StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	23583981	Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW; St. Jude Children's Research Hospital -Washington University Pediatric Cancer Genome Project	Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas	Nature Genetics	2013 Jun	5,6	Glioma	Next Generation Sequencing	Homo sapiens	SJLGG005	Illumina Genome Analyzer IIx or HighSeq	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-104635198:0;chr6:104635199-135517619:-1;chr6:135517620-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs5:140843463-140843463,hs6:104664174-104664174;hs6:135517564-135517564,hs5:140857801-140857801	PCDHGB1;MYB	Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA	The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.	GRCh37/hg19				Yes	NA
Research	23583981	Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW; St. Jude Children's Research Hospital -Washington University Pediatric Cancer Genome Project	Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas	Nature Genetics	2013 Jun	8	Glioma	Next Generation Sequencing	Homo sapiens	SJLGG033	Illumina Genome Analyzer IIx or HighSeq	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-67490865:0;chr8:67490866-89031536:1;chr8:69654188-67490578:1;chr8:78562383-89031728:-1;chr8:82753337-69654563:1;chr8:89031729-146364022:0;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs8:78562409-78562409,hs8:82753859-82753859	C8orf34;MYBL1;SNX16	Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA	The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.	GRCh37/hg19				Yes	C8orf34,MYBL1
Research	23583981	Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW; St. Jude Children's Research Hospital -Washington University Pediatric Cancer Genome Project	Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas	Nature Genetics	2013 Jun	6	Glioma	Next Generation Sequencing	Homo sapiens	SJLGG035	Illumina Genome Analyzer IIx or HighSeq	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-135491704:0;chr6:135491705-136884680:-1;chr6:136882615-135495476:1;chr6:136884681-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs6:135540965-135540965,hs8:89335432-89335432;hs8:88417780-88417780,hs6:136741489-136741489	MAP3K5;MAP7;MMP16;	Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA	The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.	GRCh37/hg19				Yes	NA
Research	23583981	Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW; St. Jude Children's Research Hospital -Washington University Pediatric Cancer Genome Project	Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas	Nature Genetics	2013 Jun	9	Glioma	Next Generation Sequencing	Homo sapiens	SJLGG038	Illumina Genome Analyzer IIx or HighSeq	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-159138663:0;chr8:0-146364022:0;chr9:0-14731423:0;chr9:14731424-78562970:-1;chr9:21749091-22015572:-1;chr9:22024624-22025145:-1;chr9:37804215-37804296:-1;chr9:78559926-78663080:-1;chr9:78654643-36070277:1;chr9:78663081-78671456:0;chr9:78671457-89348568:-1;chr9:84653505-78666783:1;chr9:89340180-78518260:1;chr9:89348569-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs9:78566224-78566224,hs9:116237623-116237623;hs9:89337633-89337633,hs9:78583405-78583405;hs12:12018549-12018549,hs15:88646889-88646889;hs12:12018559-12018559,hs15:88646886-88646886	CDKN2B-AS1;ETV6;NTRK3;PCSK5;RECK;	Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA	The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.	GRCh37/hg19				Yes	PCSK5,RECK
Research	23583981	Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW; St. Jude Children's Research Hospital -Washington University Pediatric Cancer Genome Project	Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas	Nature Genetics	2013 Jun	1,3,11,12	Glioma	Next Generation Sequencing	Homo sapiens	SJLGG039	Illumina Genome Analyzer IIx or HighSeq	chr10:0-135534747:0;chr11:0-135006516:0;chr12:0-133851895:0;chr13:0-115169878:0;chr14:0-107349540:0;chr15:0-102531392:0;chr16:0-90354753:0;chr17:0-81195210:0;chr18:0-78077248:0;chr19:0-59128983:0;chr1:0-249250621:0;chr20:0-63025520:0;chr21:0-48129895:0;chr22:0-51304566:0;chr2:0-243199373:0;chr3:0-12649233:0;chr3:12649234-46001511:-1;chr3:46001512-198022430:0;chr4:0-191154276:0;chr5:0-180915260:0;chr6:0-171115067:0;chr7:0-9539556:0;chr7:6300099-159138663:0;chr7:9539557-6300098:1;chr8:0-146364022:0;chr9:0-141213431:0;chrX:0-155270560:0;chrY:0-59373566:0	hs1:3643330-3643330,hs11:115411715-115411715;hs1:3643581-3643581,hs11:69538645-69538645;hs1:3649438-3649438,hs22:47557135-47557135;hs1:12582471-12582471,hs12:103110023-103110023;hs1:12584121-12584121,hs11:118491727-118491727;hs3:49168971-49168971,hs11:66966686-66966686;hs3:186716601-186716601,hs4:1899271-1899271;hs4:5039611-5039611,hs3:183723574-183723574;hs10:98887882-98887882,hs16:2158836-2158836;hs11:69540077-69540077,hs1:9555182-9555182;hs11:69541460-69541460,hs12:103111315-103111315;hs12:103110079-103110079,hs10:95588803-95588803;hs12:103112184-103112184,hs3:9662023-9662023;hs12:106295961-106295961,hs1:12581667-12581667;hs16:410315-410315,hs4:5037703-5037703;hs16:2170637-2170637,hs12:103110956-103110956;hs16:2172065-2172065,hs1:1196437-1196437	ABCC5;CYTH3;FYCO1;KDM2A;PHLDB1;PKD1;RAF1;SLIT1;ST6GAL1;TP73;UBE2J2;WHSC1;	Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA	The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.	GRCh37/hg19				Yes	FYCO1,RAF1;ST6GAL1,WHSC1;UBE2J2,PKD1