Do different microarray chips yield different accuracy of polygenic scores?
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8 months ago
a5864557 • 0

When replicating a polygenic score, labs have multiple microarray chips to choose from. (E.g., GSA, GDA, UK Biobank Axiom Array, UK BiLEVE Axiom array, GeneChip 2.0 array, Infinium Core-24 Kit, etc.). Will using different chips impact the accuracy of the polygenic score? If so, by how much? I've been unable to find research on this question.

Note: it is standard to impute both in the original study and the replication.

Some complications might include competing factors: what if a possible chip used for replication is closer (more variant overlap) to the chip used in study X, but has fewer variants overall than an alternative possible chip?

My thought is that it probably doesn't matter much, as long as the chip has a decent number of SNPs spread out over most LD blocks, so imputing would make different chips have somewhat similar accuracy.

See also: https://bioinformatics.stackexchange.com/questions/21769/do-different-microarray-chips-yield-different-accuracy-of-polygenic-scores

microarray genome SNP polygenic-risk-score • 342 views
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