{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001003274"],"host":["EGA"],"description":["EGA study EGAS00001003274"],"dataset_title":["RNA sequencing of tumor samples from patients with BPLL"],"repository":["EGA"],"category":["restricted"],"name_synonyms":["CG10798, B-Cell Prolymphocytic Leukemias, dm/myc, dmyc1, AU016757, l(1)G0139, p53, familial, B-Cell, myc-B, DmelCG10798, MYC, Myc, RNA-seq., congenital defects, LFS1, Leukemias, dMyc, dMYC, Tp53, aplasia, deformities, B430311C09Rik, Xp53, anon-WO03040301.171, c-MYC, c-Myc, B-Cell Prolymphocytic Leukemia, MYCC, Dm, B-Cell Prolymphocytic, EG:BACN5I9.1, agenesis, bbl, NOP, c-myc II, ARC, Whole Transcriptome Shotgun Sequencing, Nop30, bfy, bHLHe57, myc, defects, mMyc, l(1)G0354, atresia, c-myc, Leukemia, BCC7, dm/dMyc, l(1)G0359, BPLL, malformations, hypoplasia, Dmyc, DMYc, d-myc, D-Myc, Myc2, genetic, BHLHE39, Niard, Prolymphocytic Leukemia, Trp53, Nird, RNCMYC, myc2, B Cell Prolymphocytic Leukemia, birth defects, anomalies, Prolymphocytic Leukemias, P53, p44, bhy, inherited genetic, TRP53, dMyc1, constitutitional genetic, bHLHe39, MRTL, hereditary, dmyc"],"description_synonyms":["8430401K06Rik, Complete Trisomy 18 Syndrome, 145kDa, Materials, stromal cell-derived factor-1 receptor activity, acetylglucosaminyltransferase-like protein, dMyD88, Chromosomal Triplications, Myd88F, MYC, Myc, SET2, Progress Reports, congenital defects, deletion 8p, aplasia, Chromatin Assembly, B430311C09Rik, Mutations, Relative, 8p deletion, EG:BACN5I9.1, Summary Report, LAP-3, bbl, dMyd88, symptoms, Whole Transcriptome, Transcriptome Sequencing, myc, Analysis, myd, lestr, ATP-dependent chromatin remodeling, D930024N20Rik, SDF-1 receptor activity, like-acetylglucosaminyltransferase, partial monosomy of chromosome 8p, Progress Report, BCC7, Analyses, Molecular, dm/dMyc, Mbp-1, Edwards Syndrome, set, high frequency, Field Reports, BPLL., npyr, 4921524K10Rik, s, AI851092, NPYR, screening, MAA2, B-Cell Prolymphocytic Leukemias, dmyc1, MyD88, Exome, AI450190, npyy3r, ANOP2, RNA metabolism, Sap155, Trisomy 18, Dm, B-Cell Prolymphocytic, mKIAA0609, Relative Risks, bfy, Technics, 155kDa, mMyc, cxcr4, activation, fg, Complete Transcriptome, partial deletion of chromosome 8p, Molecular Cytogenetic Technic, Cytogenetic Technic, Field, signs, INSDC_feature:gene, D-Myc, LD20892, 2610102K23Rik, DmelCG2078, MDC1D, Rare, Report, enr, B Cell Prolymphocytic Leukemia, Material, bK211L9.1, Whole Exome Sequencing, bhy, dMyc1, Orphan Diseases, Trisomy E Syndrome, SF3b1, TA-8, CG10798, Trisomy, dm/myc, Molecular Cytogenetic, hFat1, LFS1, LARGE1, dMyc, dMYC, BcorR, HBP231, 8p monosomy, CD184, CDHF7, chromosome 8p deletion, chromosome 18 trisomy, Nop30, npyrl, bHLHe57, KIAA1732, defects, Chromatin Disassembly, Cytogenetic Technique, Technique, XMyD88, CXCR-4-A, Orphan Disease, CXCR-4-B, Trisomies, Leukemia, Complete, Exome Sequencings, HIP-1, MCOPS2, MDDGB6, HIF1, CD38H, absent from organism, Dmyc, DMYc, Expressions, monosomy 8p, Sequencing, Whole Exome, KMT3A, clustered, Nird, RNCMYC, Whole, T10, Expression, Investigative Reports, bHLHe39, 2810040A01Rik, dmyc, MYD88, lcr1, findings, Complete Exome Sequencings, grupo, partial monosomy 8p, DmMyd88, npy3r, ME5, Leukemias, MDS, PRP10, CXCL12 receptor activity, Exome Sequencing, Trisomy 18 Syndromes, agenesis, Research Reports, Prp10, Hsh155, CHD-2, LESTR, Relative Risk, AA409119, Cyclic ADP-ribose hydrolase 1, Chromatin, Cytogenetic, lap3, ensemble, Chromatin Modeling, EP(2)2535, HSY3RR, huntingtin-interacting protein 1, BCoR, ATP-dependent chromatin remodelling, Orphan, Cmkar4, like-glycosyltransferase, xcxcr4, Reports, LCR1, Sdf1r, biopsy, SF3b145, p231HBP, Partial Trisomies, I-19, Cus1, Mbp1, myc-B, DmelCG10798, Cytogenetic Analyses, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase, Principal Component Analyses, Technic, Tp53, Molecular Cytogenetic Technics, hsy3rr, Cytogenetic Technics, Techniques, c-MYC, c-Myc, SAP145, 2610311M13Rik, ARC, mKIAA1575, SF3B145, BTF, Btf, cytopathology, Summary Reports, SF3b155, LAP3, cADPr hydrolase 1, Molecular Cytogenetic Techniques, SF3b150, 18 trisomy, Targ4, c-myc, MYD88D, 2810013C04Rik, Gene Expressions, Complete Exome Sequencing, Whole Transcriptome Sequencing, BPLL, Chromatin Remodeling, hypoplasia, EEOC, CG2078, Progress, 2810454G14Rik, Pathologies, DmMyD88, TL, Cd38-rs1, Partial Trisomy, partial deletion of the short arm of chromosome type 8, 5730534O06Rik, NIM-R5 antigen, RGD1562735, AU016757, gyltl1b-b, Chromosomal Triplication, Partial, CD38, deformities, results, Investigative Report, MDDGA6, NOP, Genetic Materials, Kif9, PB-CKR, median, 2700025J07Rik, KIAA0609, PRPF10, acetylglucosaminyltransferase-like 1A, Genetic Material, mKIAA0164, atresia, l(1)G0354, absence, gyltl1b, histopathology, CXCR4, Risk, CXCR7, Remodeling, l(1)G0359, mdc1d, malformations, SAP155, trisomy E (formerly), Cytogenetic Techniques, d-myc, LARGE_HUMAN, DMMYD88, Myc2, HYPB, 2810441F20Rik, Niard, trisomy 16-18 (formerly), chromosomal triplication, Principal Component, HM89, 2'-phospho-ADP-ribosyl cyclase|2'-phospho-cyclic-ADP-ribose transferase, myc2, Patient, anomalies, P53, p44, Cistron, hm89, FAT, MRTL, Transcriptome Sequencings, myd88d, Gruppe, myd88, ADPRC 1, xCXCR4, 5630401D06Rik, Complete Exome, l(1)G0139, Disassembly, p53, Chromatin Disassemblies, B-Cell, Gene, HSPC069, froggy, Gyltl1a, NPYRL, anon-WO03040301.171, 5830466J11Rik, B-Cell Prolymphocytic Leukemia, Investigative, MYCC, 2'-phospho-cyclic-ADP-ribose transferase, c-myc II, D2S201E, BC029703, WES, Genetic, cd184, CXC-R4-B, CXC-R4-A, Mosaic Trisomy 18 Syndrome, LARGE, clumped, BHLHE39, BPFD#36, Trp53, Karyotypes, grupos, Clients, Prolymphocytic Leukemias, 3.2.2.6, TRP53, 2'-phospho-ADP-ribosyl cyclase, 2.4.99.20, Disease, AW556225, 2810001M05Rik, Cistrons, Client, WHIM, Xp53, group, cyclic ADP-ribose hydrolase 1, Molecular Cytogenetic Technique, Kra, CDHR8, Rare Disease, Complete Transcriptome Sequencing, frequent, distinct, NPYY3R, B230398H18Rik, Risks, HIF-1, Rest, fb22, kra, PBSF/SDF-1, FB22, Prolymphocytic Leukemia, NPY3R, DEL, birth defects, BC031601, Summary, groupe, partial monosomy of the short arm of chromosome 8, ADP-ribosyl cyclase 1, Field Report, glycosyltransferase-like protein LARGE1"],"additional_accession":[]},"is_claimable":false,"name":"Genetic characterization of B-cell prolymphocytic leukemia: a hierarchical prognostic model involving MYC and TP53 abnormalities - RNA-seq","description":"B-cell prolymphocytic leukemia (B-PLL) is a rare disease, whose molecular pathology is largely unknown. We report here the cytogenetic and molecular findings in a large series of 34 B-PLL. Karyotype (K) was complex (≥3 abnormalities) in 73%, and highly complex (HCK≥5) in 45%. The most frequent chromosomal aberrations were: translocation targeting the MYC gene [t(MYC)] (62%), 17p deletion including TP53 gene (38%), trisomy 18/18q (30%), 13q14 deletion (29%), trisomy 3 (24%), trisomy 12 (24%) and 8p deletion (23%). Whole-Exome Sequencing performed in 16 patients revealed recurrent mutations in TP53 (6/16, 38%), MYD88 (n=4), BCOR (n=4), MYC (n=3), SF3B1 (n=3), FAT1 (n=3), SETD2 (n=2), CHD2 (n=2), CXCR4 (n=2) and BCLAF1 (n=2). The main group of patients (21/34, 62%) had a t(MYC) associated with a higher percentage of prolymphocytes (p=0.03), CD38 expression (p<0.001), lower K complexity (p=0.0004), mutations in MYC and in genes involved in RNA metabolism and chromatin remodeling. Principal component analysis of gene expression data showed that patients with t(MYC) clustered together. A second group with MYC gain (5/34, 15%), was associated with HCK≥5 (p=0,01) and trisomy 3 (p=0,008). Altogether, 26/34 patients (76%) had a MYC activation, translocation or gain, that were mutually exclusive. We identified 3 distinct cytogenetic prognostic groups (p=0.0006): lower risk: absence of MYC activation (median not reached); intermediate risk: MYC activation without del17p (125 months); high risk: MYC activation + del17p (11 months). Our results show that cytogenetic analysis is a useful diagnostic tool in B-PLL that improves prognostic stratification.","dates":{"updated":"2020-07-16 15:33:08"},"accession":"EGAS00001003274","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001004412","EGAC00001000010"]}}