A practical guide to cancer subclonal reconstruction from DNA sequencing

M Tarabichi, A Salcedo, AG Deshwar… - Nature …, 2021 - nature.com
Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer
evolution studies, providing insight into the clonality and relative ordering of mutations and …

Advancing cancer research and medicine with single-cell genomics

B Lim, Y Lin, N Navin - Cancer cell, 2020 - cell.com
Single-cell sequencing (SCS) has impacted many areas of cancer research and improved
our understanding of intratumor heterogeneity, the tumor microenvironment, metastasis, and …

Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis

Y Fu, AW Jung, RV Torne, S Gonzalez, H Vöhringer… - Nature cancer, 2020 - nature.com
We use deep transfer learning to quantify histopathological patterns across 17,355
hematoxylin and eosin-stained histopathology slide images from 28 cancer types and …

The evolutionary history of 2,658 cancers

M Gerstung, C Jolly, I Leshchiner, SC Dentro… - Nature, 2020 - nature.com
Cancer develops through a process of somatic evolution,. Sequencing data from a single
biopsy represent a snapshot of this process that can reveal the timing of specific genomic …

[HTML][HTML] Genomic basis for RNA alterations in cancer

PCAWG Transcriptome Core Group Calabrese Claudia … - Nature, 2020 - nature.com
Transcript alterations often result from somatic changes in cancer genomes. Various forms of
RNA alterations have been described in cancer, including overexpression, altered splicing …

[HTML][HTML] Cancer genome evolutionary trajectories in metastasis

NJ Birkbak, N McGranahan - Cancer cell, 2020 - cell.com
Metastatic cancer is a major cause of death and remains largely incurable. A better
understanding of metastasis is therefore desperately needed to improve prognosis for late …

Characterizing allele-and haplotype-specific copy numbers in single cells with CHISEL

S Zaccaria, BJ Raphael - Nature biotechnology, 2021 - nature.com
Single-cell barcoding technologies enable genome sequencing of thousands of individual
cells in parallel, but with extremely low sequencing coverage (< 0.05×) per cell. While the …

Immuno-genomic landscape of osteosarcoma

CC Wu, HC Beird, J Andrew Livingston… - Nature …, 2020 - nature.com
Limited clinical activity has been seen in osteosarcoma (OS) patients treated with immune
checkpoint inhibitors (ICI). To gain insights into the immunogenic potential of these tumors …

Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes

E Pleasance, E Titmuss, L Williamson, H Kwan… - Nature Cancer, 2020 - nature.com
Advanced and metastatic tumors with complex treatment histories drive cancer mortality.
Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and …

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

S Zaccaria, BJ Raphael - Nature communications, 2020 - nature.com
Copy-number aberrations (CNAs) and whole-genome duplications (WGDs) are frequent
somatic mutations in cancer but their quantification from DNA sequencing of bulk tumor …