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--- catslife:instruments:polygenic_scores_pgss [2025/04/16 11:37]
gustavsd [Information About the PGS Pipeline]
+++ catslife:instruments:polygenic_scores_pgss [2025/04/18 13:18] (current)
gustavsd [Polygenic Scores Currently Available]
@@ Line 9: / Line 9: @@
 Plink files for computing PGSs in CATSLife can be found on Research Computing:
 /pl/active/IBG/data/CATSLife/derived/PGS/
@@ Line 19: / Line 18: @@
 ===== Ancestry and Principal Components =====
-The "CATSLife_Ancestry_1KGPCs_Jan2024.txt" file includes a few important pieces of information recommended for PGS analyses.
+Information about [[https://ibg.colorado.edu/mydms/out/out.ViewDocument.php?documentid=5782 | Genetic Ancestry and Principal Components]] can be downloaded here and can also be found on RC: /pl/active/IBG/data/CATSLife/derived/PGS/
-  * Conversion from genetic IID to study ID needed to merge PGS output with phenotypic information
-  * Continental ancestry group. These were determined based on mapping CATSLife data to 1KG Phase 3. EUR, AFR, SAS, and EAS 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) 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.
+The current file includes important pieces of information recommended for PGS analyses.
-  * 20 PCs are provided in this datafile. This PCA was run after combining CATSLife with 1KG Phase 3 so these values can be interpreted on the same scale as the 1KG Phase 3 participants.
+  * 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.
+===== READMEs for Computing Polygenic Scores in CATSLife  =====
+[[ https://ibg.colorado.edu/dokuwiki/lib/exe/fetch.php?media=catslife:instruments:prscs_readme_april2025.pdf | Readme for PRScs]] (Ge et al., 2019)
+Readme for SbayesR (Lloyd-Jones et al., 2019)
@@ Line 33: / Line 42: @@
 | Educational Attainment | Okbay 2022 | X | X |
 | Executive Function | Hatoum 2023 | X |  |
-| Impulsivity (3 BIS subscales) | Sanchez-Roige 2023 | X |  |
+| Impulsivity (3 BIS subscales) | Sanchez-Roige 2023 | X* |  |
-| Impulsivity (5 UPPS subscales) | Sanchez-Roige 2023 | X |  |
+| Impulsivity (5 UPPS subscales) | Sanchez-Roige 2023 | X* |  |
 | General Cognitive Ability | Davies 2018 | X |  |
 | Intelligence (Childhood) | Benyamin 2014 | X |  |
 | Neuroticism | Baselmans 2019 | X |  |
+| Frailty | Atkins 2021 | X |  |
+* (Restricted to 23andMe agreement, contact Dan Gustavson & Naomi Friedman)
+[[https://ibg.colorado.edu/mydms/out/out.ViewDocument.php?documentid=5783 | Download merged PGSs computed using PRScs]]

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