Mutational signatures: emerging concepts, caveats and clinical applications

G Koh, A Degasperi, X Zou, S Momen… - Nature Reviews …, 2021 - nature.com
Whole-genome sequencing has brought the cancer genomics community into new territory.
Thanks to the sheer power provided by the thousands of mutations present in each patient's …

Sarcoma treatment in the era of molecular medicine

TGP Grünewald, M Alonso, S Avnet… - EMBO molecular …, 2020 - embopress.org
Sarcomas are heterogeneous and clinically challenging soft tissue and bone cancers.
Although constituting only 1% of all human malignancies, sarcomas represent the second …

Signatures of copy number alterations in human cancer

CD Steele, A Abbasi, SMA Islam, AL Bowes… - Nature, 2022 - nature.com
Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-
related processes of replication stress, mitotic errors, spindle multipolarity and breakage …

A pan-cancer compendium of chromosomal instability

RM Drews, B Hernando, M Tarabichi, K Haase… - Nature, 2022 - nature.com
Chromosomal instability (CIN) results in the accumulation of large-scale losses, gains and
rearrangements of DNA. The broad genomic complexity caused by CIN is a hallmark of …

Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA

EN Bergstrom, J Luebeck, M Petljak, A Khandekar… - Nature, 2022 - nature.com
Clustered somatic mutations are common in cancer genomes and previous analyses reveal
several types of clustered single-base substitutions, which include doublet-and multi-base …

Metastasis and immune evasion from extracellular cGAMP hydrolysis

J Li, MA Duran, N Dhanota, WK Chatila, SE Bettigole… - Cancer discovery, 2021 - AACR
Cytosolic DNA is characteristic of chromosomally unstable metastatic cancer cells, resulting
in constitutive activation of the cGAS–STING innate immune pathway. How tumors co-opt …

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 …

Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity

F Newell, JS Wilmott, PA Johansson, K Nones… - Nature …, 2020 - nature.com
To increase understanding of the genomic landscape of acral melanoma, a rare form of
melanoma occurring on palms, soles or nail beds, whole genome sequencing of 87 tumors …

SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events

EN Bergstrom, MN Huang, U Mahto, M Barnes… - BMC genomics, 2019 - Springer
Background Cancer genomes are peppered with somatic mutations imprinted by different
mutational processes. The mutational pattern of a cancer genome can be used to identify …

Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression

KK Huang, H Ma, RHH Chong, T Uchihara, BSX Lian… - Cancer Cell, 2023 - cell.com
Intestinal metaplasia (IM) is a pre-malignant condition of the gastric mucosa associated with
increased gastric cancer (GC) risk. Analyzing 1,256 gastric samples (1,152 IMs) across 692 …