Tag: gcta

Genetic and chemotherapeutic influences on germline hypermutation

DNM filtering in 100,000 Genomes Project We analysed DNMs called in 13,949 parent–offspring trios from 12,609 families from the rare disease programme of the 100,000 Genomes Project. The rare disease cohort includes individuals with a wide array of diseases, including neurodevelopmental disorders, cardiovascular disorders, renal and urinary tract disorders, ophthalmological…

Continue Reading Genetic and chemotherapeutic influences on germline hypermutation

Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

Continue Reading Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

What software to use for GWAS with repeated longitudinal quantitative phenotype data?

What software to use for GWAS with repeated longitudinal quantitative phenotype data? 0 I have quantitative data that has been collected at 4 different time points. Before treatment, 1 month after, 1 year after and 2 year after. I have generated Linear Mixed Models in R to obtain the residuals….

Continue Reading What software to use for GWAS with repeated longitudinal quantitative phenotype data?

Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

Continue Reading Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

Reference panel data to be used for GCTA-COJO

Reference panel data to be used for GCTA-COJO 0 I performed a genome-wide meta-analysis based on summary statistics from the four cohorts to identify significant loci. Next, I would like to perform a conditional analysis using GCTA-COJO to search for SNPs independent of significant lead SNPs. I know that GCTA…

Continue Reading Reference panel data to be used for GCTA-COJO

How long does it take to carry out the GWAS workflow?

How long does it take to carry out the GWAS workflow? 0 Including these steps: 1) raw data format transformation for five companies 2) update positions for all SNPs to hg37 version 3) Quality control within companies 4) Pre-phasing (SHAPEIT2) and imputation (IMPUTE2) for all SNPs of each company 5)…

Continue Reading How long does it take to carry out the GWAS workflow?

Understanding Conditional analysis

Understanding Conditional analysis 1 Hello, I’m new to data analysis and I’m having some trouble understanding the process and need help with a few questions. I am running a conditional analysis on chromosome 19 in relation to Alzheimer’s disease, I understand that conditional analysis tests whether SNPs have association independent…

Continue Reading Understanding Conditional analysis

Calculation of the GRM in GCTA

Calculation of the GRM in GCTA 0 Hi experts, I am new to the field. I have some questions wrt the calculation of the GRM: by using the GCTA software: Let’s say I have a population of genome data for N= 4800000, and the original genotype SNPs, and also the…

Continue Reading Calculation of the GRM in GCTA