Batch Effects in Tumor-Only NGS Panel Sequencing and Implications for CNV Detection

Next generation sequencing (NGS) is routinely performed in clinical practice to detect various types of mutations for targeted therapy, diagnosis, and prognosis. Actionable alterations detected by NGS include not only non-synonymous mutations that lead to functional or structural changes of proteins but also copy number variants (CNV) that affect gene dosage, such as gene copy gains, amplifications or deletions. Among tumor-only CNV detection methods, the use of a Panel of Normals (PoN) for relative comparison has become a common practice, largely due to the lack of matched normal samples.