune checkpoint inhibitors (ICI), accounting for a 20% of all ICI-associated deaths. Despite numerous efforts to identify risk factors and develop predictive models, there is no clinically deployed risk prediction model for patient risk stratification or for guiding subsequent monitoring. We believe this is due to systemic suboptimal approaches in study designs and methodologies in the literature. The nature and prevalence of different methodological approaches has not been thoroughly examined in prior systematic reviews.MethodsThe PubMed, medRxiv and bioRxiv databases were used to identify studies that aimed at risk factor discovery and/or risk prediction model development for ICI-induced pneumonitis (ICI pneumonitis). Studies were then analysed to identify common methodological pitfalls and their contribution to the risk of bias, assessed using the QUIPS and PROBAST tools.ResultsThere were 51 manuscripts eligible for the review, with Japan-based studies over-represented, being nearly half (24/51) of all papers considered. Only 2/51 studies had a low risk of bias overall. Common bias-inducing practices included unclear diagnostic method or potential misdiagnosis, lack of multiple testing correction, the use of univariate analysis for selecting features for multivariable analysis, discretization of continuous variables, and inappropriate handling of missing values. Results from the risk model development studies were also likely to have been overoptimistic due to lack of holdout sets.ConclusionsStudies with low risk of bias in their methodology are lacking in the existing literature. High-quality risk factor identification and risk model development studies are urgently required by the community to give the best chance of them progressing into a clinically deployable risk prediction model. Recommendations and alternative approaches for reducing the risk of bias were also discussed to guide future studies.

Project description:BackgroundMuch research is being carried out using publicly available Twitter data in the field of public health, but the types of research questions that these data are being used to answer and the extent to which these projects require ethical oversight are not clear.ObjectiveThis review describes the current state of public health research using Twitter data in terms of methods and research questions, geographic focus, and ethical considerations including obtaining informed consent from Twitter handlers.MethodsWe implemented a systematic review, following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, of articles published between January 2006 and October 31, 2019, using Twitter data in secondary analyses for public health research, which were found using standardized search criteria on SocINDEX, PsycINFO, and PubMed. Studies were excluded when using Twitter for primary data collection, such as for study recruitment or as part of a dissemination intervention.ResultsWe identified 367 articles that met eligibility criteria. Infectious disease (n=80, 22%) and substance use (n=66, 18%) were the most common topics for these studies, and sentiment mining (n=227, 62%), surveillance (n=224, 61%), and thematic exploration (n=217, 59%) were the most common methodologies employed. Approximately one-third of articles had a global or worldwide geographic focus; another one-third focused on the United States. The majority (n=222, 60%) of articles used a native Twitter application programming interface, and a significant amount of the remainder (n=102, 28%) used a third-party application programming interface. Only one-third (n=119, 32%) of studies sought ethical approval from an institutional review board, while 17% of them (n=62) included identifying information on Twitter users or tweets and 36% of them (n=131) attempted to anonymize identifiers. Most studies (n=272, 79%) included a discussion on the validity of the measures and reliability of coding (70% for interreliability of human coding and 70% for computer algorithm checks), but less attention was paid to the sampling frame, and what underlying population the sample represented.ConclusionsTwitter data may be useful in public health research, given its access to publicly available information. However, studies should exercise greater caution in considering the data sources, accession method, and external validity of the sampling frame. Further, an ethical framework is necessary to help guide future research in this area, especially when individual, identifiable Twitter users and tweets are shared and discussed.Trial registrationPROSPERO CRD42020148170; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=148170.

Dataset Information

Genome-based prediction of common diseases: methodological considerations for future research.

Publications

Genome-based prediction of common diseases: methodological considerations for future research.

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