#21 · Epigenomics
Whole-genome doubling tracked as subclonal evolution across human cancers
The dominant thread is how whole-genome doubling (WGD) relates to tumour evolution and how it is detected. A pan-cancer analysis of 41,332 tumours across 12 cancer types relates WGD to drivers, chromosomal losses and immune programmes. Single-cell analysis identifies WGD subclones in tumours classed as non-WGD, and the expression-based WAGES method maps WGD clonal fraction in bulk tumours. This is consistent with subclonal doubling escaping binary bulk classification. What is new is the shift from binary WGD status toward clonal fraction and single-cell resolution. Related work on chromosomal mosaicism across 19 tissues from 722 WGS samples reports recurrent mitotic error and purifying selection outside tumours, although it is adjacent rather than doubling-specific. The remaining items, covering methylome segmentation, cfDNA methylation correction, PDX contamination estimation and canine k-mer age analysis, address distinct methods and are not part of this thread.
Published papers
Enhanced cfDNA methylation profiling by detection and correction of jagged ends.
JEEPERS detects and corrects jagged-end-induced methylation errors in cfDNA sequencing, preserving duplex integrity and enabling mutation-methylation…
XenoMix: estimating mouse content from DNA methylation data of Patient-Derived Xenograft models.
XenoMix is an R tool that quantifies mouse DNA contamination in PDX DNA methylation microarray data by exploiting human-mouse sequence homology, reaching…
Evidence of active whole-genome doubling (WGD) subclones in non-WGD tumors.
Single-cell analysis finds WGD subclones in tumors classed as non-WGD; the new expression-based WAGES method maps WGD clonal fraction in bulk tumors and links…
Preprints
Evolutionary characterization of whole-genome doubling across human cancers
Analyses 41,332 tumours from 12 cancer types to date whole-genome doubling against drivers, chromosomal losses and immune programmes.
Alignment-Free k-mer Analysis Reveals Age-Associated k-mer Signals in Canine Buccal DNA and Cell-Free DNA
k-mer analysis of canine buccal and cfDNA genomes finds age-linked sequence signals, stronger in buccal DNA; ridge models predict age.
Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues
Maps mosaic chromosomal alterations across 19 tissues from 722 WGS samples, revealing tissue-specific mitotic error and selection.
The Segmentome: a novel representation of the DNA methylome identified by a Bayesian HMM framework
Introduces the segmentome, a segment-level methylome representation inferred by an unsupervised Bayesian HMM from WGBS data, grouping 207 samples of 39 cell…
Topic history
| Date | Rank |
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| #21 | |
| #11 | |
| #34 |