{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Cancer Genomics"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001005250"],"host":["EGA"],"description":["EGA study EGAS00001005250"],"dataset_title":["panALL exome data set3, 650 samples","WGS files for Genomic Landscape ALL paper","panALL exome data set","RNAseq data set of panALL study","panALL exome sequencing, data set2, 700 samples","Additional WGS files for Genomic Landscape ALL paper"],"category":["restricted"],"repository":["EGA"],"name_synonyms":["acute lymphoblastic leukemia (ALL)., acute lymphoblastic leukaemia (ALL)"],"description_synonyms":["acute T cell lymphoblastic leukemia, T-cell leukemia, RAS, Ras, l(1)G0098, Materials, dP60, Vps34, precursor T-cell acute lymphoblastic leukemia/lymphoma, tyrosine-protein kinase receptor FLT3, DPTEN, B acute lymphoblastic leukaemia, BcDNA:LD15217, acute T-cell lymphocytic leukemia, SET2, growth and development, Ras-1, Tumor, VPS34, 11621, scl, Mutations, PI-3 kinase, p110-alpha, ras, c-ras2, HOP, Hop, BHLHA17, T-Lymphocytic Leukemia, CEBP, 4, TEP1, Fs(3)Hor, Precursor T Cell Lymphoblastic Leukemia, adult, T-ALL, T-Lymphocytic Leukemias, TCL5, Cell Division Cycles, C/EBP, Dp60, Tum-1, T-cell leukemia/lymphoma protein 5, Genomes, PI3K_59F, Cebp, NFATc4, PI3-kinase activity, NTef2, amlcr1, D17Mit170, PI3Kgamma, MCAP, C|ebpalpha, C/EBP alpha, sample, 4921524K10Rik, PI3K 68D, Lymphoid, B cell acute lymphocytic leukaemia, CBF-A, AW557856, precursor T-cell acute lymphoblastic leukemia, B-cell acute lymphocytic leukaemia, ATP - 1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, CG1799, Tumors, dVps34, B acute lymphoblastic leukemia, Ras2, RAS2, C230089I12Rik, Acute T-Cell Leukemias, Ras1, RAS1, SCL/tal-1, DBPCEP, acute B cell lymphocytic leukaemia, rea, HRX, p50alpha, KAT3A, Tl3, A630076E03Rik, Tl2, not genetically inherited, CG2699, DmelCG5373, Fs(3)Sz11, RSTS, C530050K14, Benign, Flk-2, PTEN3, PTEN1, Flk2, FLK2, type-1 PI3K, dRas85D, acute T cell leukaemia, Lymphoid Cell, rsts, TAL1, ras1, precursor T-lymphoblastic leukemia, evi-1, ras2, d-jak, BcDNA:RE36103, CG11621, DmHD-160, T Cell Leukemia, Acute T-Lymphocytic Leukemias, WDSTS, Hras-1, Benign Neoplasms, Dm Ras1, INSDC_feature:gene, PTENa, surveillance, mKIAA4050, DmelCG4141, F8A5_4, Malignant Neoplasms, APDS, precursor T-cell acute lymphocytic leukemia, RasI, Material, HD-160, PI3KBETA, Cells, CG2684, AW107667, T Cell, CG1594, Harvey-ras, Hras1, 2310035O07Rik, sumoylation, Hop1, SUMO-Conjugations, GLM2, dRas, Neoplasms, CG1167, H-ras, DRAS1, Period Prevalences, DRas2, IMPDH, LD06825, MLL1A, HBP231, T-Cell Leukemias, Dras2, Dras1, SCL|tal-1, PIK3, T-Cell Acute Lymphocytic Leukemia, D-Ras, dVps34/PI3K59F, Pi3Kp60, Core Genome, PI3K-dp110, AI463227, Kras-2, dPI3K, anon-92Ed, KIAA1732, IMPdH, acute T-cell lymphoblastic leukemia, Ha-ras, 8030499H02Rik, Dras, class I, ras 1, Cycles, RGD1560053, Leukemia, occurrence, HIP-1, raspberry/impd, HIF1, Accessory Genome, prevalence, Cell Division Cycle, cell-division cycle, ALL-1, Ras[V12], Pi3Kp110, DUX4L, EK3-4, pebp2ab, DmelCG5671, DRas, P110BETA, DRas85D/Ras, Neoplasias, Dmras64B, KMT3A, PI3K21B, 6430520K01, L4, Ly72, B430203M17Rik, MCM, TEL|ABL, Cpk, Cancer, C/EBP-alpha, FLT3, cou, Malignant Neoplasm, PTEN, AA414921, FLT-3, class II, T-cell acute lymphoblastic leukemia, type III phosphoinositide 3-kinase activity, T-cell transcription factor NFAT3, T acute lymphoblastic leukemia, dPten, STK-1, D-ras-1, T-cell type acute leukemia, pten, MLL/GAS7, Pangenome, Cell, Leukemias, PI(3)K, CD135, T-Cell Leukemia, cpk, E(faf), DUX10, PI3K-92E/Dp110, DmelCG1167, PIK3C1, dpten, Lr, MT, CWS5, CWS1, S35097, Neoplasm, AI462102, bHLHa17, aml1-evi-1, dPTEN, TEL/ABL, outbreaks, acute T cell lymphocytic leukemia, Lymphoid Cells, Acute T Cell, stem cell tyrosine kinase 1, aml, CEBPA, NF-AT3, C21, NFAT3, RAS85D, AML1-EVI-1, primary cancer, Mmac, Dmras85D, CG5671, l(1)9Eb, tyrosine-protein kinase receptor flk-2, CXXC7, 3110041H08Rik, postnatal growth, huntingtin-interacting protein 1, DmelCG11621, Cancers, CBFA2, C|EBP-alpha, Understanding, Lds, malignant tumor, TAL-1, caPI3K, Pan-genome, Acute, CLOVE, DmVps34, Point, IMD14, Precursor T Cell Lymphoblastic Leukemia Lymphoma, PI3K_68D, PI3K-92D, Tum, Bra, TRX1, fetal liver kinase 2, epidemics, Nfat3, acute lymphoblastic leukaemia (ALL), Dmp110, JAK, Jak, SUMO-Conjugation, stem cell protein, l(1)10Be, Neoplasia, crebbp, HTRX1, Ras1/RAs85D, p231HBP, CG5373, postnatal development., single-organism developmental process, ATVPS34, Period Prevalence, adult stage, c-rasHa, PI3K, E(sev)3C, Dp110, jak, B-cell lymphoblastic leukaemia, CG11485, Precursor T Cell Lymphoblastic Lymphoma, Cxxc7, Readability, Point Prevalence, PHOSPHATIDYLINOSITOL 3-KINASE, Cbfa2, Acute T-Cell Leukemia, DmelCG2699, l(1)L4, F8A5.4, wmfl, Sumoylations, Point Prevalences, Smt3-protein conjugation, pathogenesis, p110alpha, phosphatidylinositol 3-kinase activity, FL cytokine receptor, D-Ras1, class A basic helix-loop-helix protein 17, DmelCG1594, T-cell acute lymphocytic leukemia, Pebp2a2, me75, DmelCG2684, B-cell acute lymphoblastic leukaemia, Ubiquitylation, precursor T-lymphoblastic leukemia (T-cell ALL), RTK, acute B-cell lymphocytic leukemia, Prevalences, T-cell ALL, Pi3K92D, CG4141, l(1)G0436, catalyst activity, RTS, Pi3k, ras85B, ras85D, PI[[3]]K, aml1, T1, B-cell acute lymphoblastic leukemia, XAML, D-ras-2, p55alpha, malignant neoplasm, acute T-cell leukemia, Cell Cycles, Janus kinase activity, Pi3K, PI3k, Malignancies, ubiquitination, Smt3p-protein conjugation, Flt-3, MCMTC, C/ebpalpha, Prevalence, TBLR1, xC/EBP, l(3)s1747, PI3K68D, CBF-alpha-2, NF-ATC4, Ki-ras, P110DELTA, Mll, MLL, PtdIns-3-kinase activity, Aml1, frequency, AML1, vacuolar protein sorting 34, results, Division Cycles, dPIK, 1-phosphatidylinositol 3-kinase activity, EVI-1, PEBP2aB, T-Cell, NF-ATc4, Genetic Materials, Kif9, p21[Ras1], acute T cell leukemia, dRas1, dRAS1, AW539987, Adults, Dras85D, Genetic Material, ras-2, Lymphoblastic Leukemia, B-ALL, T-cell acute lymphocytic leukaemia, TET1-MLL, acute lymphoblastic leukemia (ALL), l(1)G0351, LD02673, p85alpha, Division Cycle, DmelCG1799, c-Ha-ras, D-ras1, l(1)G0238, MMAC1, D-ras2, All1, Exomes, C-ras1, common, C/EBPalpha, precursor T-cell acute lymphocytic leukemia/lymphoma, AW123102, Dras64B, Acute T-Lymphocytic Leukemia, PI3K 68_D, Ira1, IRA1, morbidity, C-ras2, early, l(3)06677, l(1)G0002, HYPB, l(1)G0482, p110D, Patient, c-H-ras, Horka, l(1)G0127, aml-1, msvl, Fs(3)Horka, Cistron, p120-PI3K, acute B cell lymphocytic leukemia, BZS, droPIK57, kat3a, RasV12, Lymphocytic Leukemia, DUX4, PI3K92E, Kras2, Benign Neoplasm, tal-1, Gene, Pi3K_59F, MLL|GAS7, DmelCG9375, type I phosphatidylinositol kinase activity, Malignant, B-cell lymphoblastic leukemia, HSPC069, phosphatidylinositol 3-kinase, l(1)G0388, DC42, precursor T-lymphoblastic lymphoma/leukemia, MHAM, B-cell type acute leukaemia, p60, Cycle, T Acute Lymphoblastic Leukemia, PHOSPATIDYLINOSITOL 3-KINASE, Low, DmF2, Precursor T-Cell Lymphoblastic Leukemia, l(1)G0380, Dp110/PI3K, PI3K-68D/E, lod, p21B, Runx-1, Lymphocytic, STK1, dras1, Dm-ras-64B, B230315G04, lymphoblastic leukaemia, Genetic, AMLCR1, Malignancy, Precursor T-Cell Lymphoblastic Lymphoma, FLK-2, tyrosine-protein kinase FLT3, Cell Division, PI3'K, causes, l(1)G0391, l(1)hop, B-cell acute lymphocytic leukemia, Mll1, MLL1, Ras 85D, AW546455, PI3K-68D, lymphoblastic leukemia, Acute T-Lymphocytic, Pebpa2b, Clients, T-cell lymphoblastic leukemia/lymphoma, causality, ras-l, Acute T-Cell, Lymphocyte, incidence, l(1)G0056, dP110, B cell acute lymphocytic leukemia, 6330412C24Rik, CG9375, p120, B-cell type acute leukemia, p110, K-ras, Vps34p, Cistrons, Client, development, fs(3)05703, ATP:1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, Period, vps34, EP(X)1093, dp110, rare (European definition), AI929937, PI3CG, cbfa2, PI-3-K, acute B-cell lymphocytic leukaemia, PI3K-59F, 10q23del, PI3K-Dp110, Xaml1, tcl5, CBP, HIF-1, Lymphoblastic, class III, A130070J02Rik, Fms-like tyrosine kinase 3, p110gamma, Su(tor)3-2, sample population, endemics, T Lymphocytic Leukemia, SUMO Conjugation, DEC, Dm JAK, cbp, l(1)G18, Precursor T Lymphoblastic Leukemia, BC031601, TEL, Tel, growth, Scl, SCL"],"additional_accession":[]},"is_claimable":false,"name":"The genomic landscape of pediatric acute lymphoblastic leukemia","description":"Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer and arises from B- or T-lineage lymphocyte precursors. ALL comprises dozens of subtypes, and genomic analyses have largely been performed within these subtypes. Here we analyze pediatric ALL genomes across all subtypes, including 768 whole genomes, 1,729 exomes, and 1,889 transcriptomes in 2,754 patients. Most ALL subtypes harbor 4 or more driver alterations per sample, similar to adult cancers, despite low mutation burdens. Hyperdiploid B-ALL copy gains are likely acquired early and synchronously, with copy gains occurring before ultraviolet-induced mutations. By contrast, ultraviolet-induced mutations precede copy gains in iAMP21 B-ALL. Overall, we identified 378 putative ALL driver genes. Most driver alterations vary in prevalence across ALL subtypes, with B-ALL enriched for Ras and B-lineage-related alterations, and T-ALL enriched for PI3K, JAK, and cell cycle alterations. Most B-ALL (54.3%) and T-ALL (51.2%) samples bear at least one rare driver gene alteration (present in less than 2% of samples), including 30 putative novel cancer driver genes associated with ubiquitination, SUMOylation, non-coding, and other functions. Known or novel alterations associated with poor outcomes in specific subtypes include TBL1XR1 alterations in ETV6-RUNX1 patients, CREBBP in Ph-like-CRLF2, SETD2 in hyperdiploid, and PTEN in TAL1 patients. Intriguingly, DUX4 and KMT2A subtypes separate into CEBPA/FLT3- or NFATC4-expressing subgroups with potential clinical implications. Together, these results deepen understanding of ALL etiology and outcomes, and facilitate ALL model development.","dates":{"updated":"2023-04-12 14:15:16"},"accession":"EGAS00001005250","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001008193","EGAD00001008268","EGAD00001008290","EGAD00001010270","EGAD00001008600","EGAD00001008134","EGAC00001000044"]}}