bims-ovdlit 2023-04-09 papers

Int J Gynecol Cancer. 2023 Apr 03. 33(4): 645

The fallopian tube origin of an ovarian carcinoma.

Jesus Paula Carvalho, Giovanni Miglino Suárez.

Keywords: fallopian tube neoplasms; lymph nodes; ovarian neoplasms

DOI: https://doi.org/10.1136/ijgc-2022-003976

Int J Gynecol Cancer. 2023 Apr 06. pii: ijgc-2023-004478. [Epub ahead of print]

Overall survival after PARP maintenance treatment in platinum-sensitive relapsed ovarian cancer: opposing views of the US Food and Drug Administration and European Medicines Agency.

Bradley J Monk, Robert L Coleman, Mansoor Raza Mirza.

Keywords: Ovarian Cancer

DOI: https://doi.org/10.1136/ijgc-2023-004478

Proc Natl Acad Sci U S A. 2023 Apr 11. 120(15): e2220704120

Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.

The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.

Keywords: biomarker; cfDNA; copy number alteration; methylation; mutation

DOI: https://doi.org/10.1073/pnas.2220704120

JAMA. 2023 Apr 05.

Pembrolizumab Immunotherapy Improved Endometrial Cancer Survival.

Emily Harris.

DOI: https://doi.org/10.1001/jama.2023.5623

Nat Commun. 2023 Apr 03. 14(1): 1864

Cellcano: supervised cell type identification for single cell ATAC-seq data.

Wenjing Ma, Jiaying Lu, Hao Wu.

Computational cell type identification is a fundamental step in single-cell omics data analysis. Supervised celltyping methods have gained increasing popularity in single-cell RNA-seq data because of the superior performance and the availability of high-quality reference datasets. Recent technological advances in profiling chromatin accessibility at single-cell resolution (scATAC-seq) have brought new insights to the understanding of epigenetic heterogeneity. With continuous accumulation of scATAC-seq datasets, supervised celltyping method specifically designed for scATAC-seq is in urgent need. Here we develop Cellcano, a computational method based on a two-round supervised learning algorithm to identify cell types from scATAC-seq data. The method alleviates the distributional shift between reference and target data and improves the prediction performance. After systematically benchmarking Cellcano on 50 well-designed celltyping tasks from various datasets, we show that Cellcano is accurate, robust, and computationally efficient. Cellcano is well-documented and freely available at https://marvinquiet.github.io/Cellcano/ .

DOI: https://doi.org/10.1038/s41467-023-37439-3