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SKAT-O

Definition
AI-generated

SKAT-O is an omnibus rare-variant test that optimally combines burden-type and SKAT variance-component statistics into a single association score.

Topics
GWAS
Synonyms
Optimal unified sequence kernel association test
Related
Burden Test Gene-Based Test Rare Variant Aggregation Test

Why it matters in GWAS

Because the true genetic architecture at a gene is unknown, SKAT-O is a common default in gene-based sequencing analyses alongside separate burden and SKAT runs.

Example usage

"Gene-wise p-values were computed with SKAT-O for LoF and missense masks in cases and controls."

Burden Test Gene-Based Test Rare Variant Aggregation Test SKAT
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Lee S, et al. (2012). Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet.
  • Boutry S, Helaers R, et al. (2023). Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations. Brief Bioinform. https://doi.org/10.1093/bib/bbad412
← Sequence Kernel Association Test (SKAT) Skewness →

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