Methodological Issues in Multistage Genome-wide Association Studies (Q42035322)

15 October 2017

Methodological Issues in Multistage Genome-wide Association Studies (English)

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genome-wide association study

15 October 2017

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3

David V Conti

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15 October 2017

Duncan C Thomas

1

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15 October 2017

Graham Casey

2

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15 October 2017

Robert W Haile

4

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15 October 2017

Juan Pablo Lewinger

5

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15 October 2017

Daniel O Stram

6

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15 October 2017

language of work or name

English

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publication date

1 November 2009

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15 October 2017

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15 October 2017

24

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15 October 2017

4

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15 October 2017

414-429

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maintained by WikiProject

15 October 2017

WikiProject Mathematics

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cites work

Rapid and accurate multiple testing correction and power estimation for millions of correlated markers

1 reference

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Detecting gene-environment interactions using a combined case-only and case-control approach

5 June 2018

1 reference

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Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Gene-environment interaction in genome-wide association studies

5 June 2018

1 reference

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Genetic mapping in human disease

5 June 2018

1 reference

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Identification of genetic variants using bar-coded multiplexed sequencing

5 June 2018

1 reference

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Curses--winner's and otherwise--in genetic epidemiology

5 June 2018

1 reference

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Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Calibrating the performance of SNP arrays for whole-genome association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Tests for gene-environment interaction from case-control data: a novel study of type I error, power and designs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Study designs for genome-wide association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Estimation of the multiple testing burden for genomewide association studies of nearly all common variants

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

A genome-wide association study in 574 schizophrenia trios using DNA pooling

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Bias-reduced estimators and confidence intervals for odds ratios in genome-wide association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Multiple loci identified in a genome-wide association study of prostate cancer

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

The impact of next-generation sequencing technology on genetics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Genome-wide significance for dense SNP and resequencing data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

The genetic basis of complex traits: rare variants or "common gene, common disease"?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Pathway-based approaches for analysis of genomewide association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Fine mapping versus replication in whole-genome association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Power to detect risk alleles using genome-wide tag SNP panels

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Flexible design for following up positive findings

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Enriching the analysis of genomewide association studies with hierarchical modeling

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

A Bayesian measure of the probability of false discovery in genetic epidemiology studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Evaluation of genome-wide power of genetic association studies based on empirical data from the HapMap project

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Genomewide association analysis of coronary artery disease

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Replicating genotype-phenotype associations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Non-replication and inconsistency in the genome-wide association setting

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Semiparametric Bayesian analysis of case-control data under conditional gene-environment independence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Scanning the horizon: what is the future of genome-wide association studies in accelerating discoveries in cancer etiology and prevention?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Most rare missense alleles are deleterious in humans: implications for complex disease and association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Overcoming the winner's curse: estimating penetrance parameters from case-control data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

A note on permutation tests in multistage association scans.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Incorporating biological information as a prior in an empirical bayes approach to analyzing microarray data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Coverage and power in genomewide association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Two-stage designs in case-control association analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Evaluating statistical significance in two-stage genomewide association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Using linkage genome scans to improve power of association in genome scans

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Efficiency and power in genetic association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Ranks of genuine associations in whole-genome scans.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Genomic screening and replication using the same data set in family-based association testing

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Genome-wide association studies for common diseases and complex traits

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Multiple rare variants in different genes account for multifactorial inherited susceptibility to colorectal adenomas

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Research issues and strategies for genomic and proteomic biomarker discovery and validation: a statistical perspective

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Cost-effective designs for linkage disequilibrium mapping of complex traits

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Association testing by DNA pooling: an effective initial screen

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

DNA Pooling: a tool for large-scale association studies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Are rare variants responsible for susceptibility to complex diseases?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

The problem of multiple inference in studies designed to generate hypotheses

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

On the utility of gene set methods in genomewide association studies of quantitative traits

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Exploiting gene-environment independence for analysis of case-control studies: an empirical Bayes-type shrinkage estimator to trade-off between bias and efficiency

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Multistage sampling for latent variable models

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Drinking from the fire hose--statistical issues in genomewide association studies.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Including sampling and phenotyping costs into the optimization of two stage designs for genomewide association studies.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Most pooling variation in array-based DNA pooling is attributable to array error rather than pool construction error.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Genomic DNA pooling for whole-genome association scans in complex disease: empirical demonstration of efficacy in rheumatoid arthritis

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Efficient two-stage genome-wide association designs based on false positive report probabilities

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Detecting local high-scoring segments: a first-stage approach for genome-wide association studies.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Bayesian method for gene detection and mapping, using a case and control design and DNA pooling.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Evaluating coverage of genome-wide association studies

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Evaluating and improving power in whole-genome association studies using fixed marker sets.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Optimal two-stage genotyping designs for genome-wide association scans

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Two-Stage sampling designs for gene association studies

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Two-stage designs for gene-disease association studies with sample size constraints.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

The impacts of errors in individual genotyping and DNA pooling on association studies.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Optimal two-stage genotyping in population-based association studies

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Sample size requirements for matched case-control studies of gene-environment interaction

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

A two stage design for the study of the relationship between a rare exposure and a rare disease.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Improving power in genome-wide association studies: weights tip the scale

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Optimal designs for two-stage genome-wide association studies

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Genome-wide single nucleotide polymorphism analysis of lung cancer risk detects the KLF6 gene

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895324

Non-hierarchical logistic models and case-only designs for assessing susceptibility in population-based case-control studies

2 December 2018

1 reference

12 December 2020

Strategies for genome-wide association studies: optimization of study designs by the stepwise focusing method.

1 reference

12 December 2020

Two-Stage Designs for Gene-Disease Association Studies

1 reference

12 December 2020

1 reference

12 December 2020

Exploiting gene-environment independence in family-based case-control studies: increased power for detecting associations, interactions and joint effects

1 reference

12 December 2020

Reporting and interpretation in genome-wide association studies

1 reference

12 December 2020

Exploiting gene-environment interaction to detect genetic associations

1 reference

12 December 2020

A maximum likelihood method for studying gene-environment interactions under conditional independence of genotype and exposure

1 reference

12 December 2020

Genetic variation and cancer: improving the environment for publication of association studies

1 reference

12 December 2020

Population-based estimate of the average age-specific cumulative risk of breast cancer for a defined set of protein-truncating mutations in BRCA1 and BRCA2. Australian Breast Cancer Family Study

1 reference

12 December 2020

Limitations of the case-only design for identifying gene-environment interactions

1 reference

12 December 2020

Probability of detecting disease-associated single nucleotide polymorphisms in case-control genome-wide association studies.

1 reference

12 December 2020

Identifiers

DOI

10.1214/09-STS288

1 reference

15 October 2017

0 references

1 reference

15 October 2017

1 reference