bims-ovdlit 2023-07-02 papers

Issue of 2023–07–02
four papers selected by
Lara Paracchini, Humanitas Research

Gynecol Oncol. 2023 07;pii: S0090-8258(23)00353-0. [Epub ahead of print]174 A1-A2

Jiaxin Ge, Amanda N Fader, Jonathan C Dudley.

DOI: https://doi.org/10.1016/j.ygyno.2023.06.010

Cancer Discov. 2023 Jun 28. OF1

MCED Testing Enters New Diagnostic Realms.

Real-world performance data and trial results in symptomatic individuals continue to validate the promise of screening for multiple cancers with a single blood draw. However, some worry about the performance of GRAIL's commercially available multicancer early detection test in certain high-risk groups that were not the focus of early clinical development efforts.

DOI: https://doi.org/10.1158/2159-8290.CD-ND2023-0006

Science. 2023 Jun 30. 380(6652): eadd3067

Spatially resolved single-cell translatomics at molecular resolution.

Hu Zeng, Jiahao Huang, Jingyi Ren, Connie Kangni Wang, Zefang Tang, Haowen Zhou, Yiming Zhou, Hailing Shi, Abhishek Aditham, Xin Sui, Hongyu Chen, Jennifer A Lo, Xiao Wang.

The precise control of messenger RNA (mRNA) translation is a crucial step in posttranscriptional gene regulation of cellular physiology. However, it remains a challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolution. Here, we report the development of ribosome-bound mRNA mapping (RIBOmap), a highly multiplexed three-dimensional in situ profiling method to detect cellular translatome. RIBOmap profiling of 981 genes in HeLa cells revealed cell cycle-dependent translational control and colocalized translation of functional gene modules. We mapped 5413 genes in mouse brain tissues, yielding spatially resolved single-cell translatomic profiles for 119,173 cells and revealing cell type-specific and brain region-specific translational regulation, including translation remodeling during oligodendrocyte maturation. Our method detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks.

DOI: https://doi.org/10.1126/science.add3067

Nat Genet. 2023 Jun 29.

Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes.

Simone Rubinacci, Robin J Hofmeister, Bárbara Sousa da Mota, Olivier Delaneau.

The release of 150,119 UK Biobank sequences represents an unprecedented opportunity as a reference panel to impute low-coverage whole-genome sequencing data with high accuracy but current methods cannot cope with the size of the data. Here we introduce GLIMPSE2, a low-coverage whole-genome sequencing imputation method that scales sublinearly in both the number of samples and markers, achieving efficient whole-genome imputation from the UK Biobank reference panel while retaining high accuracy for ancient and modern genomes, particularly at rare variants and for very low-coverage samples.

DOI: https://doi.org/10.1038/s41588-023-01438-3