StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	22237106	Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG	The genetic basis of early T-cell precursor acute lymphoblastic leukaemia	Nature	2012 Jan 	1,11,12	Acute lymphoblastic leukemia	Next Generation Sequencing	Homo sapiens	STJALL001		chr10:0-135374737:0;chr11:0-61155471:0;chr11:134436401-134452384:0;chr11:61155472-70912249:-1;chr11:70912250-77979119:0;chr11:77979120-79868685:-1;chr11:79868686-80914909:0;chr11:80914910-81015904:1;chr11:81015905-82756272:0;chr11:82756273-83023070:1;chr11:83023071-83642443:0;chr11:83642444-134436400:-1;chr12:0-0:0;chr12:1-4034408:1;chr12:11787382-11852551:-1;chr12:11852551-21227923:-1;chr12:21227923-22066294:1;chr12:22066294-26671330:-1;chr12:26671330-28194413:1;chr12:28194414-132349534:0;chr12:4034408-11787382:-1;chr13:0-36416293:0;chr13:114028001-114142980:0;chr13:36416294-114028000:-1;chr14:0-106368585:0;chr15:0-100338915:0;chr16:0-88827254:0;chr17:0-78774742:0;chr18:0-75851817:0;chr18:75851818-76106200:-1;chr18:76106201-76117153:0;chr19:0-63811651:0;chr1:0-635200:0;chr1:183681561-184318407:1;chr1:184318408-185391929:0;chr1:185391930-222493387:1;chr1:222493388-226744537:0;chr1:226744538-232978811:1;chr1:232978812-233022500:0;chr1:233022501-247149600:1;chr1:247149601-247249719:0;chr1:635201-8847300:-1;chr1:8847301-183681560:0;chr20:0-62435964:0;chr21:0-46944323:0;chr22:0-49691432:0;chr2:0-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-94419549:0;chr6:94419550-95073427:-1;chr6:95073428-170899992:0;chr7:0-99532387:0;chr7:142194036-142205270:0;chr7:142205271-158821462:1;chr7:158821463-158821424:0;chr7:99532388-142194035:1;chr8:0-180567:0;chr8:180568-25681600:1;chr8:25681601-25681600:0;chr8:25681601-89256109:1;chr8:89256110-146274826:0;chr9:0-80097141:0;chr9:103678699-140273252:0;chr9:80097142-103678698:-1;chrX:0-0:0;chrX:1-40412672:1;chrX:40412673-154913754:0;chrY:0-57772954:0	hs1:185391933-185391933,hs1:183681561-183681561;hs1:211055963-211055963,hs1:226744535-226744535;hs1:211056775-211056775,hs1:185394336-185394336;hs1:222493387-222493387,hs1:211057022-211057022;hs4:6947258-6947258,hs4:6960707-6960707;hs4:53945291-53945291,hs7:27172066-27172066;hs4:53945348-53945348,hs8:89256006-89256006;hs6:95073427-95073427,hs11:80914910-80914910;hs7:27171985-27171985,hsX:40412627-40412627;hs10:21278245-21278245,hs10:21279404-21279404;hs11:81015904-81015904,hs6:94419550-94419550;hs11:43874661-43874661,hs11:77957935-77957935;hs11:61155472-61155472,hs11:70912250-70912250;hs11:77979120-77979120,hs11:82756273-82756273;hs11:79868681-79868681,hs11:43875121-43875121;hs11:79873315-79873315,hs11:83007059-83007059;hs11:83023070-83023070,hs12:28194412-28194412;hs12:4034408-4034408,hs12:21227923-21227923;hs12:11787386-11787386,hs12:11852551-11852551;hs12:22066294-22066294,hs12:26671330-26671330;hs14:21977845-21977845,hs14:21988920-21988920;hsX:40412669-40412669,hs8:89256109-89256109	A2M;A2ML1;AASDHPPT;ABCB10;ABCC9;ABCG4;ACAD8;ACAP3;ACAT1;ACOT7;ACRBP;ACRV1;ACSM4;ACTA1;ACTN2;ACTN3;ACTRT2;ACY3;ADAMTS15;ADAMTS8;ADIPOR1;ADIPOR2;ADORA1;ADRBK1;ADSS;AEBP2;AGRN;AGT;AHCTF1;AHNAK;AICDA;AIDA;AIP;AJAP1;AKAP3;ALDH3B1;ALDH3B2;ALG9;ALKBH3;ALKBH8;AMICA1;AMOTL1;ANGEL2;ANGPTL5;ANKK1;ANKRD13D;ANKRD49;ANO1;ANO2;APLP2;APOA1;APOA4;APOA5;APOBEC1;APOC3;APOLD1;ARCN1;ARHGDIB;ARHGEF16;ARID4B;ARL2;ARL8A;ARNTL2;ART4;ARV1;ASPM;ASRGL1;ATAD3A;ATAD3B;ATAD3C;ATF3;ATF7IP;ATG2A;ATL3;ATN1;ATP2B4;ATPGD1;AURKAIP1;AURKAPS1;AVPR1B;B3GALNT2;B3GALT2;B3GALT6;B3GAT3;B4GALNT3;BAD;BANF1;BATF2;BATF3;BBS1;BCAT1;BCL2L14;BHLHE41;BPNT1;BTG2;C12orf11;C12orf32;C12orf36;C12orf39;C12orf4;C12orf5;C12orf53;C12orf57;C12orf59;C12orf60;C12orf67;C12orf69;C12orf70;C12orf71;C12orf77;C1orf100;C1orf101;C1orf106;C1orf107;C1orf115;C1orf116;C1orf124;C1orf131;C1orf150;C1orf159;C1orf170;C1orf174;C1orf198;C1orf229;C1orf31;C1orf57;C1orf70;C1orf86;C1orf96;C1R;C1RL;C1S;C3AR1;C7orf34;C8orf48;C8orf58;C9orf129;C9orf153;C9orf156;C9orf170;CACNA1C;CACNA2D4;CALML6;CAMTA1;CAPN9;CAPZA3;CASC1;CCDC27;CCDC77;CCND2;CD163L1;CDKN1B;CEP170;CHML;CHRM3;CMAS;CNST;COG2;CREBL2;DAD1L;DCP1B;DDX47;DERA;DISC1;DISC2;DLG2;DUSP16;DUSP5P;EDARADD;EFCAB2;EFCAB4B;EGLN1;EMP1;EPS8;ERC1;ERO1LB;ERP27;ETNK1;ETV6;EXO1;EXOC8;FAM138D;FAM36A;FAM89A;FBXL14;FGFR1OP2;FH;FKBP4;FOXM1;GALNT2;GNPAT;GOLT1B;GPR19;GYS2;HMCN1;HSN2;IAPP;IFLTD1;IQSEC3;ITFG2;ITPR2;KCNJ8;KDM5A;KIAA0528;KLHDC5;KRAS;LDHB;LOC100130522;LOC100133893;LOC100292680;LRMP;LRTM2;LYRM5;MED21;MIR920;MRPS35;NINJ2;NVL;ODZ4;PPFIBP1;PTHLH;PYROXD1;RASSF8;RECQL;REP15;RNF187;RPLP0P2;SLCO1A2;SLCO1B1;SOX5;SSPN;ST8SIA1;STK38L;TATDN3;TM7SF3;	Department of Computational Biology and Bioinformatics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA	Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.	NCBI 36/hg18		phs000340		Yes	NA
Research	22237106	Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG	The genetic basis of early T-cell precursor acute lymphoblastic leukaemia	Nature	2012 Jan 	2,9	Acute lymphoblastic leukemia	Next Generation Sequencing	Homo sapiens	STJALL002		chr10:0-135374737:0;chr11:0-134452384:0;chr12:0-8545706:0;chr12:27480227-132349534:0;chr12:8545707-27480226:-1;chr13:0-114142980:0;chr14:0-106368585:0;chr15:0-100338915:0;chr16:0-75555812:0;chr16:75555813-75582197:1;chr16:75582198-88827254:0;chr17:0-78774742:0;chr18:0-76117153:0;chr19:0-0:0;chr19:1-63793700:1;chr19:63793701-63811651:0;chr1:0-91721921:0;chr1:100818677-103024856:-1;chr1:103024857-247249719:0;chr1:91721922-93409158:-1;chr1:93409159-93589481:0;chr1:93589482-97369434:-1;chr1:97369435-97385719:0;chr1:97385720-97385843:-1;chr1:97385844-100818676:0;chr20:0-62435964:0;chr21:0-46944323:0;chr22:0-0:0;chr22:1-49491400:1;chr22:49491401-49691432:0;chr2:0-206579746:0;chr2:206579747-207028592:1;chr2:207028592-207725565:1;chr2:207725565-209229004:1;chr2:209229004-210601250:1;chr2:210601250-210911367:1;chr2:210911367-211035238:1;chr2:211035238-213106802:1;chr2:213106802-213129128:1;chr2:213129128-242651100:-1;chr2:242651101-242951149:0;chr3:0-199501827:0;chr4:0-191273063:0;chr5:0-180857866:0;chr6:0-30822391:0;chr6:30822392-32895237:-1;chr6:32895238-170899992:0;chr7:0-50144815:0;chr7:50144816-50421851:-1;chr7:50421852-158821424:0;chr8:0-115945867:0;chr8:115945868-116017817:1;chr8:116017818-146274826:0;chr9:0-29999:0;chr9:104248373-105070517:-1;chr9:105070518-118874264:0;chr9:118874265-120461292:-1;chr9:120461293-140273252:0;chr9:21096626-22880450:-1;chr9:22880450-70510800:-1;chr9:30000-21096626:-1;chr9:70510800-70705182:-1;chr9:70705182-72993063:-1;chr9:72993063-73941820:-1;chr9:73941820-76718037:-1;chr9:76718037-77929470:-1;chr9:77929470-78271717:-1;chr9:78271718-78705695:0;chr9:78705696-83900722:-1;chr9:83900723-87880619:0;chr9:87880620-89388052:-1;chr9:89388053-104248372:0;chrX:0-68505335:0;chrX:68505336-69493999:1;chrX:69493999-69701501:1;chrX:69701501-70174245:1;chrX:70174245-70800355:1;chrX:70800356-154913754:0;chrY:0-57772954:0	hs1:91721922-91721922,hs1:97385720-97385720;hs1:93589482-93589482,hs1:100818677-100818677;hs1:97385843-97385843,hs1:97369434-97369434;hs1:103024856-103024856,hs1:93409158-93409158;hs2:213106802-213106802,hs2:207028592-207028592;hs2:213129128-213129128,hs2:207725565-207725565;hs2:209229004-209229004,hsX:68505336-68505336;hs7:50144816-50144816,hs7:50421851-50421851;hs8:116017817-116017817,hs8:115945868-115945868;hs9:21096626-21096626,hs9:118874265-118874265;hs9:72993063-72993063,hs9:78271717-78271717;hs9:76718037-76718037,hs9:105070517-105070517;hs9:83900722-83900722,hs9:70705182-70705182;hs9:87880620-87880620,hs9:89388052-89388052;hs9:104248373-104248373,hs9:120461292-120461292;hs9:126600441-126600441,hs9:126599797-126599797;hs12:11921859-11921859,hs2:206579740-206579740;hs12:91128883-91128883,hs12:27480226-27480226;hs16:75582197-75582197,hs16:75555813-75555813;hsX:69493999-69493999,hs2:210601250-210601250;hsX:70174245-70174245,hs2:211035238-211035238;hsX:70800355-70800355,hs2:206579747-206579747;hsX:70800356-70800356,hs12:11922106-11922106;hsX:69550634-69550634,hsX:69551230-69551230	AAMP;ABCA12;ABCB6;ACADL;ACCN4;ACER2;ACO1;ACSL3;ADAM23;ADAMTSL1;AGAP1;AGFG1;AGXT;AK3;ALDH1A1;ALDH1B1;ALPI;ALPP;ALPPL2;ANKMY1;ANKRD20A1;ANKRD20A2;ANKRD20A3;ANKRD20A4;ANKZF1;ANO7;ANXA1;ANXA2P2;AP1S3;APTX;AQP12A;AQP12B;AQP3;AQP7;AQP7P1;AQP7P2;AQP7P3;ARID3C;ARL4C;ARMC9;ARPC2;ASTN2;B4GALT1;BAG1;BG201338;BNC2;C12orf60;C2orf67;C2orf80;C6orf10;C6orf15;C6orf25;C9orf100;C9orf11;C9orf122;C9orf123;C9orf128;C9orf135;C9orf150;C9orf153;C9orf170;C9orf40;C9orf41;C9orf46;C9orf53;C9orf57;C9orf66;C9orf68;C9orf70;C9orf85;C9orf93;C9orf95;CBWD1;CCNYL1;CD274;CDC37L1;CDKN2A;CDKN2B;CDKN2BAS;CEP78;CER1;CNTLN;CPO;CREB1;CRYGA;CRYGB;CRYGC;CRYGD;CYLC2;DAPK1;DENND4C;DMRT1;DMRT2;DMRT3;DMRTA1;DYTN;EEF1B2;ERBB4;FAM108B1;FAM119A;FAM122A;FAM189A2;FASTKD2;FLJ43859;FLJ43950;FLJ44082;FLJ46321;FOXB2;FXN;FZD5;GAS1;GCNT1;GDA;GNA14;GNAQ;GOLM1;GPR1;IDH1;IFNA1;IFNA10;IFNA13;IFNA14;IFNA16;IFNA17;IFNA2;IFNA21;IFNA4;IFNA5;IFNA6;IFNA7;IFNA8;IFNE;IFNW1;INO80D;ISCA1;KLF7;KLF9;LANCL1;LOC100130426;LOC29034;MAP2;MDH1B;MIR204;MIR548F2;MYL1;NDUFS1;OSTF1;PCSK5;PIKFYVE;PIP5K1B;PLEKHM3;PRKACG;PRUNE2;PSAT1;PTAR1;PTH2R;RFK;RORB;RPE;RPSAP9;SMC5;SNORA70C;SNORD51;TJP2;TLE1;TLE4;TLR4;TMC1;TMEM2;TRPM3;TRPM6;UNC80;VPS13A;ZCCHC6;ZDBF2;ZFAND5;	Department of Computational Biology and Bioinformatics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA	Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.	NCBI 36/hg18		phs000340		Yes	C2orf67,KIF4A;ETV6,INO80D;INO80D,BG201338
Research	22237106	Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG	The genetic basis of early T-cell precursor acute lymphoblastic leukaemia	Nature	2012 Jan 	1,4,5,9,10	Acute lymphoblastic leukemia	Next Generation Sequencing	Homo sapiens	STJALL003		chr10:0-7430589:0;chr10:24920178-63614386:0;chr10:63614387-66275073:-1;chr10:66275074-68176655:0;chr10:68176656-68950041:-1;chr10:68950042-76649371:0;chr10:7430590-24920177:-1;chr10:76649372-78529151:-1;chr10:78529152-80761759:0;chr10:80761760-96821276:-1;chr10:96821277-135374737:0;chr11:0-134452384:0;chr12:0-132349534:0;chr13:0-114142980:0;chr14:0-97862275:0;chr14:97862276-98116066:-1;chr14:98116067-106368585:0;chr15:0-100338915:0;chr16:0-84850282:0;chr16:84850283-85033002:-1;chr16:85033003-88827254:0;chr17:0-78774742:0;chr18:0-60008337:0;chr18:60008338-60413979:-1;chr18:60413980-61115803:0;chr18:61115804-61276902:-1;chr18:61276903-76117153:0;chr19:0-63811651:0;chr1:0-65943700:0;chr1:106673274-107678605:-1;chr1:107678606-107716341:0;chr1:107716342-144004701:-1;chr1:144004702-247249719:0;chr1:65943701-77157200:-1;chr1:77157201-78144610:0;chr1:78144611-78755005:-1;chr1:78755006-106673273:0;chr20:0-62435964:0;chr21:0-46944323:0;chr22:0-49691432:0;chr2:0-242951149:0;chr3:0-199501827:0;chr4:0-84837682:0;chr4:125893225-135358957:-1;chr4:135358958-191273063:0;chr4:84837683-96243984:-1;chr4:96243985-125893224:0;chr5:0-6776459:0;chr5:116236493-116328132:1;chr5:116328133-117950913:0;chr5:117950914-122015240:-1;chr5:122015241-180857866:0;chr5:13467228-61592429:0;chr5:61592430-67173064:-1;chr5:67173065-116236492:0;chr5:6776460-7052197:-1;chr5:7052198-7070447:0;chr5:7070448-13467227:-1;chr6:0-170899992:0;chr7:0-158821424:0;chr8:0-146274826:0;chr9:0-15805305:0;chr9:15805306-15811941:1;chr9:15811942-20310301:0;chr9:20310302-21615196:-1;chr9:21615196-21778860:-1;chr9:21778860-22282780:-1;chr9:22282780-31089571:-1;chr9:31089571-31827466:-1;chr9:31827467-38084084:0;chr9:38084085-38301919:-1;chr9:38301920-38906324:0;chr9:38906325-38993888:-1;chr9:38993889-140273252:0;chrX:0-154913754:0;chrY:0-57772954:0	hs1:78144611-78144611,hs1:65935999-65935999;hs1:107716342-107716342,hs1:77157121-77157121;hs1:163486878-163486878,hs1:163486903-163486903;hs1:65943763-65943763,hs10:24920177-24920177;hs1:107678605-107678605,hs10:66275073-66275073;hs4:84837683-84837683,hs4:135358957-135358957;hs4:159764088-159764088,hs10:7430590-7430590;hs4:159770296-159770296,hs10:24923739-24923739;hs5:67173064-67173064,hs4:135348611-135348611;hs5:6776460-6776460,hs5:7070448-7070448;hs5:117950914-117950914,hs5:116328132-116328132;hs5:7052197-7052197,hs10:66301865-66301865;hs5:61592430-61592430,hs10:96821276-96821276;hs9:21778860-21778860,hs9:38301919-38301919;hs9:38084085-38084085,hs9:22282780-22282780;hs9:38993888-38993888,hs9:21615196-21615196;hs10:66275072-66275072,hs1:107678605-107678605;hs10:80761760-80761760,hs1:78755007-78755007;hs10:63614387-63614387,hs4:96243984-96243984;hs10:66301858-66301858,hs4:125893225-125893225;hs10:24923743-24923743,hs10:68950041-68950041;hs10:76649372-76649372,hs10:78529151-78529151;hs16:84850283-84850283,hs14:98116066-98116066;hs16:66071321-66071321,hs16:66071625-66071625;hs18:60008338-60008338,hs18:61276902-61276902	ABCG2;ACADM;ACBD7;ACTA2;ADAM30;ADAMTS6;ADCY2;ADO;ADORA3;AFF1;AGAP11;AHCYL1;AKNAD1;ALX3;AMIGO1;AMPD1;AMPD2;ANKRD1;ANKRD13C;ANKRD22;ANKRD33B;ANXA11;ANXA2P3;AP4B1;ARHGAP21;ARHGAP24;ARL5B;ARMC3;ASB17;ATAD1;ATOH1;ATP1A1;ATP5C1;ATP5F1;ATXN7L2;BCAS2;BCL2L15;BEND7;BMI1;BMPR1A;BMPR1B;BTAF1;C10orf11;C10orf111;C10orf113;C10orf114;C10orf116;C10orf140;C10orf4;C10orf41;C10orf47;C10orf57;C10orf58;C10orf67;C10orf99;C1orf103;C1orf141;C1orf152;C1orf161;C1orf162;C1orf173;C1orf183;C1QL3;C4orf12;C4orf29;C4orf33;C4orf36;C5orf44;C5orf49;C9orf11;C9orf53;C9orf72;C9orf82;CACNB2;CAMK1D;CCDC3;CCT5;CD180;CDC123;CDKN2A;CDKN2B;CDKN2B-AS1;CDNF;CDS1;CENPK;CEP55;CFLP1;CH25H;CMBL;COMMD3;COMTD1;CPEB3;CRYZ;CTH;CTNNA3;CTNND2;CYP26A1;CYP26C1;CYP2C18;DAP;DEPDC1;DIMT1L;DIRAS3;DMP1;DMRTA1;DMXL1;DNAJB4;DSPP;DTWD2;EGR2;ELAVL2;ERBB2IP;FAM13A;FAM13AOS;FAM159B;FAM170A;FAM173B;FAM190A;FASTKD3;FAT4;FPGT;FTMT;FUBP1;GADD45A;GIPC2;GNG12;GPR177;GPRIN3;GRID2;HERC3;HERC5;HERC6;HHLA3;HPGDS;HSD17B11;HSD17B4;HSPA4L;HTR1A;IFNA1;IFNA10;IFNA13;IFNA14;IFNA16;IFNA17;IFNA2;IFNA21;IFNA4;IFNA5;IFNA6;IFNA7;IFNA8;IFNB1;IFNE;IFNK;IFNW1;IFT74;IL12RB2;IL23R;INSL5;INTU;IPO11;ISCA1L;JMJD1C;KCNMA1;KIAA1797;KIF2A;KLHL9;LARP1B;LHX8;LINGO2;LOC554202;LOC732275;LOC84989;LOX;LRRC19;LRRC40;LRRC7;LRRC70;LRRTM3;MARCH6;MAST4;MFSD8;MGC27382;MIR1296;MIR31;MIR873;MIR876;MOBKL2B;MTAP;MTRR;NCRNA00032;NEXN;NLN;NRBF2;NTNG1;PABPC4L;PCDH10;PGRMC2;PHF17;PLAA;PLK4;POLS;PPWD1;PRMT6;PRR16;PTGFR;REEP3;RGS7BP;RNF180;ROPN1L;RTKN2;RXFP1;SCLT1;SDCCAG10;SEMA5A;SFMBT2;SFRS12IP1;SLC25A31;SNCAIP;SNORD123;SRFBP1;ST6GALNAC5;TAS2R1;TEK;TNFAIP8;TUSC1;VDAC2;ZNF365;ZNF474;ZNF503;	Department of Computational Biology and Bioinformatics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA	Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.	NCBI 36/hg18		phs000340		Yes	ARHGAP21,RXFP1;CTNNA3,ARHGAP21;NTNG1,ST6GALNAC5;RXFP1,SFMBT2