Differences

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--- gwas [2020/06/22 15:14] – trynke
+++ gwas [2026/02/16 12:04] (current) – sylvia
@@ Line 2: / Line 2: @@
 GWAS is one of Lifelines' [[additional assessments]] and contains the genome-wide [[https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism|SNP]] data of 15.400 adult Lifelines participants derived from the [[https://www.illumina.com/products/by-type/clinical-research-products/human-cytosnp-12.html|Illumina CytoSNP-12v2 array]].\\
-The name GWAS might be confusing, as the assessment is not a [[https://en.wikipedia.org/wiki/Genome-wide_association_study|"genome wide association study"]] in itself, but rather the formation of a database of SNP data that can be used to perform such studies.\\
+The name GWAS might be confusing, as the assessment is not a [[https://en.wikipedia.org/wiki/Genome-wide_association_study|"genome wide association study"]] in itself, but rather the formation of a database of SNP data that can be used, together with Lifelines phenotype data, to perform such studies.\\
 Note that a second set of participants is genotyped in the [[UGLI]] project.
 ===== Subcohort =====
-The GWAS subcohort consists of 15.400 independent (no biological family relations), Caucasian-ancestry adult Lifelines participants. DNA samples were collected at [[1a visit 2]].
+The GWAS subcohort consists of 15.400* independent (no biological family relations), Caucasian-ancestry adult Lifelines participants. DNA samples were collected at [[1a visit 2]].
 Table 1: General information on the GWAS subcohort. *Age at Baseline 2nd visit.
@@ Line 18: / Line 18: @@
 | Age category 18-64                   | N=13890        |
 | Age category 65+                     | N=1510         |
+{{:gwas_age_distribution.jpg?400|}}
+*After several QC's the sample size of the latest version (v6) is N=13869.
 ===== SNP array =====
@@ Line 87: / Line 91: @@
 ===== Releasing SNP genotype data =====
 The following files are available through the Lifelines workspace or HPC:
-•	files with phenotype data
+  * files with phenotype data
+  * files with genotyped and imputed data
-•	files with genotyped and imputed data
+  * quality control files:
+      * list of samples excluded
-•	quality control files:
+      * list of SNPs excluded
-	-list of samples excluded
+      * PCA component file
-	-list of SNPs excluded
-	-PCA component file
 ===== Abbreviations =====