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. Author manuscript; available in PMC: 2017 Jul 5.
Published in final edited form as: Oncogene. 2016 May 16;36(1):60–70. doi: 10.1038/onc.2016.175

Table 1.

Pairwise co-occurrence relationships among RB1, TP53, PTEN, NKX3-1 and MYC in primary prostate cancer and metastatic castration-resistant prostate cancer (mCRPC)

Primary prostate cancer mCRPC
Studies MSKCC, 20101 Broad/Cornell 2012 TCGA, 2015 MSKCC, 20101 Michigan, 20122 Robinson et al, 2015
Specimen #s 157 109 333 28 502 150
RB1 inactivation3 3.2% 0.0% 0.9% 10% 29% 8.6%
TP53 inactivation3 1.9% 6.4% 7.5% 10% 54% 50%
PTEN inactivation3 5.7% 7.3% 17% 39% 50% 40%
NKX3-1 inactivation3 3.8% 0.0% 16% 3.6% 18% 3.3%
MYC activation4 40% 1.8% 13% 50% 25% 19%
Co-occurrence5 PPt, RM, PM, PtM PPt PM, RM, RPt, PPt RP, RN, PN, RPt, RM, PPt, NM, RN, PN, RPt, RP RP, PPt, NM, PM, RPt, PN,
Statistic significance6 p = 0.033 p = 0.023 p = 0.039

We retrieved published data (54–58) and analyzed them on cBioPortal.

1

This study included both primary prostate cancer and mCRPC.

2

mCRPC specimens were obtained at autopsy.

3

Inactivation of RB1, TP53, PTEN, and NKX3-1 is queried for HOMDEL MUT.

4

Activation of MYC is queried for AMP MUT EXP > 2 (larger than 2 SD from the mean).

5

Tendency for co-occurrence is by Log Odds Ratio; R, P, Pt, N, and M are short for RB1, TP53, PTEN, NKX3-1, and MYC, respectively, to indicate the pairs.

6

p value is by Fisher Exact Test. p < 0.05 is considered statistically significant, which is highlighted by bold font. Other pairs show tendencies with p values between 0.083 and 0.575. Tendency pairs with p values between 0.631 (the next higher value) to 0.907 (the highest) are not shown.

RB1 and TP53 often incur Shallow Deletions, suggesting biallelic inactivation for some Mutation samples, as shown by the Oncoprints for two studies in Figure. S5.