title: Reliable detection of subclonal single-nucleotide variants in tumour cell populations.
abstract: According to the clonal evolution model, tumour growth is driven by competing subclones in somatically evolving cancer cell populations, which gives rise to genetically heterogeneous tumours. Here we present a comparative targeted deep-sequencing approach combined with a customised statistical algorithm, called deepSNV, for detecting and quantifying subclonal single-nucleotide variants in mixed populations. We show in a rigorous experimental assessment that our approach is capable of detecting variants with frequencies as low as 1/10,000 alleles. In selected genomic loci of the TP53 and VHL genes isolated from matched tumour and normal samples of four renal cell carcinoma patients, we detect 24 variants at allele frequencies ranging from 0.0002 to 0.34. Moreover, we demonstrate how the allele frequencies of known single-nucleotide polymorphisms can be exploited to detect loss of heterozygosity. Our findings demonstrate that genomic diversity is common in renal cell carcinomas and provide quantitative evidence for the clonal evolution model.
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland.
authors.forename: Moritz
authors.initials: M
authors.lastname: Gerstung
authors.forename: Christian
authors.initials: C
authors.lastname: Beisel
authors.forename: Markus
authors.initials: M
authors.lastname: Rechsteiner
authors.forename: Peter
authors.initials: P
authors.lastname: Wild
authors.forename: Peter
authors.initials: P
authors.lastname: Schraml
authors.forename: Holger
authors.initials: H
authors.lastname: Moch
authors.forename: Niko
authors.initials: N
authors.lastname: Beerenwinkel
mesh_terms: D000465:Algorithms; D000483:Alleles; D002292:Carcinoma, Renal Cell / Q000235:genetics*; D060965:Clonal Evolution; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D019656:Loss of Heterozygosity; D020641:Polymorphism, Single Nucleotide; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D051794:Von Hippel-Lindau Tumor Suppressor Protein / Q000235:genetics
chemical_list: D016159:Tumor Suppressor Protein p53; D051794:Von Hippel-Lindau Tumor Suppressor Protein; C497446:VHL protein, human