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--- catslife:instruments:polygenic_scores_pgss [2025/05/14 13:49] – gustavsd
+++ catslife:instruments:polygenic_scores_pgss [2025/07/21 15:33] (current) – [Ancestry and Principal Components] gustavsd
@@ Line 23: / Line 23: @@
   * Conversion from genetic IIDs to standard CATSLife IDs needed to merge PGS output with phenotypic information.
   * Continental ancestry group. These were determined based on mapping CATSLife data to the 1000 Genomes Phase 3 reference panel. EUR (European-like), AFR (African-like), SAS (South Asian-like), and EAS (East Asian-like) groups were classified if they were within 5 SDs of the population means based on the first 4 principal components. Because there is a lot more variability in the AMR (American-like) group, this based on 2 SDs on the first 4 principal components and required that they not already be classified in one of the other groups.
-  * Two sets of PCs are provided in this datafile. Principal components labeled "PC1", "PC2" (etc.) are derived from a PCA within this sample. Principal components labeled "PC1_1KG", "PC2_1KG" (etc.) are derived from mapping our data onto 1000 Genomes. For polygenic scores involving CATSLife data, it is recommended that you use the within-sample PCs, though there may be exceptions.
+  * Two sets of PCs are provided in this datafile. Principal components labeled "PC1", "PC2" (etc.) are derived from a PCA within this sample (on EUR ancestry only!!). These PCs were computed based on only one person per family, then the other family members were mapped onto the PCs. Principal components labeled "PC1_1KG", "PC2_1KG" (etc.) are derived from mapping our data onto 1000 Genomes. For polygenic scores involving CATSLife data, it is recommended that you use the within-sample PCs, though there may be exceptions.