In serum, CNV in CCND1 was associated with MVI (p = 0.004); CNV in PTP4A, KRAS, ERBB2, TOP2A with positive STSM (p ≤ 0.035); CNV in CCND1 with the presence of incidental prostate cancer (p = 0.018). Here, PTP4A2 is linked to prostate cancer.