Fig. 1: Prior distributions for SNP effect sizes. a We divide prediction tools based on the form of the prior distribution they assign to SNP effect sizes, and whether they use individual-level data or summary statistics. For each of our eight new tools (names in blue), there is an exis...
In the following, mapping refers to implemented rules to match genotype variants to model variants.(下面,映射是指将基因型变异与模型变异相匹配的实现规则。) ---model_db_path---model_db_snp_key:optional. If provided, will load variant ids from an alternative column in the db. By default, Pr...
two steps: first, we quantify the genotype identity of all SNP loci within each pair of two individuals in each group as well as between two different groups, using the genomic data of the larger population size (the 1KGP data) and of the broader diversity in ethnicity (the SGDP data)....
It is worth noting that codes for SNP calling or Wolbachia analyses were not integrated into the Snakemake workflow due to technical constraints (e.g., interaction with external data sources). Instead, the raw codes have been released on GitHub as well....
To elucidate the relationship between the genotype and phenotype in CKD, we carried out the GWAS study for the phenotype ACR and a multi-phenotypic GWAS that included ACR, eGFR, urine albumin, and serum creatinine. The GWAS for the phenotype ACR identified a highly significant novel SNP in the...
the parental environment as well as feedback from parents can create settings that contribute to enhanced performance. Some of these possibilities can be examined with the genotype–environment correlation approach from behavioural genetics, which distinguishes among three types of such correlation. Passive...
Extreme independent variation in the expression of pairs of HLA-associated transcripts (HLA-B/C, HLA-A/F and HLA-DRB1/DRB5) in macrophages was associated with HLA genotype. Correlation analysis indicated the downstream impacts of variation in the immediate early response to LPS. For example, ...
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis. Bioinformatics 25, 1449e1450.Li MX, Jiang L, Kao PYP, Sham PC, Song YQ. IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and ...
Genotype data for C. elegans strains were acquired from the variant call format (VCF) file (release 20200815) available from the CeNDR (http://elegansvariation.org). Source data are provided with this paper. References Montgomery, M. K. et al. Mouse strain-dependent variation in obesity and...
Data availability The LifeLines-DEEP metagenomics sequencing data are available at the European Genome-phenome Archive under accessionEGAS00001001704. In the version of this paper originally published, there was a typographical error. In the Discussion, the sentence “In line with this, Ep-CAM-deficien...