StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	23496902	Jiao X, Hooper SD, Djureinovic T, Larsson C, Warnberg F, Tellgren-Roth C, Botling J, Sjoblom T	Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing	BMC Genomics	2013 Mar	1,2,3,7,8,11,15,16,17,20,21,X,Y	Breast cancer	Next Generation Sequencing	Homo sapiens	118T	SOLiD3	chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-55004818:0;chr15:55004819-58879386:-1;chr15:58879387-100338915:0;chr16:0-88827254:0;chr17:0-78774742:0;chr18:0-76117153:0;chr19:0-63811651:0;chr1:0-63476667:0;chr1:195690043-195690469:1;chr1:195690470-230523907:0;chr1:230523908-230528509:-1;chr1:230528510-247249719:0;chr1:63476668-63482030:-1;chr1:63482031-195690042:0;chr20:0-36255835:0;chr20:36255836-36257151:1;chr20:36257152-62435964:0;chr21:0-25220500:0;chr21:25220501-31517907:-1;chr21:31517908-46944323:0;chr22:0-49691432:0;chr2:0-70513576:0;chr2:70513577-70517836:-1;chr2:70517837-242951149:0;chr3:0-108519519:0;chr3:108519520-108524650:-1;chr3:108524651-134804179:0;chr3:134804180-134808444:-1;chr3:134808445-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-92600482:0;chr8:131918874-131923624:-1;chr8:131923625-141235875:0;chr8:141235876-141237150:1;chr8:141237151-143351438:0;chr8:143351439-143352831:1;chr8:143352832-146274826:0;chr8:92600483-92611590:-1;chr8:92611591-131918873:0;chr9:0-140273252:0;chrX:0-135125055:0;chrX:135125056-135131089:-1;chrX:135131090-154913754:0;chrY:0-57772954:0	hs2:172601516-172601516,hs2:175539159-175539159;hs15:57988348-57988348,hs15:58249409-58249409;hs15:59317692-59317692,hs15:67919721-67919721;hs21:27096176-27096176,hs21:40613558-40613558;hs21:27644155-27644155,hs21:30032969-30032969;hs21:30027728-30027728,hs21:45978888-45978888;hs11:55961514-55961514,hs11:70335355-70335355;hs21:26319139-26319139,hs21:34978397-34978397;hs11:55962145-55962145,hs11:70334660-70334660;hs15:58018756-58018756,hs21:45973422-45973422;hs15:58619373-58619373,hs21:34837891-34837891;hs15:59163813-59163813,hs21:26902586-26902586;hs15:69536585-69536585,hs21:16947278-16947278;hs7:89920909-89920909,hs17:22927514-22927514;hs15:58070776-58070776,hs21:40545794-40545794;hs15:71192826-71192826,hs21:18664764-18664764;hs15:67813088-67813088,hs21:17096313-17096313;hs1:203406073-203406073,hs17:67941744-67941744;hs15:56785572-56785572,hs21:35493037-35493037;hs15:56819851-56819851,hs21:26290149-26290149;hs15:56825407-56825407,hs21:35138237-35138237;hs15:57924318-57924318,hs21:36836122-36836122;hs15:58970133-58970133,hs21:28088365-28088365;hs15:58983956-58983956,hs21:46011615-46011615;hs15:59145037-59145037,hs21:40791222-40791222;hs15:63964813-63964813,hs21:30497263-30497263;hs15:64142747-64142747,hs21:34848420-34848420;hs15:69312660-69312660,hs21:28871349-28871349;hs15:70901061-70901061,hs21:38513266-38513266;hs16:33846095-33846095,hs24:10617572-10617572	ADAM10;ADCY8;APP;C15orf50;CHN1;CLDN14;CLIC6;CRB1;DSCAM;DSTYK;GRIK1;KSR1;LOC344595;MAP1D;NEO1;PRSS7;RAB11A;RCAN1;RORA;RUNX1;SHANK2;TCF12;THSD4;TIAM1;TOPBP1;TRAPPC9;TSNARE1;	Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, SE 751 85, Sweden	BACKGROUND: Chromosomal rearrangements in the form of deletions, insertions, inversions and translocations are frequently observed in breast cancer genomes, and a subset of these rearrangements may play a crucial role in tumorigenesis. To identify novel somatic chromosomal rearrangements, we determined the genome structures of 15 hormone-receptor negative breast tumors by long-insert mate pair massively parallel sequencing. RESULTS: We identified and validated 40 somatic structural alterations, including the recurring fusion between genes DDX10 and SKA3 and translocations involving the EPHA5 gene. Other rearrangements were found to affect genes in pathways involved in epigenetic regulation, mitosis and signal transduction, underscoring their potential role in breast tumorigenesis. RNA interference-mediated suppression of five candidate genes (DDX10, SKA3, EPHA5, CLTC and TNIK) led to inhibition of breast cancer cell growth. Moreover, downregulation of DDX10 in breast cancer cells lead to an increased frequency of apoptotic nuclear morphology. CONCLUSIONS: Using whole genome mate pair sequencing and RNA interference assays, we have discovered a number of novel gene rearrangements in breast cancer genomes and identified DDX10, SKA3, EPHA5, CLTC and TNIK as potential cancer genes with impact on the growth and proliferation of breast cancer cells. 	NCBI 36/hg18				Yes	ADAM10,APP;ADAM10,RUNX1;MEGF11,RCAN1;RORA,DSCAM