Computational protocol: Analysis of circulating angiopoietin-like protein 3 and genetic variants in lipid metabolism and liver health: the DiOGenes study

Similar protocols

Protocol publication

[…] DNA was extracted from EDTA blood buffy coats with a salting out method. The DNA samples were quality checked, quantified, and normalized to approximately 100 ng/ml and 2.0 mg before genotyping. Genotyping was done using Illumina 660 W-quad according to manufacturer’s protocols (Illumina, San Diego, CA). Detailed information about this dataset can be found in Carayol et al. []. Briefly, 498,233 single nucleotide polymorphisms (SNPs) were genotyped; after quality check, additional SNPs were imputed using the Michigan Imputation Server [] and the European 1000 Genomes set reference panel. SNP information was mapped onto NCBI version 37. Information was available for 4,020,654 SNPs in 494 participants with proteomics data. [...] A complete description of the QTL mapping is available in Carayol et al. []. In summary, association between SNPs and circulating ANGPTL3 was tested at baseline and during weight loss using linear mixed effect models as implemented in GCTA software adjusting for baseline BMI or change in BMI, center, age, and gender as fixed, and a genetic relationship matrices as random effect []. In order to handle the multiple comparisons, p values were corrected using SLIDE (Sliding-window method for Locally Inter-correlated markers with asymptotic Distribution Errors corrected), a method based on a multivariate normal distribution similar to classical permutation but much faster []. Considering the large number of tests performed, significance levels were defined at adjusted alpha 10%. Genomic inflation factors (GIF) were estimated for the two pQTL analyses using estlambda function available in the GenABEL R package []. Pairwise linkage disequilibrium (LD) was calculated with LDlink, a web-based application using 1000 Genome phase 3 data []. […]

Pipeline specifications

Software tools Michigan Imputation Server, GCTA, GenABEL, LDlink
Applications WGS analysis, GWAS
Organisms Homo sapiens
Diseases Fatty Liver, Oculocerebrorenal Syndrome
Chemicals Alanine, Aspartic Acid, Triglycerides