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Citations per year

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Tool usage distribution map

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cloneHD specifications


Unique identifier OMICS_09040
Name cloneHD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Ville Mustonen

Publication for cloneHD

cloneHD citations


Clonal Heterogeneity Influences the Fate of New Adaptive Mutations

Cell Rep
PMCID: 5656752
PMID: 29045840
DOI: 10.1016/j.celrep.2017.09.046

[…] To reconstruct clonal expansions in the WAxNA populations, we used background genetic variants as markers. Using the cloneHD algorithm (), we inferred the subclonal genotypes and their frequency in the populations, both of which are unknown a priori (; ). We found at least one subclone in all WAxNA populations under […]


Computational Methods for Characterizing Cancer Mutational Heterogeneity

Front Genet
PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] ial hidden Markov model framework to simultaneously infer CNA and LOH segments from read depths and digital allele ratios at heterozygous variant loci in the genome from whole genome sequencing data. CloneHD (Fischer et al., ) provides a statistical framework using read depth, B-allele frequencies, and VAFs to infer the clonal population structure of a tumor, allowing the simultaneous analysis of […]


Advances in understanding tumour evolution through single cell sequencing*

Biochim Biophys Acta
PMCID: 5813714
PMID: 28193548
DOI: 10.1016/j.bbcan.2017.02.001

[…] SNV data have been combined to increase the discriminative power in the reconstruction process. A summary of methods following this strategy and their key features are given in .The methods CHAT  and CloneHD  estimate cellular prevalences of both SNVs and CNAs but do not set them into a phylogenetic context. SubcloneSeeker infers trees based on cellular prevalences of both SNV and CNA data . Howev […]


Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates

PMCID: 4765721
PMID: 26962434
DOI: 10.5256/f1000research.8030.r11450

[…] mation of one or more of sample purity, copy number profile and clonality. These include e.g. ABSOLUTE ( , ASCAT ( , CloneHD ( , OncoSNP-SEQ ( and QPure ( (for a more complete review see Yadav and De. ). There ar […]


Molecular effects of Lapatinib in the treatment of HER2 overexpressing oesophago gastric adenocarcinoma

Br J Cancer
PMCID: 4815800
PMID: 26484410
DOI: 10.1038/bjc.2015.342
call_split See protocol

[…] ne Ontology tools and KEGG pathway analysis. ASCAT-NGS v.2.1 (; ) was used to infer tumour copy number data, and a combination of both copy number and single nucleotide variation data was analysed in cloneHD to assess clonality (). […]


Computational methods and resources for the interpretation of genomic variants in cancer

BMC Genomics
PMCID: 4480958
PMID: 26111056
DOI: 10.1186/1471-2164-16-S8-S7

[…] usly developed methods.The methods for the detection of genetic heterogeneity in cancer can be also used to detect subclonal mutation conferring drug resistance. This idea has been investigated using cloneHD [], a new subclonal reconstruction algorithm optimized using both information about somatic mutations and correlated changes generated by copy-number changes. The method has been applied to th […]

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cloneHD institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK

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