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THetA specifications


Unique identifier OMICS_03562
Name THetA
Alternative name Tumor Heterogeneity Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


No version available


Publications for Tumor Heterogeneity Analysis

THetA citations


Overview on Clinical Relevance of Intra Tumor Heterogeneity

PMCID: 5897590
PMID: 29682505
DOI: 10.3389/fmed.2018.00085

[…] (). New research methods and a closer clinical application are also appealing for circulating tumor cells (CTCs). This type of analysis gives further information especially on heterogeneity ().Intra-tumor heterogeneity analysis is the key for more efficient treatments of cancer in our patients, but only if highly reproducible clinical research is performed. We should consider that different aspec […]


Circulating tumor DNA in early response assessment and monitoring of advanced colorectal cancer treated with a multi kinase inhibitor

PMCID: 5915153
PMID: 29707145
DOI: 10.18632/oncotarget.24879

[…] s detected by targeted gene sequencing (and confirmed with our in-house PCR) in two other patients previously diagnosed as being KRAS-wild-type. To reduce the variability in mutation detection due to tumor heterogeneity, analysis was always performed on the same FFPE tissue block ().Subsequently, via sequencing, we investigated whether these tumor-specific mutations were also detectable in plasma […]


Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

Nat Commun
PMCID: 5750210
PMID: 29296022
DOI: 10.1038/s41467-017-02424-0

[…] igin in both, anti-PD-L1 and control treated samples (Fig.  and Figure ). The fraction of clonal neoantigens was 60, 95, and 93% in the MC38, anti-PD-L1 treated, and the control tumors, respectively. Tumor heterogeneity analysis revealed more homogenous tumors undergoing treatment with checkpoint blockers compared with the control tumors and the MC38 cell line (Fig. ). The same pattern can be obse […]


Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

Sci Rep
PMCID: 5717219
PMID: 29208983
DOI: 10.1038/s41598-017-16813-4
call_split See protocol

[…] entities in the model, our model THEMIS and its predecessor TITAN directly model individual genomic positions as the entities in the model and therefore have the ability to perform CNA calling during tumor heterogeneity analysis. Both THEMIS and TITAN are dynamic graphical models with each frame representing a single genomic position, with CNA events captured by hidden Markov chains. Therefore, TH […]


The subclonal structure and genomic evolution of oral squamous cell carcinoma revealed by ultra deep sequencing

PMCID: 5369985
PMID: 28157713
DOI: 10.18632/oncotarget.15014

[…] structure of OSCC (and HNSCC) have remained unexplored mainly due to studies using only a single biopsy per patient, as the use of a single tumor biopsy severely hinders the analysis of spatial intra-tumor heterogeneity. Analysis of intra-tumor heterogeneity in HNSCC has previously been based on calculating a mutant-allele tumor heterogeneity score [], which could be useful if only one biopsy is a […]


Protein drug target activation homogeneity in the face of intra tumor heterogeneity: implications for precision medicine

PMCID: 5564706
PMID: 28159918
DOI: 10.18632/oncotarget.14019

[…] wo study sets analyzed, and direct evaluation of the genomic variability needs to be further investigated, especially in relationship to the protein kinase driven signaling data. While we focused our tumor heterogeneity analysis on the activation/phosphorylation state of specific key signaling proteins, it is it is, unknown not know whether or not these protein pathways represent the functional/ca […]


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THetA institution(s)
Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA

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