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A long noncoding RNA associated with susceptibility to celiac disease
TLDR
Lnc13 levels are significantly decreased in small intestinal biopsy samples from patients with celiac disease, which suggests that down-regulation of lnc13 may contribute to the inflammation seen in this disease.
Human mitochondrial DNA is extensively methylated in a non-CpG context
TLDR
Key differences in methodology are discussed that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation, and challenge the notion that mtDNA is lowly methylated.
Revisiting genome wide association studies (GWAS) in coeliac disease: replication study in Spanish population and expression analysis of candidate genes
TLDR
Exchange differences between treated CD patients and controls along with SNP expression associations suggest a possible primary role for these four genes and their variants in pathogenesis.
Expression analysis in intestinal mucosa reveals complex relations among genes under the association peaks in celiac disease
TLDR
The results strongly suggest that the effects of disease-associated SNPs go far beyond the oversimplistic idea of transcriptional control at a nearby locus, and are needed to determine how each variant disrupts fine-tuning mechanisms in the genome that eventually lead to disease.
Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas
TLDR
A novel epigenetic signature of HPV infection in HNSCCs is identified which is independent of the anatomic site, is functionally correlated with gene expression and may be leveraged for improved stratification of prognosis in H NSCCs.
Coregulation and modulation of NFκB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation
TLDR
The results confirm the upregulation of the NFκB pathway and show that constitutively altered genes usually belong to the core of the pathway and have central roles, whereas genes overexpressed only in active CD are more peripheral.
Comparison of Illumina 450K and EPIC arrays in placental DNA methylation
TLDR
It is concluded that EPIC and 450K placental data can be combined, and two lists of CpGs that should be excluded to avoid misleading results are provided.
Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing
TLDR
This study provides the most comprehensive compendium of lncRNAs expressed in HCC, as well as in control or cirrhotic livers and finds that more than 20% of differentially expressed lnc RNAs are associated to actively transcribed enhancers and that the co-expression patterns with their closest genes change dramatically during HCC development.
DNA hypermethylation is associated with invasive phenotype of malignant melanoma
TLDR
Several methylation changes that can have role during melanoma progression are identified, including hypermethylation of the promoter regions of the ARHGAP22 and NAV2 genes that are commonly altered in locally invasive primary melanomas as well as during metastasis.
Accuracy in Copy Number Calling by qPCR and PRT: A Matter of DNA
TLDR
Analysis of three genes in a large sample set showed that both quantitative PCR and paralog ratio test are prone to false copy number assignments if sufficient attention is not paid to DNA concentration and quality.
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