Profiling of copy number alterations using low-coverage whole-genome sequencing informs differential diagnosis and prognosis in primary cutaneous follicle center lymphoma

Primary cutaneous follicle center lymphoma (PCFCL) has an excellent prognosis using local treatment, while nodal follicular lymphoma (nFL) occasionally presenting with cutaneous spread, often requires systemic therapy. Distinction of the two diseases based on histopathology alone might be challenging. Copy number alterations (CNAs) have scarcely been explored on a genome-wide scale in PCFCL, yet they might serve as potential biomarkers during differential diagnosis and risk stratification. Low-coverage whole genome sequencing (lcWGS) is a robust, high-throughput method for genome-wide copy number profiling. In this study, we analyzed 28 PCFCL samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nFL patients. Although the copy number profile of PCFCL was similar to that of nFL, PCFCL lacked amplifications of 18q, with the frequency peaking at 18q21.33 in nFL cases involving the BCL2 locus (PCFCL: 5.0% vs. nFL: 31.3%, p=0.018, Fisher's exact test). Development of distant cutaneous spread was significantly associated with higher genomic instability including the proportion of genome altered (0.02 vs. 0.13, p=0.033) and number of CNAs (2 vs. 9 p=0.017), as well as the enrichment of 2p22.2-p15 amplification involving REL and XPO1 (6.3% vs. 60.0%, p=0.005), 3q23-q24 amplification (0.0% vs. 50.0%, p=0.004), 6q16.1-q23.3 deletion (6.3% vs. 50.0%, p=0.018) and 9p21.3 deletion covering CDKN2A and CDKN2B loci (0.0% vs. 40.0%, p=0.014, all Fisher's exact test) in PCFCL. Analysis of sequential tumor samples in two cases harboring an unfavorable clinical course pointed to the acquisition of 2p amplification in the earliest common progenitor underlining its pivotal role in malignant transformation. By performing genome-wide copy number profiling on the largest patient cohort to date, we identified distinctive CNA alterations conceivably facilitating the differential diagnosis of PCFCL and secondary cutaneous involvement of nFL, and potentially aiding the risk stratification of patients with PCFCL in the future.