FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

Abstract

Allele-specific copy number analysis (ASCN) from next generation sequencing (NGS) data can greatly extend the utility of NGS beyond the identification of mutations to precisely annotate the genome for the detection of homozygous/heterozygous deletions, copy-neutral loss-of-heterozygosity (LOH), allele-specific gains/amplifications. In addition, as targeted gene panels are increasingly used in clinical sequencing studies for the detection of ‘actionable’ mutations and copy number alterations to guide treatment decisions, accurate, tumor purity-, ploidy- and clonal heterogeneity-adjusted integer copy number calls are greatly needed to more reliably interpret NGS-based cancer gene copy number data in the context of clinical sequencing. We developed FACETS, an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. It is a fully integrated stand-alone pipeline that includes sequencing BAM file post-processing, joint segmentation of total- and allele-specific read counts, and integer copy number calls corrected for tumor purity, ploidy and clonal heterogeneity, with comprehensive output and integrated visualization. We demonstrate the application of FACETS using The Cancer Genome Atlas (TCGA) whole-exome sequencing of lung adenocarcinoma samples. We also demonstrate its application to a clinical sequencing platform based on a targeted gene panel.

Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma

“…FACETS is an ASCN analysis tool and open-source software with a broad application to WGS, WES, as well as targeted-panel sequencing platforms developed by V.E.S. (33). We employed FACETS for WES data from 66 primary tumor samples from the TCGA-KICH project and for 73 primary tumor and 12 metastases samples profiled by the MSK-IMPACT platform.…”

“…Moreover, reliable interpretation of NGS-based gene copy number calls in clinical sequencing panels was possible due to accurate, purity-, ploidy-, and clonal heterogeneity-adjusted, integer copy number calls delivered by FACETS. For detailed information please refer to the related publication (33).…”

“…One unique feature of FACETS is the integer copy number output, where the total copy number and the minor allele copy number were corrected for tumor purity, ploidy, and clonal heterogeneity (33). Indeed, the loss of 1 copy of chromosome 2 detected by OncoScan and FACETS ( Figure 3, A and B) in the tumor was visualized with FISH assays using a 2p23/ALK probe (orange), and the retention of 2 copies of chromosomes 1q and 4 was confirmed using a 1q23/NTRK1 (red) and a chromosome 4 pericentromere (green) probe, respectively ( Figure 3C).…”

Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future

“…The majority of tools focus on somatic point mutations, and either restrict the analysis to copy neutral regions of the genome or make the assumption that a single mutation will be present at the same copy number state in every cancer cell (Carter et al, 2012;Miller et al, 2014;Roth et al, 2014). While tools to infer copy number heterogeneity have also been developed (Ha et al, 2014;Shen and Seshan, 2016), more recent tools seek to combine copy number and mutational data (Fischer et al, 2014;Jiang et al, 2016) and furthermore, attempt to infer evolutionary relationships between subclonal populations (Deshwar et al, 2015;. Relatedly, orthogonal tools to dissect heterogeneity by using data from single-cell sequencing have also been developed (Roth et al, 2016).…”

Genomic analysis of hairy cell leukemia identifies novel recurrent genetic alterations

“…[16][17][18] The FACETS algorithm was used to estimate tumor purity, ploidy, and allele-specific CN from sequencing data of tumor-normal pairs as previously described. 18,19 Additional experimental details are described in the supplemental Methods.…”