Precise quantification of copy number alterations (CNAs) in a tumor genome is difficult. We have applied a comprehensive copy number analysis method, digital multiplex ligation-dependent probe amplification (digitalMLPA), for targeted gene copy number analysis in clear cell renal cell carcinoma (ccRCC). Copy number status of all chromosomal arms and eleven genes was determined in 60 ccRCC samples. Chromosome 3p loss and 5q gain, known as early changes in ccRCC development, as well as losses at 9p and 14q were detected in 56/60 (93.3%), 31/60 (51.7%), 11/60 (18.3%) and 33/60 (55%), respectively. Through gene expression analysis, a significant positive correlation was detected in terms of 14q loss determined using digitalMLPA and downregulation of mRNA expression ratios with HIF1A and L2HGDH (p = 0.0253 and 0.0117, respectively). Patients with early metastasis (< 1 year) (n = 18) showed CNAs in 6 arms (in median) whereas metastasis-free patients (n =34) showed those in significantly less arms (3 arms in median) (p = 0.0289). In particular, biallelic deletion of CDKN2A/2B was associated with multiple CNAs (≥ 7 arms) in three tumors. Together with sequence-level mutations in genes VHL, PBRM1, SETD2, and BAP1, we performed multiple correspondence analysis, which identified association of 9p loss and 4q loss with early metastasis (both p < 0.05). And this analysis indicated association of 4p loss and 1p loss with poor survival (both, p < 0.05). These suggest that CNAs had essential roles in aggressiveness of ccRCC. We showed that our approach of measuring CNA through digitalMLPA will facilitate selection of patients who may develop metastasis.
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