In this work, we applied our method to LNCaP and 22RV1 prostate cancer cell lines with MSI, and identified previously unknown biallelic inactivating mutations in the par-3 partitioning defective 3 homolog (PARD3) gene in LNCaP cells and the androgen-induced prostate proliferative shutoff associated protein (AS3) gene in 22Rv1 cells. Here, PARD3 is linked to prostate cancer.