Quantification of tumor heterogeneity: from data acquisition to metric generation

A Kashyap, MA Rapsomaniki, V Barros… - Trends in …, 2022 - cell.com
Tumors are unique and complex ecosystems, in which heterogeneous cell subpopulations
with variable molecular profiles, aggressiveness, and proliferation potential coexist and …

Comprehensive outline of whole exome sequencing data analysis tools available in clinical oncology

Á Bartha, B Győrffy - Cancers, 2019 - mdpi.com
Whole exome sequencing (WES) enables the analysis of all protein coding sequences in
the human genome. This technology enables the investigation of cancer-related genetic …

Molecular biology and evolution of cancer: from discovery to action

JA Somarelli, H Gardner, VL Cannataro… - Molecular biology …, 2020 - academic.oup.com
Cancer progression is an evolutionary process. During this process, evolving cancer cell
populations encounter restrictive ecological niches within the body, such as the primary …

Rapid evolution and biogeographic spread in a colorectal cancer

JM Alves, S Prado-Lopez… - Nature …, 2019 - nature.com
How and when tumoral clones start spreading to surrounding and distant tissues is currently
unclear. Here we leveraged a model-based evolutionary framework to investigate the …

Accurate identification of subclones in tumor genomes

N Ahmadinejad, S Troftgruben, J Wang… - Molecular biology …, 2022 - academic.oup.com
Understanding intratumor heterogeneity is critical for studying tumorigenesis and designing
personalized treatments. To decompose the mixed cell population in a tumor, subclones are …

Comparative molecular analysis of cancer behavior cultured in vitro, in vivo, and ex vivo

NR Hum, A Sebastian, SF Gilmore, W He, KA Martin… - Cancers, 2020 - mdpi.com
Current pre-clinical models of cancer fail to recapitulate the cancer cell behavior in primary
tumors primarily because of the lack of a deeper understanding of the effects that the …

A phylogenetic approach to study the evolution of somatic mutational processes in cancer

S Miura, T Vu, J Choi, JP Townsend, S Karim… - Communications …, 2022 - nature.com
Cancer cell genomes change continuously due to mutations, and mutational processes
change over time in patients, leaving dynamic signatures in the accumulated genomic …

Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data

G Tanner, DR Westhead, A Droop, LF Stead - Nature Communications, 2021 - nature.com
Intratumour heterogeneity provides tumours with the ability to adapt and acquire treatment
resistance. The development of more effective and personalised treatments for cancers …

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

S Miura, T Vu, J Deng, T Buturla, O Oladeinde… - Scientific Reports, 2020 - nature.com
Tumors harbor extensive genetic heterogeneity in the form of distinct clone genotypes that
arise over time and across different tissues and regions in cancer. Many computational …

Tumors are evolutionary island-like ecosystems

A Chroni, S Kumar - Genome Biology and Evolution, 2021 - academic.oup.com
Integration of ecological and evolutionary features has begun to understand the interplay of
tumor heterogeneity, microenvironment, and metastatic potential. Developing a theoretical …