CLONET
Overview
CLONET (CLOnality and Ploidy Estimation from Tumor) is a computational method for estimating tumor clonality and ploidy from germline SNP allelic fractions in whole-genome sequencing data. By leveraging the allele-frequency distribution of heterozygous germline SNPs, CLONET infers local copy number, tumor purity, and the clonal versus subclonal status of somatic deletions and rearrangements. It was introduced alongside ChainFinder in a 2013 WGS study of prostate cancer to establish the temporal order of genomic events in chromoplexy-driven tumor evolution.
Used by
- Introduced and applied to 57 prostate WGS genomes to infer clonality of somatic deletions and rearrangements; used to establish the consensus progression path — early NKX3-1/TMPRSS2-ERG, intermediate CDKN1B/TP53 loss, late subclonal PTEN deletion (p=10⁻⁵ vs NKX3-1); concordance with ABSOLUTE purity was R²=0.99 with two flagged discrepant samples PMID:23622249
- CLONET used for tumor purity/ploidy estimation and allele-specific copy-number clonality analysis in 114 metastatic CRPC biopsies; enabled clonal evolution analysis supporting divergent model of CRPC-NE origin from CRPC-Adeno PMID:26855148
- Used for tumour purity/ploidy estimation and clonality classification in 72 urothelial carcinoma tumours; 53/72 samples passed QC for copy-number analysis and 44 had reliable purity/ploidy estimates. PMID:27749842
Notes
- Inputs are germline SNP allelic fractions from WGS; does not require SNP array data.
- Designed specifically for use with paired tumor/normal WGS; works in concert with SV callers (dRanger, BreakPointer) and GISTIC for SCNA calling.
- Two samples showed discordant CLONET/ABSOLUTE purity estimates and were flagged in the original publication.
Sources
This page was processed by crosslinker on 2026-05-09. - PMID:26855148
This page was processed by entity-page-writer on 2026-05-15. - PMID:27749842
This page was processed by entity-page-writer on 2026-05-15.