StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	22927308	Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJ, Zhao Y, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC	Poly-gene fusion transcripts and chromothripsis in prostate cancer.	Genes Chromosomes Cancer	2012 Dec	1,8,12	Prostate cancer	Next Generation Sequencing	Homo sapiens	LTL-313H	Illumina Genome Analyzer II			GRIN3B;MARCH10;ITGAE;CMYA5;SULT1C3;VN1R2;SLC2A9;AL160314.1;STARD8;SMC1B;DNAH6;KIF1A;KLHDC7A;SLC18A1;NOD2;TMX4;SPAG17;F13A1;STK31;RTTN;CXorf22;SYT6;FRAS1;CYB561;DNAH9;ATAD1;NR5A2;DACT1;STRA6;ZNF804B;NOTCH4;ACCN2;RAG1;PPPDE1;GPR98;CAPN14;FERMT1;TTN;DUOX1;KRT75;LRP4;FAT1;C12orf63;STARD13;ZNF192;DLGAP5;TRPV4;OAS1;SLC27A6;FAM55B;C14orf39;ERCC6;FRK;DMXL2;SYNPO2;ZMIZ1;TECTA;NAT8;TGFBR3;BTNL2;SCNN1B;UGT2B15;KIAA1109;ZBBX;NPBWR1;ODF3;AKR7L;RNF212;PDILT;C6orf170;EFHB;PAPLN;AC145676.2;SLC9A10;ARHGAP42;GNRHR2;YSK4;MMP26;FAM179A;SYDE2;OR5H2;SLC6A17;DNAH17;LCN8;C10orf131;SLC14A2;PTX4;C20orf201;SCD5;GSDMC;CRNKL1;CD6;VWDE;MYO7A;INPP5B;GSG2;IYD;OR2C1;PCDHA4;OR2W3;LMLN;DISC1;ZNF407;BCMO1;ADAMTSL1;SLCO1B3;HGF;FBXW12;C6orf97;CRYGB;AL353597.1;ALG8;TBC1D22A;SLC28A1;CX3CR1;ENG;AK7;ZFAT;GLI3;ZNF474;UNC13D;CELA2B;SUSD3;MUC5AC;ADNP2;GPR19;C7orf57;C11orf72;AMPH;BTN3A2;SPATA7;DNAH3;FAM57A;ANKS1B;TEP1;SCAND3;FAM196A;MBD5;HRNR;MARCH8;ZRANB3;SIVA1;FRMPD2;C9orf96;ATR;WDR27;DNAH14;THBS1;E2F7;ZNF681;KIAA1009;KALRN;PCLO;A2ML1;MATN2;GABRR2;FLG;ANKRD18B;SLC12A7;MSX1;GAB1;CIT;ATAD5;PDE4DIP;AC007601.1;DNAH7;MBOAT2;C19orf45;FNIP2;RPS27;CCDC141;KDM4D;SCFD2;ALPK1;MED12L;TRANK1;ALS2CR8;WDR78;C9orf171;FLG2;NLRP8;ARMC2;IFIH1;KIF21B;SLC7A8;NEU3;ZNF772;FAM161A;DNAH11;TCHH;NAV2;OTUD4;SCIN;PAQR5;MBLAC2;KIAA1211;SLC26A8;FTCD;SLC4A7;ANKRD44;LTN1;UTP20;ZNF519;KIAA0319;SV2C;PSMB8;DSC3;PTCH1;SEMG2;MLXIPL;SPZ1;ACAA2;LTK;DFFB;FAM186B;SETBP1;CLOCK;GLYATL3;BCAS1;LARP1;TOPBP1;TMPRSS3;EDAR;DNAH1;SLC5A4;TLN2;CECR2;EXPH5;URB2;C5orf42;MATN3;CAST;SPRY1;SRD5A1;ZNF184;TPO;THAP6;KDM1B;DECR2;CCDC48;AC083883.1;BIRC6;LRTOMT;IL28RA;OMA1;BRCA1;PDIA3;ZNF671;PLAC8L1;MYOF;CELSR2;PPARGC1B;TES;C9orf68;MFSD6;MRAP;ZNF484;GRIN3A;TARBP1;SPRED2;GLB1;MAN2B2;UBA6;SCAMP3;ZNF382;KIAA0556;VEZT;MLF1IP;TNKS1BP1;SP2;PARD3B;MAGI1;SON;EFHC1;TAF1D;WDR60;ZNF226;CLCN2;KIAA1324;MCM3AP;DNAJC2;SH3BP1;TSEN2;CHTF18;ST3GAL6;RASA1;COBLL1;DAGLB;NSD1;DOT1L;PPOX;SLC4A3;USPL1;SLC5A6;SCNN1D;UBN1;ODF3B;TOP3B;NMRAL1;DCP1B;EIF2AK1;CHID1;NAT10;SEC14L2;NUMB;ALDH3B2;RET;KIAA1543;SMARCA2;ZNF662;XXbac-B461K10.4;ZNF737;TRDMT1;POLN;ZNF584;MAPT;SMPDL3B;SCYL3;CAPN13;THADA;ACOT6;PKP2;C21orf59;DHX58;CCDC36;DNAJB7;ATM;C14orf145;CEP55;SLC38A9;CASP2;TOR1AIP1;RIN2;ZSWIM6;ZNF202;SGSM3;ERV3;TUBGCP5;NEIL3;ETAA1;MARCH3;ALG14;SEC16A;ESF1;C7orf63;CALML4;PPIF;CCDC66;CLCC1;DDX51;ANKRD12;ZDHHC6;MYNN;STAT2;NRSN2;SUPT16H;FAM184B;WNK2;CCDC85C;DMAP1;COMMD5;GALNT11;C14orf79;DERL3;WDR41;NCAPH2;PAAF1;ANKRD16;ITIH4;ZNF773;ACTR8;C1orf112;CHD7;SLC25A45;ANKK1;THEG;PLCH2;CTDSPL;PRDM15;CPT1A;STH;SLC23A1;ANKRD5;BLM;ADI1;SYNRG;AGMAT;MKI67;POP1;R3HDM1;RAD17;CWC22;PUS1;KRI1;DOM3Z;ZDHHC5;ZRANB2;CCT7;KIF15;TACC2;KIF13A;AC006547.14;LRRC63;CAPN12;CLMN;ARHGAP11A;OBSCN;MCF2L;NUPL2;CYP1A1;ARHGEF12;PREPL;SGOL2;HMMR;GTF3C3;GCC2;CCDC14;UIMC1;RSPH3;ZNF808;LIFR;CBS;LIMCH1;VSIG2;ARID5B;LTBP4;CCDC116;ZNF530;ZNF93;FEZ2;C10orf18;C9orf102;NOC3L;KIAA0802;RAB3GAP1;SYNE1;ZXDC;SMARCAL1;COX17;TCF20;ZNF830;ZNF708;USP8;LAMP1;PITRM1;ALG3;NKTR;MRPS15;DNAJC28;SDCCAG8;STON2;RPAP1;TRIOBP;CSMD3;CCDC138;PISD;ZNF440;GTPBP5;IQSEC1;SFI1;GEMIN5;PIK3R3;HYAL2;VKORC1L1;GTPBP10;PCDHB8;WDR76;NIT1;MOV10L1;TRAK2;DICER1;ABCC4;EMID2;SMC2;CASP9;GEN1;USP19;ZNF571;ABHD14B;IL4R;SLC22A18;NCDN;MUC20;OSCP1;NEK11;HES2;FBXO17;AC008074.1;ACTR1B;GFER;MYO6;DGKQ;HLA-DMA;SLC35C1;MARCH7;EFCAB10;TTC21B;PDZD2;PACRGL;C1orf50;CLK1;RP11-382J12.1;TCIRG1;PLEKHG2;GPATCH8;HNRNPF;IDUA;KTN1;ANKRD31;FBP2;C12orf43;ALMS1;F12;DOK7;IDO2;RHBDF2;FAM178B;C10orf62;FBF1;POFUT1;AKAP1;RGAG4;NUP210;PRKDC;YLPM1;AC127496.3;FAM186A;CYP2A7;SCN1B;TG;PI3;EXOC3;PM20D1;RP11-50B3.2;ZMAT4;SLC7A9;CXorf30;C2orf73;C10orf68;BSN;AC022415.1;SYNGR1;BCR;VTN;EPHA8;TP53;PCDHA1;C16orf46;RIBC2;CDKL5;UGGT2;CYP2D7P1;OCRL;RP4-695O20;SAC3D1	Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada	Complex genome rearrangements are frequently observed in cancer but their impact on tumor molecular biology is largely unknown. Recent studies have identified a new phenomenon involving the simultaneous generation of tens to hundreds of genomic rearrangements, called chromothripsis. To understand the molecular consequences of these events, we sequenced the genomes and transcriptomes of two prostate tumors exhibiting evidence of chromothripsis. We identified several complex fusion transcripts, each containing sequence from three different genes, originating from different parts of the genome. One such poly-gene fusion transcript appeared to be expressed from a chain of small genomic fragments. Furthermore, we detected poly-gene fusion transcripts in the prostate cancer cell line LNCaP, suggesting they may represent a common phenomenon. Finally in one tumor with chromothripsis, we identified multiple mutations in the p53 signaling pathway, expanding on recent work associating aberrant DNA damage response mechanisms with chromothripsis. Overall, our data show that chromothripsis can manifest as massively rearranged transcriptomes. The implication that multigenic changes can give rise to poly-gene fusion transcripts is potentially of great significance to cancer genetics.	NCBI 36/hg18				Yes	ARF3,RUNX1T1;ATP6V1C1,TSTA3;BAALC,TRAPPC9;BCAT1,ATF7IP;BCAT1,LOH12CR1;BCAT1,TMTC2;C12orf59,TTLL9;C12orf59,UBE2V2;C6orf145,FARS2;C6orf145,PRPF4B;C6orf145,RNF165;CA2,C4BPA;CA2,RUNX1T1;CELSR1,PTDSS1;EEF1D,SDC4;KIAA1467,C12orf59;PACS1,PTEN;PDRG1,ARF3;PDRG1,RUNX1T1;PDRG1,ZNF623;PTDSS1,LOH12CR1;PTDSS1,SOX5;PTDSS1,SPRYD3;PTDSS1,UBE2V2;RNF165,SSR1;RUNX1T1,ARF3;RUNX1T1,C12orf35;RUNX1T1,HHAT;RUNX1T1,SDC4;RUNX1T1,SOX5;SDC4,PTDSS1;SLC25A21,C14ORF25;SLC35B1,PEMT;SLC35B11,PEMT;SLC6A17,CA2;SNX16,CA2;SPRYD3,PTDSS1;SSR1,RNF165;ST8SIA1,PDRG1;TENC1,TTLL9;TMPRSS2,ERG;TRAPPC9,SPRYD3;TRAPPC9,ZNF623;TTLL9,C12ORF57;TTLL9,C21orf59;TTLL9,KIAA1467;UCRC,C1orf194;USP34,AHSA2;USP34,C2orf74;ZNF623,TRAPPC9
Research	22927308	Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJ, Zhao Y, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC	Poly-gene fusion transcripts and chromothripsis in prostate cancer.	Genes Chromosomes Cancer	2012 Dec	6,10	Prostate cancer	Next Generation Sequencing	Homo sapiens	LNCaP	Illumina Genome Analyzer II				Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada	Complex genome rearrangements are frequently observed in cancer but their impact on tumor molecular biology is largely unknown. Recent studies have identified a new phenomenon involving the simultaneous generation of tens to hundreds of genomic rearrangements, called chromothripsis. To understand the molecular consequences of these events, we sequenced the genomes and transcriptomes of two prostate tumors exhibiting evidence of chromothripsis. We identified several complex fusion transcripts, each containing sequence from three different genes, originating from different parts of the genome. One such poly-gene fusion transcript appeared to be expressed from a chain of small genomic fragments. Furthermore, we detected poly-gene fusion transcripts in the prostate cancer cell line LNCaP, suggesting they may represent a common phenomenon. Finally in one tumor with chromothripsis, we identified multiple mutations in the p53 signaling pathway, expanding on recent work associating aberrant DNA damage response mechanisms with chromothripsis. Overall, our data show that chromothripsis can manifest as massively rearranged transcriptomes. The implication that multigenic changes can give rise to poly-gene fusion transcripts is potentially of great significance to cancer genetics.	NCBI 36/hg18				Yes	CYP2C19,PDE6C;CYP2C19,FAM190B;CYP2C18,SOD2;SNX9,CYP2C19
Research	22927308	Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJ, Zhao Y, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC	Poly-gene fusion transcripts and chromothripsis in prostate cancer.	Genes Chromosomes Cancer	2012 Dec	2,9	Prostate cancer	Next Generation Sequencing	Homo sapiens	890	Illumina Genome Analyzer II				Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada	Complex genome rearrangements are frequently observed in cancer but their impact on tumor molecular biology is largely unknown. Recent studies have identified a new phenomenon involving the simultaneous generation of tens to hundreds of genomic rearrangements, called chromothripsis. To understand the molecular consequences of these events, we sequenced the genomes and transcriptomes of two prostate tumors exhibiting evidence of chromothripsis. We identified several complex fusion transcripts, each containing sequence from three different genes, originating from different parts of the genome. One such poly-gene fusion transcript appeared to be expressed from a chain of small genomic fragments. Furthermore, we detected poly-gene fusion transcripts in the prostate cancer cell line LNCaP, suggesting they may represent a common phenomenon. Finally in one tumor with chromothripsis, we identified multiple mutations in the p53 signaling pathway, expanding on recent work associating aberrant DNA damage response mechanisms with chromothripsis. Overall, our data show that chromothripsis can manifest as massively rearranged transcriptomes. The implication that multigenic changes can give rise to poly-gene fusion transcripts is potentially of great significance to cancer genetics.	NCBI 36/hg18				Yes	FUBP1,ETV1;KCNS3,PPM1G;SLC35D2,LPPR1;SLC35D2,MRPL50;ZNF638,KCNS3