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gwas [2020/06/22 15:13] – trynkegwas [2025/02/05 13:49] (current) – external edit 127.0.0.1
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 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]].\\   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. Note that a second set of participants is genotyped in the [[UGLI]] project.
  
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 | Age category 18-64                   | N=13890        | | Age category 18-64                   | N=13890        |
 | Age category 65+                     | N=1510         | | Age category 65+                     | N=1510         |
 +
 +{{:gwas_age_distribution.jpg?400|}}
  
 ===== SNP array ===== ===== SNP array =====
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   * Unimputed: Genotypes determined on the basis of the SNP array, not imputed against genomic reference panels.   * Unimputed: Genotypes determined on the basis of the SNP array, not imputed against genomic reference panels.
  
-==== Non-Caucasian samples ====+===== Non-Caucasian samples =====
 To prevent false-positive association, non-Caucasian samples are excluded.  To prevent false-positive association, non-Caucasian samples are excluded. 
  
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   * Population stratification (using Eigenstrat)   * Population stratification (using Eigenstrat)
  
-==== Cryptic relationships ==== +===== Cryptic relationships ===== 
 Samples are selected using self reported family relations. After cleaning of the data, samples are compared with each other to determine the relationship by genetic similarity. If a pair of samples are indicated as first degree relatives, the sample with the best genotyping quality will be included. Samples are selected using self reported family relations. After cleaning of the data, samples are compared with each other to determine the relationship by genetic similarity. If a pair of samples are indicated as first degree relatives, the sample with the best genotyping quality will be included.
  
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 ===== Releasing SNP genotype data ===== ===== Releasing SNP genotype data =====
 The following files are available through the Lifelines workspace or HPC: 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 ===== ===== Abbreviations =====
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