ArticleF1000Research2023
Epigenetic germline variants predict cancer prognosis and risk and distribute uniquely in topologically associating domains.
Article in F1000Research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
- Update of
Authors and funding
5 authors.
Funding
Abstract
Background: Methylation quantitative trait loci (meQTLs) associate with different levels of local DNA methylation in cancers. Here, we investigated whether the distribution of cancer meQTLs reflected functional organization of the genome in the form of chromatin topologically associated domains (TADs) and evaluated whether cancer meQTLs near known driver genes have the potential to influence cancer risk or progression. Methods: Published cancer meQTLs were analyzed according to their location in transcriptionally active or inactive TADs and TAD boundary regions. Cancer meQTLs near known cancer genes were analyzed for association with cancer risk in the UKBioBank , and prognosis in The Cancer Genome Atlas (TCGA). Results: In TAD boundary regions, the density of cancer meQTLs was higher near inactive TADs. Furthermore, we observed an enrichment of cancer meQTLs in active TADs near tumor suppressors, whereas there was a depletion of such meQTLs near oncogenes. Several meQTLs were associated with cancer risk in the UKBioBank, and we were able to reproduce breast cancer risk associations in the DRIVE cohort. Survival analysis in TCGA implicated a number of meQTLs in 13 tumor types. In 10 of these, polygenic cancer meQTL scores were associated with increased hazard in a CoxPH analysis. Risk and survival-associated meQTLs tended to affect cancer genes involved in DNA damage repair and cellular adhesion and reproduced cancer-specific associations reported in prior literature. Conclusions: This study provides evidence that genetic variants that influence local DNA methylation are affected by chromatin structure and can impact tumor evolution.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.