StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	22553170	Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC	From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer	Journal of Pathology	2012 Jul	2,9	Prostate cancer	Next Generation Sequencing	Homo sapiens	890	Illumina GA-IIx			FUBP1;ETV1;DENND1A;ANXA4;ANXA4;TMEM67;ABL1;ANXA4;ABL1;ANXA4;RALGPS1;EXOC6B;GPR107;C2orf28;MAP3K5;TCF12;ZNF638;KCNS3;PPM1G;SLC35D2;LPPR1;MRPL50;DTNB;SPTLC1;TMEM55A;LCLAT1;ABL1;ANXA4	Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada	The current paradigm of cancer care relies on predictive nomograms which integrate detailed histopathology with clinical data. However, when predictions fail, the consequences for patients are often catastrophic, especially in prostate cancer where nomograms influence the decision to therapeutically intervene. We hypothesized that the high dimensional data afforded by massively parallel sequencing (MPS) is not only capable of providing biological insights, but may aid molecular pathology of prostate tumours. We assembled a cohort of six patients with high-risk disease, and performed deep RNA and shallow DNA sequencing in primary tumours and matched metastases where available. Our analysis identified copy number abnormalities, accurately profiled gene expression levels, and detected both differential splicing and expressed fusion genes. We revealed occult and potentially dormant metastases, unambiguously supporting the patients' clinical history, and implicated the REST transcriptional complex in the development of neuroendocrine prostate cancer, validating this finding in a large independent cohort. We massively expand on the number of novel fusion genes described in prostate cancer; provide fresh evidence for the growing link between fusion gene aetiology and gene expression profiles; and show the utility of fusion genes for molecular pathology. Finally, we identified chromothripsis in a patient with chronic prostatitis. Our results provide a strong foundation for further development of MPS-based molecular pathology.	NCBI 36/hg18				Yes	ADAMTS12,PXDNL;CPLX2,UBXD8;EBF1,FBXL17;EBF1,FEM1C;EFNA5,PCDHB7;JMY,DMGDH;KCNN2,EBF1;LMAN2,AP3S1;NDUFAF2,MAST4;PDE4D,C5orf47;PDE4D,FAM172A;PDE4D,PPP2R2B;PDE8B,UIMC1;PPP2R2B,FAM172A;RASGRF2,RNF145;TRIM40,FBXO38;YTHDC2,PPP2R2B;ZFP62,RGNEF