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Protocols

MetaSKAT specifications

Information


Unique identifier OMICS_00241
Name MetaSKAT
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for MetaSKAT

MetaSKAT citations

 (7)
library_books

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

2017
Sci Data
PMCID: 5735917
PMID: 29257133
DOI: 10.1038/sdata.2017.179

[…] ‘broad’ criteria for deleteriousness, and the PTV+missense mask included variants in the PTV+NSbroad mask as well as those with MAF<1% annotated as missense.We performed gene-level analysis using the MetaSKAT software package (v0.32), employing the SKAT v0.93 library to perform a SKAT-O analysis within each ancestry group as well as across all ancestry groups via meta-analysis. Within each ancestr […]

library_books

Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer’s disease

2017
Acta Neuropathol
PMCID: 5563332
PMID: 28447221
DOI: 10.1007/s00401-017-1714-x

[…] riant (MAF < 0.01) association meta-analysis by ethnicity was performed separately for PTC and predicted deleterious missense mutations using heterogeneous genetic effect SKAT-O statistics within the MetaSKAT framework []. APOE dosage (number of ε4 alleles) was tested as a covariate. Summary odds ratios (ORMH) were calculated with a Cochran–Mantel–Haenszel test in PLINK [], stratified by country o […]

library_books

The genetic architecture of type 2 diabetes

2016
Nature
PMCID: 5034897
PMID: 27398621
DOI: 10.1038/nature18642

[…] for each ancestry using high-quality genotype calls (GQ>20) for all samples passing extended QC. We considered a variant to have MAF<1% if MAF estimates for every ancestry group were <1%.We used the MetaSKAT R package (v0.32) with the SKAT v0.93 library to perform SKAT-O analysis within each ancestry, and in meta-analysis. Within each ancestry group, we analyzed genotype dosages with adjustment f […]

library_books

Exome wide Association Study Identifies CLEC3B Missense Variant p.S106G as Being Associated With Extreme Longevity in East Asian Populations

2016
PMCID: 5861862
PMID: 27154906
DOI: 10.1093/gerona/glw074

[…] end test; then the heterogeneity between men and women was assessed by use of the above-described meta-analysis procedures. Meta-analysis of the results from the SKAT-O test was carried out by use of MetaSKAT ().To verify that the SNPs identified as being associated with extreme longevity were also associated with overall life span, we performed Kaplan–Meier survival analysis of 2,274 quality cont […]

call_split

A Pharmacogenetic Investigation of Intravenous Furosemide in Decompensated Heart Failure: A Meta Analysis of 3 Clinical Trials

2016
Pharmacogenomics J
PMCID: 5009007
PMID: 26927285
DOI: 10.1038/tpj.2016.4
call_split See protocol

[…] ross studies. The framework is based on study-specific summary statistics for each region and is flexible enough to accommodate a range of heterogeneity of genetic effects across studies. We used the MetaSKAT package (version 0.40, R3.1.1) provided by the same authors to calculate a multi-marker score statistics for fixed-effect meta-analysis and a multi-marker score statistics for random-effects […]

library_books

Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer

2015
Sci Rep
PMCID: 4639776
PMID: 26553438
DOI: 10.1038/srep16286

[…] ferent number of variants in each individual study we performed SKAT-O test separately for each individual study and combined summary statistics from individual SKAT results in a meta-analysis using “MetaSKAT” package in R Similarly to single-variant analysis we tested for over-dispersion of P-values by generating QQ plots and deriving an inflation factor (λ). To account for multiple testing in th […]


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MetaSKAT institution(s)
Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA

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