Related papers: Using somatic mutation data to test tumors for clo…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Tumours develop in an evolutionary process, in which the accumulation of mutations produces subpopulations of cells with distinct mutational profiles, called clones. This process leads to the genetic heterogeneity widely observed in tumour…
The majority of cancer treatments end in failure due to Intra-Tumor Heterogeneity (ITH). ITH in cancer is represented by clonal evolution where different sub-clones compete with each other for resources under conditions of Darwinian natural…
Computed tomography imaging is a standard modality for detecting and assessing lung cancer. In order to evaluate the malignancy of lung nodules, clinical practice often involves expert qualitative ratings on several criteria describing a…
Next-generation sequencing technologies allow the measurement of somatic mutations in a large number of patients from the same cancer type. One of the main goals in analyzing these mutations is the identification of mutations associated…
Cancer results from a sequence of genetic and epigenetic changes which lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells, and thus, to a selective advantage of pre-cancerous cells. The…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
The emerging field of precision oncology relies on the accurate pinpointing of alterations in the molecular profile of a tumor to provide personalized targeted treatments. Current methodologies in the field commonly include the application…
Examination of T-cell receptor (TCR) clonality has become a way of understanding immunologic response to cancer and its interventions in recent years. An aspect of these analyses is determining which receptors expand or contract…
Recent advances in cancer research largely rely on new developments in microscopic or molecular profiling techniques offering high level of detail with respect to either spatial or molecular features, but usually not both. Here, we present…
With the advance of imaging technology, digital pathology imaging of tumor tissue slides is becoming a routine clinical procedure for cancer diagnosis. This process produces massive imaging data that capture histological details in high…
Changes in the number of copies of certain parts of the genome, known as copy number alterations (CNAs), due to somatic mutation processes are a hallmark of many cancers. This genomic complexity is known to be associated with poorer…
We study the spatial evolutionary dynamics of solid tumors as they obtain additional driver mutations. We start with a cancer clone that expands uniformly in three dimensions giving rise to a spherical shape. We assume that cell division…
Patient similarity analysis is important in health care applications. It takes patient information such as their electronic medical records and genetic data as input and computes the pairwise similarity between patients. Procedures of…
Mutational signatures are patterns of somatic mutations in tumor genomes that provide insights into underlying mutagenic processes and cancer origin. Developing reliable methods for their estimation is of growing importance in cancer…
Tumor shape is a key factor that affects tumor growth and metastasis. This paper proposes a topological feature computed by persistent homology to characterize tumor progression from digital pathology and radiology images and examines its…
Identifying subgroups and properties of cancer biopsy samples is a crucial step towards obtaining precise diagnoses and being able to perform personalized treatment of cancer patients. Recent data collections provide a comprehensive…
In this work we explore the temporal dynamics of spatial heterogeneity during the process of tumorigenesis from healthy tissue. We utilize a spatial stochastic process model of mutation accumulation and clonal expansion in a structured…
Recent experimental evidence suggests that acute myeloid leukemias may originate from multiple clones of malignant cells. Nevertheless it is not known how the observed clones may differ with respect to cell properties such as proliferation…
Lung cancer has a high rate of recurrence in early-stage patients. Predicting the post-surgical recurrence in lung cancer patients has traditionally been approached using single modality information of genomics or radiology images. We…