Genome-wide association studies and the genetic dissection of complex traits.

paper Cited Public

Authors: Sebastiani, Paola; Timofeev, Nadia; Dworkis, Daniel A; Perls, Thomas T; Steinberg, Martin H
Year: 2009
Journal: American journal of hematology
PMID: 19569043
DOI: 10.1002/ajh.21440
PMCID: PMC2895326

#	Section	Preview
0	Background	Over the past 30 years, about 1,200 disease-causing genes have been identified by studying well…
1	Background	Three major factors have made GWAS popular and feasible in a relatively short time and are…
2	Background	The most common genetic variations are single nucleotide polymorphisms (SNPs)—variation of a…
3	Background	By 2005, the genetic community was ready to embark on several GWAS. The first published GWAS…
4	Background	artery disease and diabetes [6,31,32], fetal hemoglobin expression [33], and other traits [34].…
5	The State of the Art	Several reviews describe in great detail the necessary steps to plan, analyze, and report the…
6	Study design	Typically, a GWAS uses a case–control design, in which cases are ascertained based on the trait of…
7	Study design	Referent cohort subjects used in other studies can also be used as controls. This was the strategy…
8	Study design	[51] and EIGENSOFT [52]. Figure 2 provides an example using data from the New England Centenarian…
9	Study design	When the trait of interest is a quantitative measure, such as blood pressure or fetal hemoglobin…
10	Choice of genotyping platform and resource allocation	Despite some different choices of SNPs to be typed—either tag-SNPs chosen to capture substantial…
11	Choice of genotyping platform and resource allocation	the same chromosome [56]. Equivalent arrays produced by Affymetrix had lower coverage of common SNPs…
12	Choice of genotyping platform and resource allocation	the coverage of the full set of common and rare variants have been recently reviewed using sequence…
13	Quality control	Once the DNA samples are hybridized to the arrays and the arrays are read and quantified using some…
14	Quality control	Issues with sample quality can be easily identified by the proportion of SNPs that fail to have…
15	Quality control	in the study using estimates of the alleles that are shared identity by descent (IBD). Two alleles…
16	Quality control	III [64], and can identify repeated samples, as well as unknown relations. If the study includes…
17	Quality control	Other SNP-specific analyses are often carried out to remove low quality or unreliable data. For…
18	Statistical analysis	The core of the analysis is typically a statistical test conducted for each individual SNP in the…
19	Statistical analysis — Frequentist approaches	The frequentist approach is most commonly used to test these hypotheses and weighs the evidence…

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Bayesian Polynomial Regression Models to Fit Multiple Genetic Models for Quantitative Traits.	Bae H et al.	—	2015	→
Genetic Analysis Reveals a Longevity-Associated Protein Modulating Endothelial Function and Angiogenesis.	Villa F et al.	—	2015	→
Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.	Ilyas M et al.	—	2015	→
Classification, epidemiology, and genetics of orofacial clefts.	Watkins SE et al.	—	2014	→
Toward a road map for global -omics: a primer on -omic technologies.	Coughlin SS	—	2014	→
Implications of genome wide association studies for addiction: are our a priori assumptions all wrong?	Hall FS et al.	—	2013	→
The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies.	Lindquist KJ et al.	—	2013	→
Translating genome wide association study results to associations among common diseases: in silico study with an electronic medical record.	Anand V et al.	—	2013	→
Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs.	Krithika S et al.	—	2012	→
Genetic modifiers of sickle cell disease.	Steinberg MH et al.	—	2012	→
Genetic risk sum score comprised of common polygenic variation is associated with body mass index.	Peterson RE et al.	—	2011	→
Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS et al.	—	2011	→
Genome-wide association studies and susceptibility to infectious diseases.	Newport MJ et al.	—	2011	→
Microarray evidences the role of pathologic adipose tissue in insulin resistance and their clinical implications.	Mathur SK et al.	—	2011	→
Quantitative Models for Causal Analysis in the Era of Genome Wide Association Studies.	Coughlin SS	—	2011	→
Severe sickle cell anemia is associated with increased plasma levels of TNF-R1 and VCAM-1.	Dworkis DA et al.	—	2011	→
Therapy-related myeloid neoplasms: pathobiology and clinical characteristics.	Sill H et al.	—	2011	→
Genetic and environmental risk factors for adolescent-onset substance use disorders.	Meyers JL et al.	—	2010	→
Genetic modifiers of the severity of sickle cell anemia identified through a genome-wide association study.	Sebastiani P et al.	—	2010	→
History and current status of newborn screening for hemoglobinopathies.	Benson JM et al.	—	2010	→
Leg ulcers in sickle cell disease.	Minniti CP et al.	—	2010	→
Phenotypic complexity, measurement bias, and poor phenotypic resolution contribute to the missing heritability problem in genetic association studies.	van der Sluis S et al.	—	2010	→
Smoking and atherosclerotic cardiovascular disease: part IV: genetic markers associated with smoking.	Winkelmann BR et al.	—	2010	→
A systems biology consideration of the vasculopathy of sickle cell anemia: the need for multi-modality chemo-prophylaxsis.	Hebbel RP et al.	—	2009	→