Absolute copy number fitting from shallow whole genome sequencing data

Low-coverage or shallow whole genome sequencing (sWGS) approaches can efficiently detect somatic copy number aberrations (SCNAs) at low cost. This is clinically important for many cancers, in particular cancers with severe chromosomal instability (CIN) that frequently lack actionable point mutations and are characterised by poor disease outcome. Absolute copy number (ACN), measured in DNA copies per cancer cell, is required for meaningful comparisons between copy number states, but is challenging to estimate and in practice often requires manual curation. Using a total of 60 cancer cell lines, 148 patient-derived xenograft (PDX) and 142 clinical tissue samples, we evaluate the performance of available tools for obtaining ACN from sWGS. We provide a validated and refined tool called Rascal (relative to absolute copy number scaling) that provides improved fitting algorithms and enables interactive visualisation of copy number profiles. These approaches are highly applicable to both pre-clinical and translational research studies on SCNA-driven cancers and provide more robust ACN fits from sWGS data than currently available tools.

P14.54 Association of EGFR Expression and Copy Number with Outcome in Depatux-m (ABT-414) Randomized Phase II Study of the EORTC Brain Tumor Group

BACKGROUND Patients with glioblastoma (GBM) have a dismal prognosis and are in desperate need of better therapy than the standard of care (SOC). Epidermal growth factor receptor (EGFR) gene amplification is reported in more than 50% of GBMs as an important target for therapeutic intervention and as a potential predictive biomarker. Depatuxizumab mafodotin (depatux-m, ABT-414) is an antibody-drug conjugate that preferentially binds cells with EGFR active conformation, internalized and releases the cytotoxin, leading to cell death. In the primary analysis we reported a trend (in EORTC 1410; HR: 0.71, 95% CI [0.50–1.02], p = 0.06) at topline analysis which continued to improve with ad hoc follow up (HR of 0.66, 95%CI [0.47–0.93]; p = 0.016) was observed towards improved overall survival (OS) in patients with EGFR amplified (amp) recurrent glioblastoma treated with depatux-m in combination with temozolomide. OS was equivalent in the depatux-m monotherapy and chemotherapy control arms. Here, we evaluate the association of EGFR mRNA expression and EGFR copy number with outcome using the updated efficacy data. METHODS Eligible were patients with centrally confirmed EGFR amp GBM at first recurrence after temozolomide chemo-irradiation. Patients were randomized to either a) depatux-m 1.0–1.25 mg/kg combined with temozolomide 150–200 mg/m2 day 1–5 every 4 weeks, b) depatux-m 1.0–1.25 mg/kg monotherapy or c) either temozolomide or lomustine (TMZ/LOM) depending on the time of relapse. Primary endpoint was OS. Long-term follow-up data (24 months follow-up; 237 events) were utilized for this EGFR analysis. The expression level of EGFR was determined using RT-PCR. The absolute copy number of EGFR was determined using next generation sequencing. EGFR mRNA and EGFR copy number were treated as continuous variables and compared to OS using a generalized additive cox proportional hazards model. RESULTS The outcome of the long-term follow-up was that when used in combination with TMZ, depatux-m addition resulted in improved OS as compared to TMZ/ LOM control regardless of EGFR expression or absolute copy number of EGFR. In contrast, in depatux-m monotherapy, a trend was observed that depatux-m improved the outcome only at highest expression levels and highest absolute EGFR copy number. CONCLUSIONS The long-term follow-up trial results demonstrated that addition of depatux-m to SOC showed a trend to increased survival as compared to SOC alone in EGFR amp patients as determined using Fluorescent in situ hybridization (FISH) analysis. Further retrospective analysis supports this efficacy advantage is observed at all expression and amplification levels. When used in combination with SOC and regardless of the absolute copy number of EGFR, the trend for OS improvement was observed at all expression levels.

ACE: absolute copy number estimation from low-coverage whole-genome sequencing data

Summary Chromosomal copy number aberrations can be efficiently detected and quantified using low-coverage whole-genome sequencing, but analysis is hampered by the lack of knowledge on absolute DNA copy numbers and tumor purity. Here, we describe an analytical tool for Absolute Copy number Estimation, ACE, which scales relative copy number signals from chromosomal segments to optimally fit absolute copy numbers, without the need for additional genetic information, such as SNP data. In doing so, ACE derives an estimate of tumor purity as well. ACE facilitates analysis of large numbers of samples, while maintaining the flexibility to customize models and generate output of single samples. Availability and implementation ACE is freely available via www.bioconductor.org and at www.github.com/tgac-vumc/ACE. Supplementary information Supplementary data are available at Bioinformatics online.