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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. When it comes to behavioral studies related to entertainment and gambling, researchers found that pathological gamblers have specific allele variations connected to serotonin and dopamine transporter genes. Today, kasinot ilman rekisteröitymistä attracts more number of gamblers and the gambling options are galore.

AbsCN-seq

OMIC_02202

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

OMIC_00217

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

OMIC_08946

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

OMIC_07407

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

OMIC_06141

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

OMIC_10732

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

OMIC_09039

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

OMIC_10999

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

OMIC_07696

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

OMIC_07304

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

OMIC_07438

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

OMIC_09040

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

OMIC_07958

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

OMIC_00336

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

OMIC_02239

deepSNV

Detection of subclonal SNVs in deep sequencing experiments.

Detection of subclonal SNVs in deep sequencing experiments.

Expanding Ploidy and Allele Frequency on Nested…

OMIC_00218

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

OMIC_09042

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

OMIC_09038

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…

OMIC_08806

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…

OMIC_09037

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

OMIC_05980

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

OMIC_07695

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

OMIC_03561

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

OMIC_03560

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

OMIC_03424

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

OMIC_03559

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

OMIC_05106

SciClone

An R package for inferring the subclonal architecture of tumors.

An R package for inferring the subclonal architecture of tumors.

SCUnmix

OMIC_09605

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

OMIC_07003

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

OMIC_08807

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

OMIC_05917

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

OMIC_06142

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

OMIC_03562

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

OMIC_09036

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…