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CNA Explorer and anaLyzer (CNAEL): an interactive web application and standard operating procedure enabling efficient clinical review and reporting of complex NGS-derived tumor copy number profiles

Purpose: Clinical analysis and reporting of somatically acquired copy number abnormalities (CNAs) detected through next-generation sequencing (NGS) is time consuming and requires significant expertise. Interpretation is complicated by other classes of variants such as coding mutations and gene fusions. Recent guidelines for the clinical assessment of tumor CNAs harmonize and simplify the reporting criteria but did not directly address NGS-specific concerns or the need for a standardized and scalable protocol for CNA analysis. Methods: We developed a scalable NGS-derived CNA analysis protocol paired with a novel interactive web application, CNA Explorer and anaLyzer (CNAEL), to facilitate the rapid, scalable, and reproducible analysis and reporting of complex tumor-derived CNA profiles https://CNAEL.sema4.com. Results: Novel features of CNAEL include on-the-fly data rescaling to account for tumor ploidy, purity, and modal chromosomal copy number; integration of gene expression, coding, and fusion variants into review and automated genome-wide summarization to enable rapid reporting. We found that case curation times were significantly reduced when using CNAEL [median:7 mins, IQR = 4, 10.25] compared with our previous laboratory standard operating procedure [median: 61 mins, IQR = 23.75, 176,25] with p=4.631e-05. Conclusion CNAEL enables efficient and accurate clinical review and reporting of complex NGS-derived tumor copy number profiles.