Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

Table 2

Summary of NGS-based studies on prostate cancer.

Discoveries	Method	References
Copy number loss of MTAP, CDKN2, and ARF genes	DNA-Seq	[34]
Somatic mutations in MTOR, BRCA2, ARHGEF12, and CHD5 genes		[11]
NCOA2, p300, the AR corepressor NRIP1/RIP140, and NCOR2/SMRT		[6]
Somatic mutations in SPOP, FOXA1, and MED12		[35]
Somatic mutations in MLL2 and FOXA1		[36]
Somatic mutations in TP53, DLK2, GPC6, and SDF4.		[37]
TMPRSS2:ERG, TMPRSS2:ETV1	RNA-Seq	[38]
TMPRSS2:ETV4		[39]
TMPRSS2:ETV5, SLC45A3:ETV5		[40]
TMPRSS2:ELK4		[41]
SLC45A3:ETV1, HERV-K_22q11.23:ETV1, HNRPA2B1:ETV1, and C15ORF21:ETV1		[42]
KLK2:ETV4 and CANT1:ETV4		[43]
SLC45A3:BRAF or ESRP1:RAF1		[44]
C15orf21:Myc		[45]
EPB41:BRAF		[46]
TMEM79:SMG5		[47]
Differential expression of PCAT-1		[48]
Differential expression of miR-16, miR-34a, miR-126*, miR-145, and miR-205		[49]
HDACs and EZH2 work as ERG corepressors	Chip-Seq	[50]
AP4 as a novel co-TF of AR		[51]
POU2F1 and NKX3-1		[52]
Runx2a regulates secretion invasiveness and membrane secretion		[53]
A novel transcriptional regulatory network between NKX3-1, AR, and the RAB GTPase signaling pathway		[54]
Distinct patterns of promoter methylation around transcription start sites	Methyl-Seq	[55]