gwas
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gwas [2020/06/22 17:13] trynke |
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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 ===== | ||
gwas.1592838838.txt.gz · Last modified: 2020/06/22 17:13 by trynke
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