St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project Steering Committee

This DAC controls 172 datasets

Dataset ID	Description	Samples
EGAD00001000085	Somatic Histone H3 mutations	14
EGAD00001000135	Neuroblastoma whole genome sequencing	80
EGAD00001000159	DATA FILES FOR SJOS	37
EGAD00001000160	DATA FILES FOR SJACT	16
EGAD00001000161	DATA FILES FOR SJLGG	33
EGAD00001000162	DATA FILES FOR SJEPD	44
EGAD00001000163	DATA FILES FOR SJPHALL	18
EGAD00001000164	Whole Genome Sequencing accompanying Genetic landscape of pediatric Rhabdomyosarcoma.	29
EGAD00001000165	DATA FILES FOR SJINF	46
EGAD00001000259	DATA FILES FOR SJAMLM7	8
EGAD00001000260	Hypodiploid acute lymphoblastic leukemia whole genome sequencing	40
EGAD00001000261	Retinoblastoma whole genome sequencing	8
EGAD00001000268	DATA FILES FOR SJCBF	34
EGAD00001000269	OLD DATA FILES FOR SJMB - Superseded by EGAD00001001864	68
EGAD00001000352	DATA FILES FOR SJLGG	7
EGAD00001000353	DATA FILES FOR SJLGG	45
EGAD00001000654	DATA FILES FOR BALL-PAX5	153
EGAD00001000655	DATA FILES FOR Histone-NSD2_RNASeq	8
EGAD00001000657	DATA FILES FOR Histone Capture bams	962
EGAD00001000695	DATA FILES FOR SJLGG	46
EGAD00001000700	None	8
EGAD00001000701	None	-
EGAD00001000793	RNA sequencing (RNA-Seq) for St. Jude High Grade Glioma (HGG) study	-
EGAD00001000806	Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study	63
EGAD00001000807	Whole Exome Sequencing (WES) for St. Jude High Grade Glioma (HGG) study	148
EGAD00001000853	DATA FILES FOR SJEPD	37
EGAD00001000854	DATA FILES FOR SJEPD	77
EGAD00001000878	RNA-Seq files accompanying Genetic landscape of pediatric Rhabdomyosarcoma	42
EGAD00001000976	WGS DATA FILES FOR SJPhLike	80
EGAD00001001016	DATA FILES FOR SJPhLike-RNASeq	125
EGAD00001001020	DATA FILES FOR SJEWS-WGS	38
EGAD00001001032	DATA FILES FOR SJMEL-WGS	12
EGAD00001001045	DATA FILES FOR SJRB	20
EGAD00001001052	DATA FILES FOR SJTALL	24
EGAD00001001053	DATA FILES FOR SJOS-WGS-2ndBatch	27
EGAD00001001054	DATA FILES FOR Ph-likeALL WES	23
EGAD00001001056	None	7
EGAD00001001059	Whole Exome Sequencing files accompanying Genetic landscape of pediatric Rhabdomyosarcoma	56
EGAD00001001065	DATA FILES FOR SJCPC-WGS	8
EGAD00001001098	DATA FILES FOR SJINF RNASeq	63
EGAD00001001245	DATA FILES FOR PCGP SJINF WES	40
EGAD00001001246	DATA FILES FOR PCGP SJMEL WXS	28
EGAD00001001247	DATA FILES FOR PCGP SJMEL RNASEQ	7
EGAD00001001248	DATA FILES FOR PCGP SJETP WXS	13
EGAD00001001352	Data files for CONSERTING (WGS)	38
EGAD00001001415	DATA FILES FOR PCGP Dyer_iPSC WGS	2
EGAD00001001416	DATA FILES FOR PCGP Dyer_iPSC TEBS	18
EGAD00001001418	DATA FILES FOR PCGP Dyer_iPSC 5hmc	8
EGAD00001001432	PCGP Germline Study Whole Genome Sequencing	1337
EGAD00001001433	PCGP Germline Study Whole Exome Sequencing	906
EGAD00001001664	LGG Epilepsy Cohort WGS	18
EGAD00001001665	LGG Epilepsy Cohort WXS	61
EGAD00001001666	LGG Epilepsy Cohort RNA-Seq	34
EGAD00001001864	DATA FILES FOR PCGP MB WGS - Supersedes (EGAD00001000269)	76
EGAD00001001874	None	16
EGAD00001002530	Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed RNASeq data referenced in this paper.	36
EGAD00001002654	This dataset contains RNA-seq, ATAC-seq, and ChIP-seq samples from the SJERG cohort. We applied ChIP-Seq for Dux4 on two B-cell ALL cell-lines(REH, Nalm6) along with INPUT. ATAC-Seq on two B-cell ALL cell-lines(REH, Nalm6) and xenograft of a B-cell ALL patient(ERG000016).	13
EGAD00001002667	Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed Excap data referenced in this paper.	327
EGAD00001002676	DATA FILES FOR PCGP SJERG (WGS)	44
EGAD00001002677	DATA FILES FOR PCGP SJERG (WXS)	42
EGAD00001002679	This dataset contains WES files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing.	38
EGAD00001002680	This dataset contains RNA-Seq files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing.	26
EGAD00001002681	RNA-seq, ChIP-seq, and ATAC-seq files for PCGP SJERG paper titled "Deregulation of DUX4 and ERG in acute lymphoblastic leukemia"	53
EGAD00001002692	DATA FILES FOR MULLIGHAN MEF2D RNASEQ STRANDED	200
EGAD00001002704	DATA FILES FOR MULLIGHAN MEF2D RNASEQ UNSTRANDED	217
EGAD00001002741	Additional Xenograph files for PCGP SJERG	11
EGAD00001003126	WGS data of medulloblastoma tumor/control pairs.	74
EGAD00001003134	DATA FILES FOR GRUBER SJAMLM7 EXOME	114
EGAD00001003135	DATA FILES FOR GRUBER SJAMLM7 RNASEQ	86
EGAD00001003154	RNA-Seq files for SJOS study	14
EGAD00001003155	WES files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'	6
EGAD00001003156	WGS files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'	4
EGAD00001003197	None	-
EGAD00001003198	None	-
EGAD00001003199	None	-
EGAD00001003389	WGS and WXS files for Dyer ATRX study	6
EGAD00001003396	WGS minibam files for SJLIFE	3036
EGAD00001003412	None	152
EGAD00001003413	None	145
EGAD00001003432	ChIP-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"	20
EGAD00001003433	RNA-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"	98
EGAD00001003434	Whole Exome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"	149
EGAD00001003435	Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"	150
EGAD00001003781	Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files.	94
EGAD00001003782	When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files.	43
EGAD00001003905	RNA-Seq files accompanying the paper titled "Somatic Histone H3 Mutations in Diffuse Intrinsic Pontine Gliomas and Non-Brainstem Paediatric Glioblastomas".	66
EGAD00001004280	This dataset contains whole genome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome"	78
EGAD00001004287	This dataset contains whole exome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome"	156
EGAD00001004290	This dataset contains whole genome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome"	156
EGAD00001004312	ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".	158
EGAD00001004315	WGBS files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".	37
EGAD00001004337	Whole Genome Sequencing files accompanying the paper titled "Structure and evolution of double minutes in diagnosis and relapse brain tumors". Please read the paper for more details.	2
EGAD00001004381	WGS files for ALL relapse paper titled "Mutational landscape and temporal evolution during treatment of relapsed acute lymphoblastic leukemia".	-
EGAD00001004382	RNA-Seq files for ALL relapse paper titled "Mutational landscape and temporal evolution during treatment of relapsed acute lymphoblastic leukemia".	-
EGAD00001004383	Capture validation files for ALL relapse paper titled "Mutational landscape and temporal evolution during treatment of relapsed acute lymphoblastic leukemia".	-
EGAD00001004429	ChIP-Seq files for PCGP ATRX study paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"	121
EGAD00001004446	WGS files for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"	16
EGAD00001004447	WES files for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"	128
EGAD00001004461	RNAseq files (dataset 1 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"	1083
EGAD00001004463	RNAseq files (dataset 2 of 2) for Mullighan PAX5_B-ALL paper titled "PAX5-driven Subtypes of B-cell Acute Lymphoblastic Leukemia"	204
EGAD00001004506	WES files for CHEN WTPDX paper titled "Forty-Five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor"	107
EGAD00001004507	RNAseq files for CHEN WTPDX RNASEQ paper titled "Forty-Five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor"	88
EGAD00001004559	WGBS files for PCGP NBL_MYCN_ATRX paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"	24
EGAD00001004566	WES files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"	2
EGAD00001004567	RNASeq files for MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"	2
EGAD00001004579	WGS files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"	2
EGAD00001004595	VALCAP files for Ma et al. (2019) Genome Biology (accepted) titled “Analysis of error profiles in deep next-generation sequencing data"	47
EGAD00001005484	WXS files for Zhang PanNBL paper titled "Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations"	634
EGAD00001005506	WGS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"	99
EGAD00001005509	WXS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"	276
EGAD00001005510	RNAseq files for Mullighan_GL_reALL RNASEQ2 paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"	34
EGAD00001005511	RNASeq files for Mullighan_GL_reALL RNASEQ1 paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"	81
EGAD00001005729	WGS files for Mullighan BiTE WGS paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"	56
EGAD00001005730	WXS files for Mullighan BiTE WXS paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"	60
EGAD00001005731	RNAseq files for Mullighan BiTE RNASEQ1 paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"	41
EGAD00001005732	lowinput RNASEQ files for Mullighan BiTE RNASEQ2 paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"	10
EGAD00001005733	single cell RNASEQ files for Mullighan BiTE RNASEQ3 paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"	10
EGAD00001005936	WXS files for Mullighan Leventaki ALCL paper titled "Integrative molecular analysis of pediatric Anaplastic large cell lymphoma reveals subtypes with distinct immune suppression signatures."	42
EGAD00001005951	RNASeq files for Mullighan Leventaki ALCL Project paper titled "Integrative molecular analysis of pediatric Anaplastic large cell lymphoma reveals subtypes with distinct immune suppression signatures."	32
EGAD00001006196	Additional Neuroblastoma whole genome sequencing data	3
EGAD00001006344	Additional Neuroblastoma whole genome sequencing data	30
EGAD00001006380	RNASeq files for paper titled "Molecular classification improves risk assessment in adult B-lineage ALL: Patients on the international UKALLXII-ECOG2993 trial."	57
EGAD00001006398	ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".	242
EGAD00001006442	WGS files for paper titled "Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses"	184
EGAD00001006443	WXS files for paper titled "Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses"	260
EGAD00001006444	RNASeq files for paper titled "Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses"	132
EGAD00001006609	RNASeq files for paper titled "Prognostic and therapeutic significance of leukemia subtypes and minimal residual disease measurements in pediatric acute lymphoblastic leukemia treated with contemporary risk-directed trial: a cohort study"	122
EGAD00001006674	RNASeq files for paper titled "The Acquisition of Molecular Drivers in Pediatric Therapy-Related Myeloid Neoplasms"	56
EGAD00001006675	WXS files for paper titled "The Acquisition of Molecular Drivers in Pediatric Therapy-Related Myeloid Neoplasms"	137
EGAD00001006676	WGS files for paper titled "The Acquisition of Molecular Drivers in Pediatric Therapy-Related Myeloid Neoplasms"	35
EGAD00001006678	HiC files for GenomePaint paper titled "Exploration of coding and non-coding variants in cancer using GenomePaint."	8
EGAD00001006679	WGS files for GenomePaint paper titled "Exploration of coding and non-coding variants in cancer using GenomePaint."	1
EGAD00001006680	RNASeq files for GenomePaint paper titled "Exploration of coding and non-coding variants in cancer using GenomePaint."	1
EGAD00001006905	Whole genome sequencing of 29 samples	29
EGAD00001006954	iAMP21 WGS, total of 224 samples	224
EGAD00001006998	iAMP21 WGS second batch	-
EGAD00001007530	RNAseq data of total TXVI samples	227
EGAD00001007570	WGS data set of 11 xenograft samples, Degradation of Janus kinases in CRLF2-rearranged acute lymphoblastic leukemia	11
EGAD00001007577	RNAseq samples from the iAMP21 study	88
EGAD00001007670	RNAseq data set of BCL11B, 519 samples	519
EGAD00001007863	BCL11B PacBio data set, 4 samples	4
EGAD00001007966	WGS data set used in the study, 2 samples	2
EGAD00001007967	RNAseq data set used in the study, 10 samples	10
EGAD00001007968	WGBS data set used in the study, 96 samples	96
EGAD00001008134	RNAseq data set, panALL study, 16 samples	16
EGAD00001008193	Exome sequencing of panALL exome data set, total of 1948 samples	598
EGAD00001008268	panALL exome sequencing, data set2, 700 samples	700
EGAD00001008290	panALL exome data set3, 650 samples	650
EGAD00001008328	WGS files for Wlodarski BMF MDS paper titled "Whole-genome sequencing of INSIGHT-HD BMF/MDS cohort"	-
EGAD00001008406	RNAseq files for Klco RPAML paper titled "UBTF tandem duplication defines High-risk Pediatric Acute Myeloid Leukemia"	-
EGAD00001008407	RNAseq files for Klco RPAML paper titled "UBTF tandem duplication defines High-risk Pediatric Acute Myeloid Leukemia"	173
EGAD00001008413	WGS files for Klco RPAML paper titled "UBTF tandem duplication defines High-risk Pediatric Acute Myeloid Leukemia"	158
EGAD00001008446	Remaining WGS files for paper titled "UBTF tandem duplication defines High-risk Pediatric Acute Myeloid Leukemia"	10
EGAD00001008600	WGS files for Genomic Landscape ALL paper titled "The genomic landscape of pediatric acute lymphoblastic leukemia"	278
EGAD00001008824	RNASeq files for Roussel-MPBRG paper titled "Combination of ribociclib and gemcitabine for the treatment of medulloblastoma"	98
EGAD00001008833	RNASeq files for Roussel paper titled "Combination of CDK4/6 with BET-bromodomain and PI3K/mTOR inhibitors in medulloblastoma in vitro and in vivo"	-
EGAD00001008842	RNASeq files for Roussel paper titled "Combination of CDK4/6 with BET-bromodomain and PI3K/mTOR inhibitors in medulloblastoma in vitro and in vivo"	39
EGAD00010000085	Somatic Histone H3 mutations	-
EGAD00010000462	SJLGG Case samples using Gene Expression Array	75
EGAD00010000596	PCGP Ph-likeALL GEA	837
EGAD00010000598	PCGP Ph-likeALL SNP6	1724
EGAD00010000696	PCGP ETP ALL SNP6	-
EGAD00010000698	PCGP INF ALL SNP6	-
EGAD00010001300	Medulloblastoma expression profiling	146
EGAD00010001319	Medulloblastoma methylation profiling	345
EGAD00010001596	DNA methylation data from patient RMS tumor samples from Illumina 450 K arays	32
EGAD00010001635	Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array	415
EGAD00010001636	Over 2.5 million SNP and CNV loci are screened by Illumina Infinium Omni2.5Exome-8 Kit	196
EGAD00010001637	Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array	539
EGAD00010001638	Over 2.5 million SNP and CNV loci are screened by Illumina Infinium Omni2.5Exome-8 Kit	262
EGAD00010001813	Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array	91
EGAD00010001814	Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array	195