Abstract 3617: Very low coverage whole genome sequencing improves clinically relevant copy number variation calling compared to targeted sequencing
Authors: Amallraja Anu , Fuß Janina , Williams Casey B. , Forster Michael , Hinz Sebastian , Meißner Tobias , Hendricks Alexander 
Published: September 2020

Abstract
Introduction
Despite many advances, the treatment for most patients with advanced solid tumors in the abdomen continues to be a clinical challenge. Copy number variants (CNVs) are an important part of the genomic landscape of these patients. Next-generation sequencing (NGS) tests used in the clinical setting are predominantly multi-gene targeted panels (FM, Guardant, NeoGenomics). Although this is the current standard, there is still doubt about the reliability and accuracy of such panels (PMID: 28472276), and panel based CNV-calling in clinical labs use stringent thresholds that may filter out many CNVs. The purpose of our study was to evaluate the clinical utility of a 125-gene targeted sequencing panel in detecting actionable CNVs in a cohort of colorectal cancer patients, with the eventual goal of identifying appropriate genome-guided therapy options.
Materials and Methods
We performed (i) targeted (350X) NGS based on the IDT xGen 125-gene Pan-Cancer panel on tumor and matched normal blood samples of 54 patients as well as (ii) very low-coverage (LC-WGS, 0.1X) whole genome sequencing on tumor and matched blood samples for the same set of patients. Bioinformatics methods included adapter trimming with bbduk, alignment with bwa-mem, quality control with FASTQC and Qualimap. CNVkit, ichorNCA, and Control-FREEC were used to call CNVs. For CNVkit and ichorNCA, the normal samples were combined to create a ‘reference normal'. Multiple window sizes were utilized to call CNVs at different scales.
Results
We compared the results of CNV calls from CNVkit, ichorCNA and Control-FREEC from targeted and LC-WGS data. This analysis indicates that targeted panels are at least currently not capable of reliably identifying the copy number landscape of clinical colorectal samples when matched normal samples are utilized. While within the targeted region we identified a median of five clinically actionable CNVs per sample for both targeted and whole genome sequencing (CNV amplification threshold of 5 copies), discordance of called CNVs on average was 56 percent. Numerical copy number calls tend to be higher for the targeted panel (mean: 10) vs LC-WGS (mean: 6) Beyond the targeted regions, LC-WGS detected a median of one additional clinical actionable CNV in genes such as PD-L1, JAK2, LRP1B, VEGFA, BCL2, and CCND3 which are not part of the targeted gene panel.
Conclusions
Our analysis suggests that CNV calling from targeted panels can be improved upon by incorporating very low-coverage whole genome sequencing.
Citation Format: Anu Amallraja, Janina Fuß, Casey B. Williams, Michael Forster, Sebastian Hinz, Tobias Meißner, Alexander Hendricks. Very low coverage whole genome sequencing improves clinically relevant copy number variation calling compared to targeted sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3617.