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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 11 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  = .0253 and .0117, respectively). Patients with early metastasis (<1 y) (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  = .0289). In particular, biallelic deletion of  CDKN2A/2B  was associated with multiple CNAs (≥7 arms) in 3 tumors. Together with sequence‐level mutations in genes  VHL ,  PBRM1 ,  SETD2 , and  BAP1 , we performed multiple correspondence analysis, which identified the association of 9p loss and 4q loss with early metastasis (both  P  < .05). This analysis indicated the association of 4p loss and 1p loss with poor survival (both,  P  < .05). These findings suggest that CNAs have essential roles in aggressiveness of ccRCC. We showed that our approach of measuring CNA through digitalMLPA will facilitate the selection of patients who may develop metastasis.

Risk prediction for metastasis of clear cell renal cell carcinoma using digital multiplex ligation‐dependent probe amplification