Discovery of cancer risk variants in the sequence of the germline genome can shed light on carcinogenesis. Here we describe gene burden association analyses, aggregating rare missense and loss of function variants, at 22 cancer sites, including 130,991 c
By integrating a rice pan-genome graph to identify structural variants, we obtained 6,604,898 SNP and 42,879 PAV variants for the six panels (7765 accessions). Meta-analysis significantly improved quantitative trait loci (QTLs) detection and hidden heritability by up to 43 and 37.88%, ...
Neuroticism is a personality trait, which is an important risk factor for psychiatric disorders. Recent genome-wide studies reported about 600 genes potentially influencing neuroticism. Little is known about the mechanisms of their action. Here, we aimed
The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589–594 (2005). CAS PubMed Google Scholar Blankenship, R. E. & Hartman, H. The origin and evolution of oxygenic photosynthesis. Trends Biochem. Sci. 23, 94–97 (1998). CAS PubMed Google Scholar Ondov, B. D., Bergman, N...
From the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we gathered BLCA patient data, which was classified into distinct subgroups using non-negative matrix factorization (NMF). Survival and pathway analyses were conducted between these clusters. The PMRGs model, created ...
long-read sequencing technologies. Although manual correction of GSA using toolkits such as Apollo [7] and IGV-GSAman [8] seems to be an effective approach to improve GSA, it relies on comprehensive transcriptome or proteome data and is time-consuming especially when working on pan-genome ...
Similar to Cas9-mediated genome editing, Cas-16S-seq is potentially restricted by the off-targeting effect and PAM requirement of CRISPR/Cas systems. Indeed, the number of host-specific cp-gRNAs was restricted by these two factors in our analysis (Fig.2d; Additional file2: Table S2). The ...
Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, Bogdanova EA, Staroverov DB, Rasskazov VA, Lukyanov S: A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res. 2002, 12: 1935-1942. 10.1101/gr.547...
Xiao P, Chen Y, Jiang H, Liu YZ, Pan F, Yang TL, Tang ZH, Larsen JA, Lappe JM, Recker RR, Deng HW (2008) In vivo genome-wide expression study on human circulating B cells suggests a novel ESR1 and MAPK3 network for postmenopausal osteoporosis. J Bone Miner Res 23(5):644–654...
In order to examine the mutation status in low and high-risk groups, we first measured the number of mutations present in each gene within our sample set using somatic mutation data from The Cancer Genome Atlas (TCGA). The “maftools” package was used to create waterfall graphs, and Tumor...