A method for determining a risk of prostate cancer recurrence in a human subject, the method comprising: (a) detecting a set of copy numbers for a set of genomic regions or portions thereof in a biological sample obtained from the subject; wherein the set of genomic regions or portions thereof comprises genomic regions or portions thereof located at human chromosomes 3q26.2, 3q26.32, 3q26.3, Sp15.1, 7p22.3, 7q11.22, 7q11.23, 7q22.1, 7q31.31, 9q34.1, 11p15.4, 17q21.33, 17q25.3, 22q13.1, 4p13, Sq13.1, 5q14.3, Sq21.1, Sq21.2, 5q21.3, 5q23.1, 6q14.1, 6q21, 8p22, 8p21.2, 8p12, 10q23.31, 13q14.11, 13q14.13, 13q14.2, 13q14.3 and 16q23.1; (b) scoring each genomic region or portion thereof as diseased or normal, wherein the scoring is determined based on the copy number of the biological sample compared to a reference copy number; wherein the genomic region or portion thereof is scored as diseased if there is an increase in copy number at the genomic region or portion thereof located at human chromosome 3q26.2, 3q26.32, 3q26.3, Sp15.1, 7p22.3, 7q11.22, 7q11.23, 7q22.1, 7q31.31, 9q34.1, 11p15.4, 17q21.33, 17q25.3, or22q13.1 in the biological sample compared to the reference copy number, and if there is a decrease in copy number at the genomic region or portion thereof located at human chromosome 4p13, Sq13.1, 5q14.3, Sq21.1, Sq21.2, 5q21.3, 5q23.1, 6q14.1, 6q21, 8p22, 8p21.2, 8p12, 10q23.31, 13q14.11, 13q14.13, 13q14.2, 13q14.3 or 16q23.1 in the biological sample compared to reference copy number; (c) comparing the number of diseased genomic regions from step (b) to a threshold value for disease recurrence corresponding to at least 20% of the set of genomic regions or portions thereof being scored as diseased to generate a copy number score; (d) calculating a Cancer of the Prostate Risk Assessment Postsurgical (CAPRA-S) clinical score comprising the numerical values assigned to the clinical factors: the prostate-specific antigen level, pathogenic Gleason score, surgical margin status, presence of extracapsular extension, presence of seminal vesicle invasion, and presence of lymph node involvement; and (e) predicting a risk of prostate cancer recurrence for the subject based on the combination of copy number score and the clinical score, and based on using the copy number variation values and the clinical factor values, wherein the copy number variation values assigned to the genomic regions and the values assigned to the clinical factors are analyzed statistically as continuous and individual variables in the same model. (a) detecting a set of copy numbers for a set of genomic regions or portions thereof in a biological sample obtained from the subject; wherein the set of genomic regions or portions thereof comprises genomic regions or portions thereof located at human chromosomes 3q26.2, 3q26.32, 3q26.3, Sp15.1, 7p22.3, 7q11.22, 7q11.23, 7q22.1, 7q31.31, 9q34.1, 11p15.4, 17q21.33, 17q25.3, 22q13.1, 4p13, Sq13.1, 5q14.3, Sq21.1, Sq21.2, 5q21.3, 5q23.1, 6q14.1, 6q21, 8p22, 8p21.2, 8p12, 10q23.31, 13q14.11, 13q14.13, 13q14.2, 13q14.3 and 16q23.1; (b) scoring each genomic region or portion thereof as diseased or normal, wherein the scoring is determined based on the copy number of the biological sample compared to a reference copy number; wherein the genomic region or portion thereof is scored as diseased if there is an increase in copy number at the genomic region or portion thereof located at human chromosome 3q26.2, 3q26.32, 3q26.3, Sp15.1, 7p22.3, 7q11.22, 7q11.23, 7q22.1, 7q31.31, 9q34.1, 11p15.4, 17q21.33, 17q25.3, or22q13.1 in the biological sample compared to the reference copy number, and if there is a decrease in copy number at the genomic region or portion thereof located at human chromosome 4p13, Sq13.1, 5q14.3, Sq21.1, Sq21.2, 5q21.3, 5q23.1, 6q14.1, 6q21, 8p22, 8p21.2, 8p12, 10q23.31, 13q14.11, 13q14.13, 13q14.2, 13q14.3 or 16q23.1 in the biological sample compared to reference copy number; (c) comparing the number of diseased genomic regions from step (b) to a threshold value for disease recurrence corresponding to at least 20% of the set of genomic regions or portions thereof being scored as diseased to generate a copy number score; (d) calculating a Cancer of the Prostate Risk Assessment Postsurgical (CAPRA-S) clinical score comprising the numerical values assigned to the clinical factors: the prostate-specific antigen level, pathogenic Gleason score, surgical margin status, presence of extracapsular extension, presence of seminal vesicle invasion, and presence of lymph node involvement; and (e) predicting a risk of prostate cancer recurrence for the subject based on the combination of copy number score and the clinical score, and based on using the copy number variation values and the clinical factor values, wherein the copy number variation values assigned to the genomic regions and the values assigned to the clinical factors are analyzed statistically as continuous and individual variables in the same model.