PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies

Nature Communications
Molly A HallMarylyn D Ritchie

Abstract

Genome-wide, imputed, sequence, and structural data are now available for exceedingly large sample sizes. The needs for data management, handling population structure and related samples, and performing associations have largely been met. However, the infrastructure to support analyses involving complexity beyond genome-wide association studies is not standardized or centralized. We provide the PLatform for the Analysis, Translation, and Organization of large-scale data (PLATO), a software tool equipped to handle multi-omic data for hundreds of thousands of samples to explore complexity using genetic interactions, environment-wide association studies and gene-environment interactions, phenome-wide association studies, as well as copy number and rare variant analyses. Using the data from the Marshfield Personalized Medicine Research Project, a site in the electronic Medical Records and Genomics Network, we apply each feature of PLATO to type 2 diabetes and demonstrate how PLATO can be used to uncover the complex etiology of common traits.

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Citations

Apr 6, 2018·BMC Bioinformatics·Anurag VermaMarylyn D Ritchie
Mar 17, 2018·Current Epidemiology Reports·Anurag Verma, Marylyn D Ritchie
May 2, 2018·BioData Mining·Shefali S VermaMarylyn D Ritchie
Sep 29, 2020·Circulation·Derek KlarinUNKNOWN Veterans Affairs Million Veteran Program†
Mar 28, 2019·Human Genetics·Hua ZhouKenneth Lange
May 26, 2018·Human Genetics·Elisabetta ManduchiJason H Moore
Oct 27, 2018·Journal of Obesity·Elliot D K ChaSarah A Pendergrass
Jan 11, 2020·Frontiers in Genetics·Anastasia M LucasMolly A Hall
Feb 27, 2021·American Journal of Human Genetics·Theodore George DrivasMarylyn DeRiggi Ritchie
Jun 5, 2021·PLoS Genetics·Molly A HallMarylyn D Ritchie
Jul 18, 2021·Journal of Medical Genetics·Lijuan WangXue Li

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Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

phenx
* Calc
ArrayTools
BioBin
PennCNV
PLatform for the Analysis , Translation , and Organization of ...
GSEA
PhenX Toolkit
R
Bioconductor

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