Are We Ready for Genome-wide Association Studies?

Thomas, Duncan C.

doi:10.1158/1055-9965.epi-06-0146

Cited by 50 publications

(40 citation statements)

References 63 publications

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“…Despite many similarities between genetic association studies and ''classical'' observational epidemiologic studies (that is, cross-sectional, case-control, and cohort) of lifestyle and environmental factors, genetic association studies present several specific challenges including an unprecedented volume of new data (Lawrence et al 2005;Thomas 2006) and the likelihood of very small individual effects. Genes may operate in complex pathways with gene-environment and gene-gene interactions .…”

Section: Introductionmentioning

confidence: 99%

Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement

et al. 2009

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Making sense of rapidly evolving evidence on genetic associations is crucial to making genuine advances in human genomics and the eventual integration of this information in the practice of medicine and public health. Assessment of the strengths and weaknesses of this evidence, and hence the ability to synthesize it, has been limited by inadequate reporting of results. The STrengthening the REporting of Genetic Association studies (STREGA) initiative builds on the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement and provides additions to 12 of the 22 items on the STROBE checklist. The additions concern population stratification, genotyping errors, modeling haplotype variation, Hardy-Weinberg equilibrium, replication, selection of participants, rationale for choice of genes and variants, treatment effects in studying quantitative traits, 123Hum Genet ( ) 125:131-151 DOI 10.1007 statistical methods, relatedness, reporting of descriptive and outcome data, and the volume of data issues that are important to consider in genetic association studies. The STREGA recommendations do not prescribe or dictate how a genetic association study should be designed but seek to enhance the transparency of its reporting, regardless of choices made during design, conduct, or analysis.

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Section: Introductionmentioning

confidence: 99%

Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement

et al. 2009

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“…Second, genome-wide association (GWA) studies, in which a dense array of genetic markers, capturing a substantial proportion of common variation in genome sequence, is typed in a set of DNA samples and tested for association with the trait of interest, without a priori hypotheses [38,39]. The comprehensive analyses of common variation in the human genome in association with specific diseases through GWA studies are expanding the search for genetic risk factors on an unprecedented scale [40,41]. As of July 2009, the vast majority of published genetic association studies continue to present results for candidate genes.…”

Section: Introductionmentioning

confidence: 99%

On Track? Using the Human Genome Epidemiology Roadmap

Little

Hawken²

2010

Public Health Genomics

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“…Contemporary genotyping technologies allow for thousands, and even hundreds of thousands, of genotypes to be done quickly using a relatively small amount of DNA (1)(2)(3). Interest in genome-wide scans to identify susceptibility alleles for cancer is growing, and the use of these technologies to perform genome-wide association studies is under way (2).…”

Section: Introductionmentioning

confidence: 99%

“…Interest in genome-wide scans to identify susceptibility alleles for cancer is growing, and the use of these technologies to perform genome-wide association studies is under way (2). One such study is the Cancer Genetic Markers of Susceptibility initiative that will use a genome-wide scan to identify genetic susceptibility to prostate and breast cancer.…”

Section: Introductionmentioning

confidence: 99%

Successful Genome-Wide Scan in Paired Blood and Buccal Samples

Feigelson

Rodríguez

Welch

et al. 2007

Cancer Epidemiology, Biomarkers &Amp; Prevention

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Interest in genome-wide association studies to identify susceptibility alleles for cancer is growing, and several are currently planned or under way. Although the feasibility of collecting buccal cell samples as an alternative to venous blood samples as a source of genomic DNA has been shown, the validity of using DNA from buccal cells for genome-wide scans has not been assessed. We used 46 paired buffy coat and buccal cell samples to test the feasibility of using DNA from buccal cells for genotyping with the HumanHap300 Bead Chip (v.1.0.0) on the Illumina Infinium II platform. Genotyping was successful in every sample, regardless of DNA yield or sample type. Of the 317,502 genotypes attempted, 315,314 (99.3%) were successfully called. Completion rates were similar for buffy coat and buccal cell samples (99.63% and 99.44%, respectively; P = 0.15). Completion rates <99% were observed in only four samples and did not differ by specimen type. The paired samples showed exceptionally high concordance (99.96%). These results show that buccal cell samples collected and processed under optimal conditions can be used for genome-wide association studies with results comparable to those obtained from DNA extracted from buffy coat. (Cancer Epidemiol Biomarkers Prev 2007;16(5):1023 -5)

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Are We Ready for Genome-wide Association Studies?

Cited by 50 publications

References 63 publications

Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement

Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement

On Track? Using the Human Genome Epidemiology Roadmap

Successful Genome-Wide Scan in Paired Blood and Buccal Samples

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