LIFE-Heart samples were genotyped with either Affymetrix Axiom CEU1 or Affymetrix Axiom CADLIFE. The latter is an array containing Axiom CEU as genome-wide backbone and an additional custom content of about 62,500 SNPs from CAD loci. Genotype calling relied on Affymetrix Power Tools (APT, version 1.17.0 for Axiom-CADLIFE, version 1.16.1 for Axiom-CEU) with their latest libraries (Axiom CADLIFE1, release 3 respectively Axiom GenomeWide CEU 1 Array Plate, Analysis Files, release 6). Genotype calling and SNP filtering was performed separately for the two array products. For sample filtering, high quality SNPs in the intersection of both arrays were used. The same steps of sample and SNP filtering were performed as in LIFE-Adult. In summary, 5,700 samples and 504,593 SNPs fulfilled all quality criteria for autosomal analyses. For X-chromosomal analyses, additional 12 samples were removed and a total of 12,715 SNPs fulfilled the specified quality criteria. Imputation was performed using the same reference, software and software settings as in LIFE-Adult. The intersection of SNPs of Affymetrix Axiom CEU1 and Affymetrix Axiom CADLIFE was used for this purpose.
Axiom ceu1
Manufactured by Thermo Fisher Scientific
The Axiom CEU1 is a laboratory equipment designed for cell expansion applications. It provides a controlled environment for the growth and proliferation of cells. The core function of the Axiom CEU1 is to maintain optimal conditions for cell culture, such as temperature, humidity, and gas composition, to support the expansion of cells in a laboratory setting.
Automatically generated - may contain errors
3 protocols using axiom ceu1
1
Genotyping and Imputation in LIFE-Heart
2
Genotyping and Imputation of Genetic Variants
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Genotypes were measured by using SNP micro-arrays: Affymetrix Gene Chip Human Mapping 500 K Array Set (Sorbs), Affymetrix Axiom CEU1 (LIFE-Adult, LIFE-Heart), Affymetrix custom array (LIFE-Heart), Affymetrix Genome-Wide Human SNP Array 6.0 (LURIC, Sorbs), Illumina 200k MetaboChip (LURIC), Illumina Omni 2.5/Illumina Omni Express (KORA) and Illumina Human 670k BeadChip (YFS). Sample and SNP quality control was performed according to study specific criteria, see Supplementary Data S2 for details.
Genotypes were imputed using IMPUTE266 (link) based on 1000 Genomes Phase 1 reference panel (LIFE-Adult, LIFE-Heart, LURIC, Sorbs, YFS) or 1000 Genomes Phase 3 reference panel (KORA). Genotype data was translated to forward strand annotation using NCBI b37 (hg19) coordinates.
Genotypes were imputed using IMPUTE266 (link) based on 1000 Genomes Phase 1 reference panel (LIFE-Adult, LIFE-Heart, LURIC, Sorbs, YFS) or 1000 Genomes Phase 3 reference panel (KORA). Genotype data was translated to forward strand annotation using NCBI b37 (hg19) coordinates.
3
Quality Control and Imputation of Genome-Wide SNP Data
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We genotyped 7,838 participants of LIFE-Adult using the genome-wide SNP array Affymetrix Axiom CEU1 and the software Affymetrix Power Tools (version 1.20.6). Quality control (QC) of the genotype calling was performed following Affymetrix’s best practice steps [17 ].
Sample QC included dish-QC (<0.82), sample call rate (<97%), sex-mismatch, problematic relatedness (e.g. sample mix-up) and irregularities of XY intensity plots (e.g. XXY samples filtered for gonosomal analyses). We assessed genetic heterogeneity with principal component analyses and filtered outliers (>6 SD in any of the first 10 principal components) for further analysis.
SNP QC comprised SNP call rate, parameters of cluster plot irregularities according to Affymetrix’s recommendations, violation of Hardy-Weinberg equilibrium (p<10−6 in an exact test for autosomes, p<10−4 for chromosome X with women only [18 (link)]) and plate association (p<10−7).
After sample and SNP QC, 7669 samples and 532,676 SNPs were imputed on the reference 1000 Genomes Phase 3 [19 (link)], software SHAPEIT [20 (link)] v2r900 for prephasing and IMPUTE2 [21 (link)] v2.3.2 for genotype estimation. For chromosome X, the same settings were used.
Sample QC included dish-QC (<0.82), sample call rate (<97%), sex-mismatch, problematic relatedness (e.g. sample mix-up) and irregularities of XY intensity plots (e.g. XXY samples filtered for gonosomal analyses). We assessed genetic heterogeneity with principal component analyses and filtered outliers (>6 SD in any of the first 10 principal components) for further analysis.
SNP QC comprised SNP call rate, parameters of cluster plot irregularities according to Affymetrix’s recommendations, violation of Hardy-Weinberg equilibrium (p<10−6 in an exact test for autosomes, p<10−4 for chromosome X with women only [18 (link)]) and plate association (p<10−7).
After sample and SNP QC, 7669 samples and 532,676 SNPs were imputed on the reference 1000 Genomes Phase 3 [19 (link)], software SHAPEIT [20 (link)] v2r900 for prephasing and IMPUTE2 [21 (link)] v2.3.2 for genotype estimation. For chromosome X, the same settings were used.
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