Related papers: Phylogeny-based tumor subclone identification usin…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
Tumor samples are heterogeneous. They consist of different subclones that are characterized by differences in DNA nucleotide sequences and copy numbers on multiple loci. Heterogeneity can be measured through the identification 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…
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of…
Tumor is heterogeneous - a tumor sample usually consists of a set of subclones with distinct transcriptional profiles and potentially different degrees of aggressiveness and responses to drugs. Understanding tumor heterogeneity is therefore…
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…
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…
High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the…
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…
Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural…
Extracting genetic information from a full range of sequencing data is important for understanding diseases. We propose a novel method to effectively explore the landscape of genetic mutations and aggregate them to predict cancer type. We…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
Cancer arises from successive rounds of mutations which generate tumor cells with different genomic variation i.e. clones. For drug responsiveness and therapeutics, it is necessary to identify the clones in tumor sample accurately. Many…
Due to the complexity of cancer, clustering algorithms have been used to disentangle the observed heterogeneity and identify cancer subtypes that can be treated specifically. While kernel based clustering approaches allow the use of more…
In this work, we study and analyze different feature selection algorithms that can be used to classify cancer subtypes in case of highly varying high-dimensional data. We apply three different feature selection methods on five different…
Tumor cell populations can be thought of as being composed of homogeneous cell subpopulations, with each subpopulation being characterized by overlapping sets of single nucleotide variants (SNVs). Such subpopulations are known as subclones…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and…
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…
Cancer is responsible for millions of deaths worldwide every year. Although significant progress has been achieved in cancer medicine, many issues remain to be addressed for improving cancer therapy. Appropriate cancer patient…