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Protocols

PLATO specifications

Information


Unique identifier OMICS_16741
Name PLATO
Alternative name PLatform for the Analysis Translation and Organization of large-scale data
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.1.0
Stability Beta
Maintained Yes

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Documentation


Maintainer


  • person_outline Marylyn Ritchie

Publication for PLatform for the Analysis Translation and Organization of large-scale data

PLATO citations

 (10)
library_books

Sequencing of Linkage Region on Chromosome 12p11 Identifies PKP2 as a Candidate Gene for Left Ventricular Mass in Dominican Families

2017
PMCID: 5919734
PMID: 29288195
DOI: 10.1534/g3.117.300358

[…] in NOMAS and 842 exonic RVs in the replication families. Mendelian error checking was performed in the replication families and Mendelian errors were set to missing for all the variants called using PLATO v. 0.84 (). […]

library_books

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

2017
Nat Commun
PMCID: 5660079
PMID: 29079728
DOI: 10.1038/s41467-017-00802-2

[…] le ), there is need for an integrated analytic tool to investigate genetic and environmental factors by modeling the complexity involved in the development of common traits and diseases. We offer the PLatform for the Analysis, Translation, and Organization of large-scale data (PLATO) software as a multifaceted, unified tool for investigating complexity, including genetic interactions, environment- […]

library_books

Genome wide study of resistant hypertension identified from electronic health records

2017
PLoS One
PMCID: 5319785
PMID: 28222112
DOI: 10.1371/journal.pone.0171745

[…] For the GWAS, single-SNP tests of association were performed in PLINK [] and PLATO [] using logistic regression and assuming an additive genetic model. All associations were adjusted for sex, decade of birth, median body mass index (BMI in kg/m2), genotyping platform, and gene […]

library_books

Rare Variants in NOD1 Associated with Carotid Bifurcation Intima Media Thickness in Dominican Republic Families

2016
PLoS One
PMCID: 5147882
PMID: 27936005
DOI: 10.1371/journal.pone.0167202

[…] ree structure was confirmed using the Graphical Relationship Representation software. Mendelian error checking was performed and Mendelian errors were set to missing for all the variants called using PLATO[]. We additionally removed non-exonic variants, leaving us with 136 samples from 9 families and 791 exonic RVs available for analyses. […]

call_split

Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome Wide Data

2016
Front Genet
PMCID: 4858524
PMID: 27200085
DOI: 10.3389/fgene.2016.00076
call_split See protocol

[…] ham ().Processing of genotype files into the input format for STRUCTURE and principal component analysis (PCA) analysis was performed with the genetic analysis, translation, and organization software PLATO (). To estimate genetic ancestry, we applied STRUCTURE (Version 2.3.4) to cluster participants into discrete populations (; , ; ). For references of continental ancestry, we downloaded HapMap 3 […]

call_split

Biology Driven Gene Gene Interaction Analysis of Age Related Cataract in the eMERGE Network

2015
Genet Epidemiol
PMCID: 4550090
PMID: 25982363
DOI: 10.1002/gepi.21902
call_split See protocol

[…] dent of phenotype. Once gene-gene models were verified by five or more databases, pairwise SNP-SNP combinations of all loci within each gene-gene model were created () and output for regression using PLATO software [Grady et al., ]. Because we allowed for a 50 kb gene boundary, it was possible for a given SNP to map to more than one gene, and thus, to be paired with SNPs within the same gene. Ther […]

Citations

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PLATO institution(s)
Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
PLATO funding source(s)
This work was funded by the National Institutes of Health (NIH) Pharmacogenetics Research Network (PGRN) Pharmacogenomics of Arrhythmia Therapy U01 (HL65962), R01 NS032830, U01 HG004608, and LM10040 as well as the Training Program on Genetic Variation and Human Phenotypes grant (5T32GM080178).

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