Links and References
Online Resources
Plink guides: https://www.cog-genomics.org/plink/1.9/data; http://zzz.bwh.harvard.edu/plink/
LD-hub: http://ldsc.broadinstitute.org/ldhub/
Locuszoom: http://locuszoom.sph.umich.edu/
University of Michigan Imputation Server: https://imputationserver.sph.umich.edu
Haplotype Reference Consortium: http://www.haplotype-reference-consortium.org/home
SOLAR-Eclipse Genetics: http://solar-eclipse-genetics.org/
Gene-sets: http://software.broadinstitute.org/gsea/downloads.jsp
PRSice - Polygenic Risk Scores: http://prsice.info/
1000 Genomes Browser: http://www.ensembl.org/Homo_sapiens/Info/Index
GCTA: http://cnsgenomics.com/software/gcta/index.html
Genetic Power Calculation: http://csg.sph.umich.edu/abecasis/gas_power_calculator/
GCTA Power Calculator: http://cnsgenomics.com/shiny/gctaPower/
LD-Pred (Improving PRS accuracy): http://www.cell.com/ajhg/abstract/S0002-9297(15)00365-1
MTAG (Improving PRS accuracy II): http://www.biorxiv.org/content/early/2017/07/03/118810
MR-Base: http://www.mrbase.org/
Readings & References
GWAS of Height: Defining the role of common variation in the genomic and biological architecture of adult human height
Common disorders are quantitative traits, Plomin, 2009
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder, Purcell, 2009
Biological insights from 108 schizophrenia-associated genetic loci, PGC SCZ, 2014
GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Rietveld, 2013
MAGMA: Generalized Gene-Set Analysis of GWAS Data, Christiaan, 2015
Plink: A Tool Set for Whole-Genome Association... Purcell, 2007
Second-Generation PLINK... Chang, 2015
solarius: an R interface to SOLAR for variance component analysis in pedigrees, Ziyatdinov 2016
LD Score regression distinguishes confounding from polygenicity in genome-wide association studies, Bulik-Sullivan, 2015a
An Atlas of Genetic Correlations across Human Diseases and Traits, Bulik-Sullivan, 2015b
Statistical power and significance testing in large-scale genetic studies, Sham & Purcell 2014
What should the genome-wide significance threshold be? Empirical replication of borderline genetic associations, Panagiotou 2012
A critical review of the first 10 years of candidate gene-by-environment interaction research in psychiatry, Duncan & Keller 2011
Mendelian randomization: genetic anchors for causal inference in epidemiological studies, Davey Smith & Hemani 2014
Analysis of shared heritability in common disorders of the brain (aka BRAINSTORM), Anttila 2016
Logical and methodological issues affecting genetic studies of humans reported in top neuroscience journals, Grabitz 2017
Collaborative meta-analysis finds no evidence of a strong interaction between stress and 5-HTTLPR genotype contributing to the development of depression, Culverhouse 2017
Power-up: a reanalysis of ‘power failure’ in neuroscience using mixture modelling, Nord 2017