关联检验中的reference与risk/effect allele在关联检测中，reference allele（non-risk或non-effect）是效应估计的基准，与参考基因组中的ref/alt概念分离。早期研究中，minor allele常被作为reference allele，但现在，为了消除混淆，研究者倾向于保持与reference genome的统一。risk allele则是与疾病关联的allel...
在这里的概念再次改变,同样的reference allele,在与 risk/effect allele并列时,则指的是GWAS关联检测中的reference allele (non-risk 或者 non-effect),也就是效应量beta(或odds ratio)估计时的参考,概念上与上述参考基因组的ref与alt的组合无关,但为了保持统一性,近年来研究中关联检验的reference 也会与 reference...
The A allele is thought to give rise to functional protein, whereas the G allele results in a truncated mRNA degraded through nonsense-mediated decay. Due to balancing selection of rs2248374, about one in four individuals are G/G at this locus globally and will hence be devoid of full ...
SNVs are not really “mutations,” because by definition they are relatively common in a population (most definitions of a polymorphism indicate that the variant allele should be present at a frequency of 1% or more in a population). However, common SNVs did arise through a germinal mutation...
(HWE) > 10−6. Imputed SNPs were filtered for imputation quality score >0.5 and for deviation from reference allele frequency <20%. Finally, the alleles were harmonized so that the same effect allele was used in all studies. Number of quality controlled SNPs per study is presented in...
Using the processed WGS, WGBS, and RNA-seq data for 128 benign prostate samples from the CPGEA cohort [15], we extracted genotype information for SNPs with rsIDs in dbSNP (build 151) and a minor allele frequency (MAF) greater than 0.05, and removed SNPs in high LD (squared correlation...
In order to estimate cell type composition in the empty and contamination profiles, we used the deconvolution method implemented in SCDC[16], the endogenous single cell allele counts from the respective replicate were used as reference (qcthreshold = 0.6). In addition, cell type filtering (frequen...
Quality control was ensured by perfect concordance of replicate samples, expected minor allele frequencies, and adherence to Hardy–Weinberg equilibrium. Only scans from participants with the high- or medium-affinity genotypes (known to be 490% of North Americans; Mizrahi et al, 2012) were ...
The effect of HLA-B allele on the IDDM risk defined by DRB1*04 subtypes and DQB1*0302. Diabetes 46: 1888-1892.Nejentsev S, Reijonen H, Adojaan B, Kovalchuk L, Sochnevs A, Schwartz EI, Akerblom HK, Ilonen J. The effect of HLA-B allele on the IDDM risk defined by DRB1*04 ...
the Allele C is the reference allele encoding for the p.N264; the Allele A is the minor allele resulting the p.K264 variant amino acid;CForest plot for the p.N264K association analysis showing significantly protective odds ratios across APOL1 high risk (G1G1, G2G2 and G1G2) genotypes...