Differences

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--- ugli [2025/12/19 16:05] – sylvia
+++ ugli [2026/02/16 14:40] (current) – sylvia
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 ====SNP array intensity files====
 Raw intensity data from the GSA will be made available to the researchers.
+====Updated version - v3====
+Changes in the GSA genotype and imputed data version 3 (Oct 2025)
+. During the QC of the Affymetrix data (UGLI2+3) genetic relationships of all samples genotyped with the CytoSNP, GSA or Affymetrix array were determined and compared with the reported pedigree relations. Some DNA samples appeared not to be from the expected individual and could also not be matched to any other individual using the observed genetic relationships. These samples were therefore excluded. This resulted in a new sample size of N=36,233.
+. A new phasing and imputation strategy was adopted. The online HRC imputation on the Sanger Imputation Server makes use of the SHAPEIT2 or EAGLE2 phasing tools and the PBWT imputation tool. These software tools are relatively old (2014). Instead, an in-house phasing and imputation approach was used, using a subset of ~11,000 HRC samples as a reference panel with the EAGLE2 phasing and IMPUTE5 imputation tools.
+. Based on a new PCA on the combined data of the CytoSNP, GSA and Affymetrix chips to identify non-European individuals, a new list of non-European GSA individuals now has been constructed (PC's). It is up to the researcer whether he/she wants to exclude them or correct for population ethnicity in the analysis.
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 ==== Quality Checks ====
-An UGLI2 - Affymetrix (release 2.0) Quality Control Report is available, describing in detail the QC steps that were taken during the quality control (QC) process of the second release of UGLI comprising the genotype of 29,366 participants assessed using the FinnGen Thermo Fisher Axiom® custom array. {{ :qc_report_ugli2_release_1_-v1.pdf |}}
+An UGLI2 - Affymetrix (release 2.0) Quality Control Report is available, describing in detail the QC steps that were taken during the quality control (QC) process of the second release of UGLI comprising the genotype of 29,366 participants assessed using the FinnGen Thermo Fisher Axiom® custom array. {{ :qc_report_ugli2_release_2_-v1.pdf |}}
 ====Imputation====