Solid tumor samples typically contain multiple distinct clonal populations of cancer cells, and also stromal and immune cell contamination. A majority of the cancer genomics and transcriptomics studies do not explicitly consider genetic heterogeneity and impurity, and draw inferences based on mixed populations of cells. Deconvolution of genomic data from heterogeneous samples provides a powerful tool to address this limitation. Source text: Yadav and De, 2015.
AbsCN-seq
AbsCN-seq
A simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole…
A simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole numbers for tumor cells from sequencing data. A simulation study shows that estimates have reasonable accuracy, and that the algorithm is robust against the…
ABSOLUTE
ABSOLUTE
It can estimate purity/ploidy, and from that compute absolute copy-number and mutation…
It can estimate purity/ploidy, and from that compute absolute copy-number and mutation multiplicities.
AncesTree
AncesTree
Infers the clonal evolution and tumor composition, including mixing fractions, of a tumor…
Infers the clonal evolution and tumor composition, including mixing fractions, of a tumor from multi-sample DNA sequence data. AncesTree is better able to identify ancestral relationships between individual mutations than existing approaches,…
Bayclone
Bayclone
An allocation model to describe tumor heterogeneity (TH) using next-generation sequencing…
An allocation model to describe tumor heterogeneity (TH) using next-generation sequencing (NGS) data. Taking a Bayesian approach, the Indian buffet process (IBP) is extended to define a class of nonparametric models, the categorical IBP (cIBP).
Binary Tree Partition
Binary Tree Partition
rec-BTP
A combinatorial formulation of the problem of constructing the subpopulations of tumor…
A combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations. BTP outperforms existing clustering approaches on simulated and real sequencing data.
BubbleTree
BubbleTree
An intuitive representation of purity, allele-specific copy number, and clonality for…
An intuitive representation of purity, allele-specific copy number, and clonality for human tumor specimens. BubbleTree displays the clonal composition within a tumor at the genomic segment level with allele-specific copy number – a granular…
cancerTiming
cancerTiming
A maximum-likelihood estimation procedure that fully accounts for sequencing variability…
A maximum-likelihood estimation procedure that fully accounts for sequencing variability and show that it outperforms the partial maximum-likelihood estimation method. A Bayesian estimation procedure is also proposed to stabilize the estimates in…
Canvas
Canvas
A tool for identification of copy number changes from diverse sequencing experiments…
A tool for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched and unmatched tumor-normal studies. In addition…
Clomial
Clomial
A generative model for NGS data derived from multiple subsections of a single tumor. An…
A generative model for NGS data derived from multiple subsections of a single tumor. An expectation-maximization procedure for estimating the clonal genotypes and relative frequencies using this model is described. Applying this method to larger…
CLONality Estimate in Tumors
CLONality Estimate in Tumors
CLONET
Cancer arises from initiating cells (clones) that undergo intense evolutionary selection…
Cancer arises from initiating cells (clones) that undergo intense evolutionary selection during disease progression and can be widely altered during treatment. The tumor cell evolutionary process may lead to subclonal divergence resulting in genetic…
Clonality Inference in Tumors Using Phylogeny
Clonality Inference in Tumors Using Phylogeny
CITUP
A combinatorial method that infers clonal populations and their frequencies while…
A combinatorial method that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and deep sequencing data from two cancer studies, CITUP…
cloneHD
cloneHD
A software tool for reconstructing the subclonal structure of a population from…
A software tool for reconstructing the subclonal structure of a population from short-read sequencing data. Read depth data, B-allele count data and somatic nucleotide variant (SNV) data can be used for the inference. cloneHD can estimate the number…
CNALR
CNALR
An R package to perform a stratification of tumour subtypes based on copy number…
An R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. CNALR exhibits the best agreement in the prediction between smooth-segmented and circular binary-segmented CNA…
CNAnorm
CNAnorm
A normalization method for copy number aberration in cancer samples. CNAnorm performs…
A normalization method for copy number aberration in cancer samples. CNAnorm performs ratio, GC content correction and normalization of data obtained using very low coverage (one read every 100-10,000 bp) high throughput sequencing. It performs a…
deepSNV
deepSNV
Detection of subclonal SNVs in deep sequencing experiments.
Detection of subclonal SNVs in deep sequencing experiments.
Expanding Ploidy and Allele Frequency on Nested…
Expanding Ploidy and Allele Frequency on Nested Subpopulations
ExPANdS
Characterizes coexisting subpopulations in a single tumor sample using copy number and…
Characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model detects coexisting genotypes by leveraging run-specific tradeoffs between…
FISHtrees
FISHtrees
A framework for inferring models of tumor progression from single-cell gene copy number…
A framework for inferring models of tumor progression from single-cell gene copy number data, including variable rates for different gain and loss events. Application of FISHtrees to real cervical cancer data identifies key genomic events in disease…
Genomic Rearrangement Assembly For Tumours
Genomic Rearrangement Assembly For Tumours
GRAFT
A technique to help reconstruct the history of rearrangements responsible for cancer…
A technique to help reconstruct the history of rearrangements responsible for cancer genome karyotypes. This uses allelic copy number segmentation, rearrangements, and somatic single-nucleotide mutation distributions, and so is based entirely on the…
Lineage Inference for Cancer Heterogeneity and…
Lineage Inference for Cancer Heterogeneity and Evolution
LICHeE
Automates the phylogenetic inference of cancer progression from multiple somatic samples.…
Automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and…
Minimum Event Distance for Intra-tumour…
Minimum Event Distance for Intra-tumour Copy-number Comparisons
MEDICC
A method for phylogenetic reconstruction and heterogeneity quantification based on a…
A method for phylogenetic reconstruction and heterogeneity quantification based on a minimum event distance for intra-tumour copy-number comparisons. Given multiple such evolutionarily-related copy-number profiles, for example from distinct primary…
PhyloSub
PhyloSub
A statistical model that infers the phylogeny and genotype of the major subclonal…
A statistical model that infers the phylogeny and genotype of the major subclonal lineages represented in the population of cancer cells. It uses a Bayesian nonparametric prior over trees that groups SNVs into major subclonal lineages and…
PhyloWGS
PhyloWGS
A method that can be applied to WGS data from one or more tumor samples to reconstruct…
A method that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations.…
PurBayes
PurBayes
An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor…
An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.
PurityEst
PurityEst
A computational tool for estimating purity of human tumor samples using next-generation…
A computational tool for estimating purity of human tumor samples using next-generation sequencing data.
PyClone
PyClone
A tool for inferring the cellular frequency of point mutations from deeply sequenced…
A tool for inferring the cellular frequency of point mutations from deeply sequenced data. The model supports simultaneous analysis of multiple related samples and infers clusters of mutations whose cellular prevalences shift together. Such clusters…
PyLOH
PyLOH
A model to resolve the identifiability problem by integrating two types of sequencing…
A model to resolve the identifiability problem by integrating two types of sequencing information – somatic copy number alterations and loss of heterozygosity.
SciClone
SciClone
An R package for inferring the subclonal architecture of tumors.
An R package for inferring the subclonal architecture of tumors.
SCUnmix
SCUnmix
A method for deconvoluting mixtures of genomic data with the goal of more accurately…
A method for deconvoluting mixtures of genomic data with the goal of more accurately reconstructing cellular progression processes from bulk tumor genomic data. The method is designed to take better advantage of an underlying geometric structure one…
Sequenza
Sequenza
A software package that uses paired tumor-normal DNA sequencing data to estimate tumor…
A software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. Comparison between Sequenza/exome and SNP/ASCAT revealed…
Subcloneseeker
Subcloneseeker
Examines somatic variation events (such as copy number changes, loss of heterozygosity,…
Examines somatic variation events (such as copy number changes, loss of heterozygosity, or point mutations) in order to identify the underlying subclone structure, i.e. the subclones including the normal (non-cancerous) cells and their cellular…
TITAN
TITAN
A tool for predicting subclonal copy number alterations (CNA) and loss of heterozygosity…
A tool for predicting subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) from tumour whole genome sequencing data. It infers the clonal cluster of events along with their estimates of cellular prevalence, which is proportion of…
Tree Approach
Tree Approach
TrAp
An evolutionary framework for deconvolving data from a single genome-wide experiment to…
An evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. TrAp has been developed an algorithm for solving this…
Tumor Heterogeneity Analysis
Tumor Heterogeneity Analysis
THetA
An algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations…
An algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. THetA successfully estimates normal admixture and recovers clonal and subclonal copy number aberrations in…
TuMult
TuMult
A computational method for reconstructing the sequence of copy number changes driving…
A computational method for reconstructing the sequence of copy number changes driving carcinogenesis, based on the analysis of several tumor samples from the same patient. TuMult is a valuable tool for the establishment of clonal relationships…