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Research Training

[updated 12/27/2020]

Here are a select set of high yield resources (in addition to lab publications) to review prior to starting in the lab. feedback

Review / Statement / Guideline / Editorial Papers

Browsers

Computation

Tools

Power Calculators

 Review / Statement / Guideline / Editorial Papers

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CAD epidemiology: Viran SS, et al. Circulation 2020

CAD genetics: Musunuru K, Kathiresan S. Cell. 2019

CAD polygenic risk: Natarajan P. J Am Coll Cardiol. 2018; Aragam K, Natarajan P. Circ Res. 2020

Clonal hematopoiesis: Natarajan P, et al. Circ Genom Precis Med. 2018; Khetarpal S, et al. J Am Coll Cardiol. 2019

Digital health: Budd J, et al. Nat Med. 2020

GWAS: McCarthy MI, et al. Nat Rev Genet. 2009Cantor RM, et al. Am J Hum Genet. 2010Clarke GM, et al. Nat Protoc. 2011Visscher P, et al. Am J Hum Genet. 2017; Tam V, et al. Nat Rev Genet. 2019

Mendelian randomization: Holms MV, et al. Nat Rev Cardiol. 2017; Burgess S, et al. Wellcome Open Res. 2020

Meta-analysis: Gurevitch J, et al. Nature. 2018

Precision medicine: Collins FS, Varmus H. N Eng J Med. 2015

Return of results: Kalia SS, et al. Genet Med. 2017

RVAS: Lee S, et al. Am J Hum Genet. 2014Auer PL, Lettre G. Genome Med. 2015; Sazonovs A, Barrett JC. Annu Rev Genomics Hum Genet. 2018

Sequencing: Shendure J, et al. Nature. 2017

T2D genetics: Bonneford A, Froguerl P. Cell Metab. 2015, Ingelsson E, McCarthy M. Circ Genom Precis Med. 2018

 Browsers

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Variants: dbSNPUCSC, ExAC, gnomAD, BRAVO

Annotation: VEP

Genotype-phenotype correlation: GWAS Catalog, PhenoScanner, Global Biobank Engine

Mendelian: OMIM, ClinVar, ClinGen, HGMD

Regulation: GTEx, HaploReg, RegulomeDB

Heritability: LD Hub

Proxies: LDlink

Mendelian randomization: MRBase

 Computation

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Broad cluster: Intro, Software, Job submission

Cloud collaboration: FireCloud

Google Cloud: SDKcloudtools

 Tools

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Variant discovery: GATK

QC/Manipulation: Hail (tutorial), bcftools, PLINKGATK

Association: Hail, PLINK, EPACTS, BOLT-LMM, Rvtests

Annotation: Hail, VEP, dbNSFP, Reg2Map

Population stratification: Hail, EIGENSOFT, ADMIXTURE

Heritability: GCTA, LD score

Mendelian randomization: MendelianRandomization, TwoSampleMR

Plotting: ggplots2, bokeh, qqman, LocusZoom

R: R Markdown (tutorial), Shiny

 Power Calculators

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Association: Genetic Power Calculator, PAGENT, GAS

Mendelian randomization: mRnd

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