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Sequence Kernel Association Test (SKAT)

Definition
AI-generated

SKAT is a variance-component test for association between a trait and a set of rare variants in a region.

Topics
GWAS
Synonyms
SKAT
Related
Burden Test Gene-Based Test Rare Variant

Why it matters in GWAS

SKAT is widely used in exome and whole-genome gene-based pipelines for complex traits where causal rare alleles may be protective or deleterious; it complements burden approaches and motivates omnibus hybrids (SKAT-O).

Example usage

"We ran gene-level SKAT on nonsynonymous SNVs with MAC ≥ 5 using the default linear kernel."

Burden Test Gene-Based Test Rare Variant Rare Variant Aggregation Test SKAT-O
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

  • Wu MC, et al. (2011). Rare-variant association testing for sequencing data with the sequence kernel association test. 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
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