Related papers: Quantification of tumour evolution and heterogenei…
Early detection and quantification of tumour growth would help clinicians to prescribe more accurate treatments and provide better surgical planning. However, the multifactorial and heterogeneous nature of lung tumour progression hampers…
Recently, there has been a resurgence of interest in rigorous algorithms for the inference of cancer progression from genomic data. The motivations are manifold: (i) growing NGS and single cell data from cancer patients, (ii) need for novel…
In the study of cancer evolution and therapeutic strategies, scientific evidence shows that a key dynamics lies in the tumor-environment interaction. In particular, oxygen concentration plays a central role in the determination of the…
We develop a feature allocation model for inference on genetic tumor variation using next-generation sequencing data. Specifically, we record single nucleotide variants (SNVs) based on short reads mapped to human reference genome and…
Reliably predicting the future spread of brain tumors using imaging data and on a subject-specific basis requires quantifying uncertainties in data, biophysical models of tumor growth, and spatial heterogeneity of tumor and host tissue.…
Integrating experimental data into ecological models plays a central role in understanding biological mechanisms that drive tumor progression where such knowledge can be used to develop new therapeutic strategies. While the current studies…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
Tumor cells acquire different genetic alterations during the course of evolution in cancer patients. As a result of competition and selection, only a few subgroups of cells with distinct genotypes survive. These subgroups of cells are often…
Heterogeneity in characteristics from one region (sub-population) to another, commonly observed in complex systems, such as glasses and a collection of cells, is hard to describe theoretically. In the context of cancer, intra-tumor…
Mounting evidence underscores the prevalent hierarchical organization of cancer tissues. At the foundation of this hierarchy reside cancer stem cells, a subset of cells endowed with the pivotal role of engendering the entire cancer tissue…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
We propose small-variance asymptotic approximations for the inference of tumor heterogeneity (TH) using next-generation sequencing data. Understanding TH is an important and open research problem in biology. The lack of appropriate…
In the study of therapeutic strategies for the treatment of cancer, eco-evolutionary dynamics are of particular interest, since characteristics of the tumour population, interaction with the environment and effects of the treatment,…
The Galleri (R) (GRAIL) multi-cancer early detection test measures circulating tumour DNA (ctDNA) to predict the presence of more than 50 different cancers, from a blood test. If sensitivity of the test to detect early-stage cancers is…
Intra-tumour phenotypic heterogeneity limits accuracy of clinical diagnostics and hampers the efficiency of anti-cancer therapies. Dealing with this cellular heterogeneity requires adequate understanding of its sources, which is extremely…
Heterogeneity is a fundamental characteristic of cancer. To accommodate heterogeneity, subgroup identification has been extensively studied and broadly categorized into unsupervised and supervised analysis. Compared to unsupervised…
Multi-gene panel testing allows many cancer susceptibility genes to be tested quickly at a lower cost making such testing accessible to a broader population. Thus, more patients carrying pathogenic germline mutations in various…
Molecular phenotyping is central in cancer precision medicine, but remains costly and standard methods only provide a tumour average profile. Microscopic morphological patterns observable in histopathology sections from tumours are…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
We present an applied study in cancer genomics for integrating data and inferences from laboratory experiments on cancer cell lines with observational data obtained from human breast cancer studies. The biological focus is on improving…