StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	23991058	Valentina Boeva, Stephanie Jouannet, Romain Daveau, Valerie Combaret, Cecile Pierre-Eugene, Alex Cazes, Caroline Louis-Brennetot, Gudrun Schleiermacher, Sandrine Ferrand, Gaelle Pierron, Alban Lermine, Thomas Rio Frio, Virginie Raynal, Gilles Vassal, Emma	Breakpoint Features of Genomic Rearrangements in Neuroblastoma with Unbalanced Translocations and Chromothripsis	PLoS One	2013 Aug	2,3	Neuroblastoma	Next Generation Sequencing	Homo sapiens	CLB-Re	Illumina Genome Analyzer Iix + SOLiD 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821422-51822596;hs21:18662734-18664468,hs21:18664612-18666655;hs21:39430214-39431963,hs21:39432136-39433942;hs21:43347296-43350072,hs21:43353577-43356312;hs21:43895273-43896989,hs21:43897144-43899197;hs22:23475510-23478215,hs22:23479675-23482121;hs22:46864727-46865782,hs22:46865869-46866569;hsX:117451678-117454032,hsX:117455089-117457048;hsX:136091199-136092964,hsX:136093039-136094957;hsX:147660963-147662170,hsX:147663153-147664307	ACOT12;ADAM22;ADAMTS9;ADAMTS9-AS2;ADCY8;ADRA1A;AFF2;AK8;ALK;AMPH;ANK1;APBA1;APOLD1;ARHGAP21;ARHGEF10;ARHGEF33;ARL6IP5;ASAP2;ASPRV1;ATAD2B;ATIC;ATL2;ATP13A1;ATP9B;ATXN7;BBX;BCL2;BRE;BSND;C10orf76;C1orf127;C2CD2;C2orf44;C3orf64;C3orf67;C4orf51;C8orf12;C9orf139;C9orf96;CADPS;CAPN13;CBFA2T3;CCDC164;CCDC63;CCDC75;CCDC88C;CDA;CDK5RAP2;CELF4;CELSR1;CHST9;CIB4;CLIC6;CLPTM1L;CMIP;CNTN3;CNTN4;CNTNAP2;COL17A1;COLEC11;CPM;CRIM1;CSGALNACT1;CSMD3;CYB5B;DCDC1;DHX57;DLEC1;DNAJC24;DNAJC8;DNM2;DNMT3A;DOK6;DPP6;DPYSL5;DSCR4;DTNB;DTWD2;DYM;EFR3B;EML4;EML5;EPT1;ERBB2IP;ERC1;EVC2;FAM179A;FAM19A1;FAM59B;FAM84A;FBXL14;FEZ2;FGF12;FGGY;FHIT;FKBP5;FLJ33534;FLJ43663;FNIP2;FOXP1;FRAS1;FRMD4B;FSTL4;FSTL5;G2E3;GABBR2;GALNT13;GDA;GHR;GMDS;GMIP;GPR113;GREB1;GRINA;GSK3A;GXYLT2;HAAO;HDAC4;HEATR7A;HOMER2;HPCAL1;HS1BP3;HSPG2;ICA1;IFT52;IGF1;IRF2;ISPD;ITSN2;KCNK3;KIAA1797;KIF3B;KIF3C;KLHDC4;KLHL29;KRTCAP3;LARP7;LBP;LCE1E;LDLRAD3;LINC00339;LOC100128590;LOC100271832;LOC339788;LOC387647;LOC388942;LOC400950;LOC440970;LOC641365;LOC649133;LOC728730;LPA;LPPR2;LRFN2;LRP1;LRRFIP1;LRRTM4;LTBP1;LUZP2;MAGI1;MAN1B1;MAP4K3;ME1;MEMO1;MFSD2B;MGAT4C;MIR4757;MITF;MLF1IP;MPP3;MRPL42P5;MRPS9;MTA3;MTHFD1L;MYCN;MYCNOS;MYO10;MYOCD;MYOM2;MYT1L;NBAS;NCOA1;NEDD4L;NLN;NOL10;NTF3;NTM;ODZ4;OPCML;OR7A10;OTOF;PAIP1;PARP10;PCBP1-AS1;PDIA6;PDZRN3;PEPD;PGD;PIK3C2G;PIK3CD;PITPNC1;PKDCC;PLA2G2C;PLA2R1;PLB1;PLEKHH2;POU2F3;PPP1R1C;PPP4R2;PRICKLE2;PRKCZ;PRKG1;PSD2;PTPRG;PTPRN2;PTPRZ1;PTRHD1;PVRL1;QTRT1;RAB10;RAD52;RASGEF1C;RCAN2;ROBO1;ROBO2;RPRD2;RPS23;RPS6KA2;RSPH1;RTDR1;RUFY1;SBF2;SCARA5;SDK1;SEMA3A;SGCZ;SH3PXD2A;SHISA9;SLC20A1;SLC25A25;SLC25A26;SLC8A1;SLCO3A1;SLIT3;SLK;SMAD3;SMC6;SNTG2;SOS1;SPATA13;SPI1;SRRM1;STARD3;STOX2;SYNDIG1;TAF1B;TBC1D3;TDH;TDRD5;TECPR1;TG;THADA;THSD4;TLL2;TMCC2;TMEM105;TMEM163;TMEM18;TMTC1;TP53BP2;TPO;TRIB2;TRIM37;TRIM54;TRPM2;TSHZ2;TSSC1;TTC15;TTC27;UBE2QL1;UBE2U;UBXN2A;UIMC1;USP40;VIT;VWA3B;WNK2;XRCC3;XYLT2;YPEL5;ZBTB26;ZC3H12D;ZNF236;ZNF385D;ZNF521;ZNF79	Inserm, U900, Paris, France	Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical genetic alterations of neuroblastoma and the two tumors belong to the group of neuroblastoma exhibiting a profile of chromothripsis. Inter and intra-chromosomal rearrangements were identified in the four samples, allowing in particular characterization of unbalanced translocations at high resolution. Using complementary experiments, we further characterized 51 rearrangements at the base pair resolution that revealed 59 DNA junctions. In a subset of cases, complex rearrangements were observed with templated insertion of fragments of nearby sequences. Although we did not identify known particular motifs in the local environment of the breakpoints, we documented frequent microhomologies at the junctions in both chromothripsis and non-chromothripsis associated breakpoints. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. Our study therefore indicates that both non-homologous end joining-mediated repair and replicative processes may account for genomic rearrangements in neuroblastoma. RNA-seq analysis allows the identification of the subset of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis.	GRCh37/hg19			ERP001414;ERP001988	Yes	ALK,CNTN3;ALK,LTBP1;ARHGEF33,THADA;ASAP2,MAGI1;ASPRV1,PCBP1-AS1;ATAD2B,MITF;BRE,MAGI1;C3orf64,PPP4R2;C3orf67,ADAMTS9;CIB4,ALK;CRIM1,FHIT;DPYSL5,THADA;FAM179A,MAP4K3;FAM59B,SOS1;FAM84A,FHIT;FHIT,ROBO1;GREB1,ATAD2B;HPCAL1,FAM179A;ITSN2,LTBP1;KCNK3,ALK;KIF3C,EPT1;KLHL29,ROBO2;KRTCAP3,FOXP1;LTBP1,MITF;MYT1L,ATL2;MYT1L,FHIT;NBAS,MAGI1;PLB1,LTBP1;PRICKLE2,MAGI1;PTRHD1,LOC100128590;RAB10,ADAMTS9;RAB10,PLB1;SLC8A1,CNTN3;SLC8A1,MAGI1;SNTG2,PRICKLE2;SNTG2,SOS1;THADA,CADPS;THADA,FHIT;TPO,THADA;TRIM54,TTC27;TTC15,ATXN7
Research	23991058	Valentina Boeva, Stephanie Jouannet, Romain Daveau, Valerie Combaret, Cecile Pierre-Eugene, Alex Cazes, Caroline Louis-Brennetot, Gudrun Schleiermacher, Sandrine Ferrand, Gaelle Pierron, Alban Lermine, Thomas Rio Frio, Virginie Raynal, Gilles Vassal, Emma	Breakpoint Features of Genomic Rearrangements in Neuroblastoma with Unbalanced Translocations and Chromothripsis	PLoS One	2013 Aug	1,2	Neuroblastoma	Next Generation Sequencing	Homo sapiens	NB1141	Illumina Genome Analyzer Iix + SOLiD V4/5500	chr10:15529190-15534526:-1;chr10:82748693-82755344:-1;chr10:83881117-83891684:-1;chr11:11820549-11826177:-1;chr11:21844990-21851266:-1;chr11:80897522-80954853:-1;chr12:117084488-117091290:-1;chr12:59934068-59949389:-1;chr12:80154933-80162240:1;chr14:29115847-29121527:-1;chr14:41606973-41672179:-1;chr14:84040576-84053462:-1;chr15:44134089-44140792:-1;chr15:98839166-98846740:-1;chr16:19942815-19970111:-1;chr16:58671655-58679585:-1;chr16:8063663-8070034:-1;chr18:40051191-40060344:-1;chr19:1947496-1954243:-1;chr19:35358488-35364082:-1;chr19:57472684-57478735:-1;chr1:1008696-33428101:1;chr1:102981985-118210856:1;chr1:104333229-160069178:-1;chr1:10532535-52086062:-1;chr1:10593721-22544984:-1;chr1:11000544-210352595:-1;chr1:11168798-210037600:-1;chr1:150207282-216546090:-1;chr1:150262096-220965516:-1;chr1:150267833-187360931:1;chr1:153924857-168223449:-1;chr1:173971109-186325486:-1;chr1:176021366-244022618:-1;chr1:176027486-210743602:1;chr1:176232171-183415615:-1;chr1:176662006-197116025:1;chr1:177243880-247265613:1;chr1:182809129-186315259:-1;chr1:182814024-245905715:1;chr1:186233169-186321810:1;chr1:187242483-223923379:-1;chr1:192433020-211838849:1;chr1:193312809-244172296:1;chr1:198301572-198313291:-1;chr1:203535803-241184504:-1;chr1:203660375-207790855:1;chr1:203738238-241394532:1;chr1:205493732-206227778:-1;chr1:2068550-227749001:1;chr1:208061423-212065304:1;chr1:22539918-26402564:-1;chr1:24470636-65806923:1;chr1:26491823-48278955:-1;chr1:27818230-53385947:1;chr1:30854615-76564199:-1;chr1:32828029-223917154:1;chr1:33387731-222083256:-1;chr1:33392618-228002678:1;chr1:35206835-186228869:1;chr1:41732082-208440994:1;chr1:42174094-62123246:-1;chr1:43711284-172794913:-1;chr1:43715503-116711705:1;chr1:44021796-46794418:-1;chr1:46869357-110734126:-1;chr1:47080149-57895203:1;chr1:48268839-70823296:-1;chr1:53388571-203532748:1;chr1:65434646-214126453:1;chr1:68578726-236343140:-1;chr1:70600665-227181629:1;chr1:71544272-187249590:-1;chr1:78381334-174930142:1;chr1:78438651-247270878:-1;chr1:82290565-226955829:-1;chr1:85083954-93405396:-1;chr1:86677932-86684957:-1;chr1:88286998-211865281:-1;chr1:92136276-102979292:1;chr1:9383812-115549141:1;chr1:94361854-173979899:-1;chr1:9649603-11175913:-1;chr22:19098103-19103450:-1;chr22:19568850-19575804:-1;chr22:22703334-22752441:1;chr2:108852881-108859177:-1;chr2:140990927-140997449:-1;chr2:163663230-163668712:-1;chr2:16940093-16949702:-1;chr2:196169811-196176361:-1;chr2:38956022-38972572:1;chr3:131986063-131998357:-1;chr3:165038483-165086313:-1;chr3:189222922-189227688:-1;chr3:189734079-189743455:-1;chr3:26447844-26454823:-1;chr3:41086972-41147816:-1;chr3:53024162-53041943:-1;chr3:84102144-84110568:-1;chr3:89391108-89422305:-1;chr4:175622591-175629943:-1;chr4:64131648-64157031:-1;chr4:71192597-71202301:-1;chr4:77835705-77840925:-1;chr5:150788348-150795389:-1;chr5:170127275-170133922:-1;chr5:179273528-179279633:-1;chr5:82479176-82485709:-1;chr5:88039999-88046084:-1;chr6:110393354-110417123:-1;chr6:132704943-132715688:-1;chr6:67005854-67050972:-1;chr6:74610890-74623068:-1;chr6:77433996-77461537:-1;chr7:127212044-127220658:-1;chr7:157730840-157736827:-1;chr8:5592539-5607475:-1;chr8:63032223-63043589:-1;chr8:87185470-87196722:-1;chr9:35978649-35984566:-1;chrX:11950774-11961984:-1;chrX:19463498-19472538:-1;chrX:91675313-91682189:-1;chrY:15715619-15733808:-1	hs1:54948487-54951659,hs2:16471642-16474882;hs1:168420447-168423941,hs8:30104833-30105849;hs1:215363951-215367234,hs2:15382398-15385750;hs2:808016-810857,hs3:15938261-15938856;hs2:39633376-39636378,hs5:126611809-126614967;hs5:21901609-21902330,hs13:61461250-61462231;hs5:80098576-80099975,hsX:29351349-29353077;hs1:1004867-1007660,hs1:48276716-48279021;hs1:1685962-1688147,hs1:159504785-159507102;hs1:4202418-4204433,hs1:4204549-4206063;hs1:6408891-6411178,hs1:44046003-44049001;hs1:6853393-6855834,hs1:8436418-8438863;hs1:6859214-6861316,hs1:47451425-47453557;hs1:8713341-8715164,hs1:163725403-163727518;hs1:9653601-9656094,hs1:235001227-235003141;hs1:10538687-10541143,hs1:39547723-39550155;hs1:10598035-10600813,hs1:184466137-184469221;hs1:10706786-10709474,hs1:227749851-227752064;hs1:10975755-10978962,hs1:82296483-82299429;hs1:11008495-11010874,hs1:211841853-211844204;hs1:15062466-15065058,hs1:202893997-202896280;hs1:21891623-21894398,hs1:211855786-211858232;hs1:21959686-21962265,hs1:85009249-85011179;hs1:23243501-23245597,hs1:76492376-76494808;hs1:23291097-23294022,hs1:175245472-175247940;hs1:24465977-24468106,hs1:33167271-33169437;hs1:25156470-25158623,hs1:25161550-25164564;hs1:26395646-26398296,hs1:165169781-165172145;hs1:35005180-35006837,hs1:35007277-35009059;hs1:36639361-36641627,hs1:97428248-97430881;hs1:38973578-38975999,hs1:161359375-161361020;hs1:41406644-41408702,hs1:98932089-98934354;hs1:41475631-41478286,hs1:156479673-156482383;hs1:42178727-42181808,hs1:207549769-207552778;hs1:43279431-43282744,hs1:203732827-203736051;hs1:44198440-44200976,hs1:240852477-240854708;hs1:46810408-46813517,hs1:113418964-113421203;hs1:4686178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U900, Paris, France	Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical genetic alterations of neuroblastoma and the two tumors belong to the group of neuroblastoma exhibiting a profile of chromothripsis. Inter and intra-chromosomal rearrangements were identified in the four samples, allowing in particular characterization of unbalanced translocations at high resolution. Using complementary experiments, we further characterized 51 rearrangements at the base pair resolution that revealed 59 DNA junctions. In a subset of cases, complex rearrangements were observed with templated insertion of fragments of nearby sequences. Although we did not identify known particular motifs in the local environment of the breakpoints, we documented frequent microhomologies at the junctions in both chromothripsis and non-chromothripsis associated breakpoints. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. Our study therefore indicates that both non-homologous end joining-mediated repair and replicative processes may account for genomic rearrangements in neuroblastoma. RNA-seq analysis allows the identification of the subset of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis.	GRCh37/hg19			ERP001414;ERP001988	Yes	ANP32E,USH2A;ATP2B4,CR1;CDK18,AVPR1B;DFFA,OSBPL9;DHX9,TPR;FAAH,SLC6A17;IL22RA1,DNAJC6;KCNK2,NBAS;LAX1,RGS7;LOC388630,HHLA3;MIR548F1,TPR;MOB3C,DAB1;NEXN,RABGAP1L;PAPPA2,ASPM;RFWD2,HHAT;TMEM201,MTOR;TSSK3,CAPN2;WASF2,ECHDC2;WLS,GPR137B
Research	23991058	Valentina Boeva, Stephanie Jouannet, Romain Daveau, Valerie Combaret, Cecile Pierre-Eugene, Alex Cazes, Caroline Louis-Brennetot, Gudrun Schleiermacher, Sandrine Ferrand, Gaelle Pierron, Alban Lermine, Thomas Rio Frio, Virginie Raynal, Gilles Vassal, Emma	Breakpoint Features of Genomic Rearrangements in Neuroblastoma with Unbalanced Translocations and Chromothripsis	PLoS One	2013 Aug	6,19	Neuroblastoma	Next Generation Sequencing	Homo sapiens	NB1142	Illumina Genome Analyzer Iix + SOLiD V4/5500	chr10:132985660-132995251:-1;chr10:1579059-1588908:-1;chr10:15954855-15968097:-1;chr10:71277735-71295026:-1;chr10:81721053-81731645:-1;chr11:124771072-124781839:-1;chr11:7807484-7837743:-1;chr12:56912991-56959884:1;chr13:106702169-106722732:-1;chr14:25905886-25916204:-1;chr16:52409891-52418832:-1;chr16:83667149-83679289:-1;chr17:69601715-69610672:-1;chr19:15539293-51327008:-1;chr19:19726050-33382212:-1;chr19:19730038-59064493:1;chr19:39272147-51322273:1;chr19:47844171-59068942:-1;chr19:54189926-55853550:1;chr19:562142-11115016:-1;chr19:781621-21513741:-1;chr1:155589112-155726967:1;chr1:199107104-199117349:-1;chr1:248150477-248159424:-1;chr1:60043981-60054277:-1;chr1:66020112-66033875:-1;chr20:12454760-12479026:-1;chr21:18101423-18108767:-1;chr21:25254696-25267775:-1;chr21:45615676-45624372:-1;chr2:143453088-143465894:-1;chr2:208347634-208363143:-1;chr2:227558825-227568040:-1;chr2:235838370-235846454:-1;chr2:35577680-35620309:-1;chr2:79330714-79343389:1;chr3:107034072-107044826:-1;chr3:196930241-196943330:-1;chr3:2023912-2032848:-1;chr3:25026175-25036053:-1;chr3:46791915-46854633:-1;chr4:115504089-115517922:-1;chr4:122279125-122293394:-1;chr4:164610228-164619218:-1;chr4:17198756-17207600:-1;chr4:32514066-32524007:-1;chr5:150877792-150886768:-1;chr5:26792444-26806239:-1;chr5:7639502-7649315:-1;chr5:86965343-86976794:-1;chr5:9896902-9928889:-1;chr6:100534810-100542871:-1;chr6:108911690-108920587:-1;chr6:126097658-150070724:1;chr6:136006752-170470886:-1;chr6:219613-107430301:1;chr6:23738625-23748789:-1;chr6:33736589-111279330:1;chr6:35335168-67817228:-1;chr6:35754594-35766766:1;chr6:39435171-108400197:-1;chr6:52174676-52932227:-1;chr6:52924112-87848352:-1;chr6:53924807-53938573:-1;chr6:62450477-159553363:1;chr6:73332512-160539393:1;chr6:99365311-168647732:1;chr7:13274204-13284668:-1;chr8:16259283-16277307:-1;chr8:2253552-2268331:1;chr9:96218633-96229100:-1;chrX:146034707-146045627:-1	hs2:138746679-138747353,hsX:76651556-76652306;hs6:215500-218685,hs19:55556975-55560020;hs6:35142422-35145938,hs19:55596935-55599944;hs6:37524902-37528250,hs19:55573613-55577027;hs6:45986874-45990519,hs19:55577842-55581128;hs6:125180750-125184366,hs19:55654991-55658179;hs6:136611902-136612700,hs19:55560202-55560883;hs6:152045747-152048420,hs19:55013679-55017070;hs6:157558280-157559463,hs19:55552600-55554363;hs6:157640190-157641292,hs19:55553991-55555948;hs6:160530367-160533917,hs19:55649962-55653924;hs17:21195702-21196569,hs18:15165041-15165590;hs1:3497291-3500128,hs1:3500363-3502804;hs1:28546763-28551211,hs1:28554059-28557093;hs1:106112685-106113998,hs1:106114598-106116634;hs1:113540719-113541837,hs1:113543186-113545023;hs1:219159258-219161464,hs1:219160830-219164490;hs1:227598318-227600253,hs1:227600264-227602390;hs1:246680458-246683437,hs1:246685322-246689142;hs2:71842780-71845722,hs2:71845556-71847897;hs2:104041156-104042668,hs2:104043987-104045472;hs2:108850805-108855426,hs2:108856247-108859628;hs2:166011059-166014630,hs2:166016836-166020285;hs2:180998391-181000046,hs2:181000523-181001747;hs2:194922032-194923154,hs2:194924830-194926182;hs2:195293240-195297166,hs2:195298592-195302232;hs3:3476764-3481012,hs3:3483369-3487391;hs3:18828208-18829399,hs3:18830672-18832075;hs3:22859858-22862035,hs3:22862828-22863813;hs3:32715304-32716156,hs3:32717142-32718337;hs3:39759108-39761179,hs3:39762318-39764259;hs3:42834260-42838401,hs3:42840869-42844527;hs3:174478186-174479914,hs3:174480147-174482224;hs3:183376919-183379044,hs3:183379086-183381759;hs4:1037556-1040435,hs4:1039753-1041425;hs4:10207226-10211271,hs4:10234580-10238735;hs4:19076032-19079475,hs4:19085750-19090524;hs4:137070698-137073394,hs4:137076171-137079269;hs4:152786696-152789884,hs4:152794800-152799109;hs4:189956531-189957543,hs4:189958600-189959209;hs5:21232204-21237237,hs5:21238515-21242985;hs5:109565750-109567478,hs5:109568734-109570623;hs5:114320517-114325263,hs5:114334985-114339220;hs6:35146380-35149594,hs6:71696846-71700967;hs6:35339473-35343551,hs6:52179146-52183214;hs6:37520118-37523236,hs6:108432031-108435299;hs6:39045094-39048407,hs6:62444279-62448067;hs6:39401847-39404731,hs6:160535975-160539067;hs6:49593450-49597312,hs6:170725950-170729952;hs6:52174742-52177612,hs6:64986030-64990307;hs6:64982285-64985665,hs6:126222575-126226244;hs6:64999063-65000516,hs6:65000972-65003277;hs6:67004893-67008689,hs6:67048927-67052957;hs6:67808955-67812730,hs6:95859383-95863573;hs6:71691783-71695322,hs6:122279176-122282712;hs6:73713582-73715765,hs6:73716078-73718288;hs6:73991925-73996338,hs6:126227352-126231084;hs6:84569987-84573247,hs6:90539496-90543057;hs6:87840419-87844059,hs6:99355361-99359121;hs6:90535144-90538047,hs6:99276177-99279776;hs6:95865284-95868629,hs6:159241278-159244471;hs6:99271810-99275631,hs6:126092793-126096866;hs6:108435896-108440138,hs6:111280630-111284071;hs6:109694349-109698659,hs6:156445677-156449341;hs6:151888147-151891900,hs6:168197596-168201129;hs6:160527913-160531976,hs6:170730583-170734012;hs7:23093513-23096892,hs7:23105700-23109552;hs7:89806779-8981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U900, Paris, France	Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical genetic alterations of neuroblastoma and the two tumors belong to the group of neuroblastoma exhibiting a profile of chromothripsis. Inter and intra-chromosomal rearrangements were identified in the four samples, allowing in particular characterization of unbalanced translocations at high resolution. Using complementary experiments, we further characterized 51 rearrangements at the base pair resolution that revealed 59 DNA junctions. In a subset of cases, complex rearrangements were observed with templated insertion of fragments of nearby sequences. Although we did not identify known particular motifs in the local environment of the breakpoints, we documented frequent microhomologies at the junctions in both chromothripsis and non-chromothripsis associated breakpoints. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. Our study therefore indicates that both non-homologous end joining-mediated repair and replicative processes may account for genomic rearrangements in neuroblastoma. RNA-seq analysis allows the identification of the subset of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis.	GRCh37/hg19			ERP001414;ERP001988	Yes	BCLAF1,RDH13;C6orf127,CLPS;CLIC5,RDH13;GPR77,CHMP2A;MIR4462,RDH13;PBX4,CEP89;PBX4,TRIM28;WIZ,KLK1