EGAGenomicsIllumina HiSeq 2000Otherhttps://ega-archive.org/studies/EGAS00001000673EGAEGA study EGAS00001000673CBF AMLEGArestrictedprimary cancer, Malignant Neoplasm, Malignancy, Neoplasms, familial, Benign Neoplasm, Benign Neoplasms, Cancers, Tumor, Malignant, malignant tumor, genetic, Neoplasias, MT, Benign, malignant neoplasm, Neoplasm, inherited genetic, Malignancies, constitutitional genetic, hereditary, Neoplasia, Cancer, Tumors, Malignant Neoplasms.Myelocytic, v-abl, RAR, Hunter Carpenter Macdonald syndrome, Materials, Chronic Granulocytic Leukemia, Myeloid, acute non lymphoblastic leukemia, Stem cell Leukemia, CDR, MTC1, mental retardation, Myelocytic Leukemia, growth and development, Tumor, MYL, Trim19, chronic myelogenous, C-abl, Reto, neurodegeneration with brain iron accumulation caused by mutation in PLA2G6, mili, INAD, p150, BCR, syndromic 6 (formerly), 1, CG40494, JTK7, Whole Transcriptome, Transcriptome Sequencing, Wilson Turner mental retardation syndrome (formerly), AI325092, X-linked intellectual disability - gynecomastia - obesity, Abl, ABL, D-ret, 1200009E24Rik, epoxyethane, cbfbeta, amlcr1, Dimethylene oxide, CDLS5, DmelCG12072, AI853148, stem cell leukaemia, Cgh, Cancer of the Prostate, abl, Ph1-Positive Myeloid Leukemia, adult chronic leukemia, AV071570, CBF-B, Nucleotide, Tumors, acute myelogenous, RET, stem cell leukemia (disease), with gynecomastia and obesity (formerly), Granulocytic Leukemias, early onset of peripheral gangrene, Exome, D-Abl, familial, MENE (3R)-G, MTG8, Oxyfume, ret, Benign, HSCR1, DmelCG14396, MRXS6, D-abl, evi-1, DmelCG4032, nucleotides, AI561783, Chronic granulocytic leukemia, Complete Transcriptome, 4674, Seitelberger disease, MTP deficiency, Myeloblastic, Ph1-Positive Myelogenous, progressive multifocal, Acute Myeloid Leukemia, Benign Neoplasms, INSDC_feature:gene, Ph1-Positive Myeloid, non-small cell lung adenocarcinoma, Malignant Neoplasms, oxyde d'ethylene, nonsmall cell adenocarcinoma, PEA2, congenital generalised, Material, CML - chronic Myelogenous Leukemia, Whole Exome Sequencing, Warts/Lats, SMHC, Phospholipase A2-associated neurodegeneration, cbf-beta, Wts/Lats, Myelogenous Leukemias, Adenocarcinoma, INAD1, CLL, 2-Epoxyaethan, HD-59, Macias-Flores Garcia-Cruz Rivera syndrome, NBLST3, Lung, multinuclear leukocyte, X-linked, abl1, Nonsmoker, Neoplasms, 5133400C09Rik, number, SM1, PLA2G6 neurodegeneration with brain iron accumulation, WTS, Wts, MEN2, SM2, stem cell leukaemia (disease), l(3)04674, CML, infantile, cAbl, Bassen-Kornzweig syndrome, CG1061, Tcrz, hypertrichosis, DmHD-59, congenital betalipoprotein deficiency syndrome, atypical, wts, Cancer of Prostate, DmelCG40494, Chronic Granulocytic Leukemias, FACT80, CBFB, Leukemia, Complete, Exome Sequencings, Whole Genome, dAbl, RNF71, Granulocytic Leukemia, Complete Genome Sequencing, PHL, Abl1, PP8675, pebp2ab, Sequencing, microsomal triglyceride transfer Protein deficiency, WTS/LATS, Neoplasias, Whole Exome, pebp2-beta, Ph1-Positive Myelogenous Leukemias, Whole, Prostatic, Chronic, constitutitional genetic, stem cell leukemia, Cancer, AblK, ALK, leukemia, ALL, ETO, Anprolene, heredity., Oxacyclopropane, Betalipoprotein deficiency disease, Dabl, Malignant Neoplasm, c-abl, Complete Exome Sequencings, DAlk53, DAbl, Leukemias, chronic, DRet, DRET, Cell, c-Ret, AML, whole transcriptome, Exome Sequencing, MT, chronic myelogenous leukemia, Myeloid Leukemias, Prostatic Cancer, chemical analysis, Neoplasm, Dihydrooxirene, dRET, dRet, CDHF12, aml1-evi-1, Lung Adenocarcinomas, aml, Xcml, primary cancer, underdeveloped, postnatal growth, bcr|abl, Cancers, Understanding, SMMHC, malignant tumor, included, Acute, lung adenocarcinoma, chronic myelogenous leukaemia, warts/lats, PML, chronic myeloid leukaemia, AI893578, T160, polymorphonuclear leucocyte, abetalipoproteinemia neuropathy, hereditary, Neoplasia, CD246, Dret, nr1b1, Chronic Myelocytic Leukemia, Ableson, single-organism developmental process, Chronic Myeloid Leukemia, determination, ZMYND2, postnatal development, apolipoprotein B deficiency, Lats/Warts, Bassen Kornzweig syndrome, Philadelphia-Positive Myeloid Leukemias, acanthocytosis, Readability, Nonsmokers, FAA4, Pebpb2, l(3)100Aa, Ph1 Positive, TRIM19, Chronic Myelocytic Leukemias, BCR1, pea2-beta, FACT, Acute Myeloblastic Leukemia, Complete Exome Sequencing, Whole Transcriptome Sequencing, hypoplasia, Chronic Myelogenous Leukemias, Myelogenous Leukemia, leukoencephalopathy, adult chronic leukaemia, aml1, Granulocytic, genetic, XAML, Prostatic Neoplasm, c-Abl, c-ABL, malignant neoplasm, CG4032, pebp2b, ANLL, Malignancies, dmLATS, ethene oxide, RET51, HTC2, Amprolene, Myelogenous, Anproline, lats, chromosome Xq27.1 Interchromosomal insertion syndrome, neuroaxonal dystrophy, Am ABL, Ph1-Positive Myelogenous Leukemia, Genome Sequencing, Philadelphia-Positive, LATS, Adenocarcinomas, AAT4, congenital generalized, Ph1-Positive, D22S662, DAlk, Ph1-Positive Myeloid Leukemias, adenocarcinoma of the lung, CDHR16, infantile neuroaxonal dystrophy/atypical neuroaxonal dystrophy, Complete Genome, Philadelphia-Positive Myeloid, Oxidoethane, CBFA2T1, Genetic Materials, dALK, Hunter-Carpenter-McDonald syndrome, D-ash, HDACL1, wart, Genetic Material, HD8, Hopes, PTC, bcr/abl, Acute myelogenous leukemia, Nfya, Chronic Granulocytic, Chronic Myelogenous, Chronic Myeloid Leukemias, 2-epoxyethane, hCG, adenocarcinoma of lung, susceptibility to, MEN2A, MEN2B, CG17960, PEBP2b, Lung Adenocarcinoma, Dsrc7, chronic granulocytic leukemia, hypertrichosis congenital generalized X-linked, wts/lats, aml-1, Lats, microarray, Cistron, inherited genetic, Transcriptome Sequencings, PEBP2B, Prostate, bronchogenic lung adenocarcinoma, Dmel_CG00000, Hopefulness, Dlats, Philadelphia Positive, Stem cell leukaemia, Prostate Neoplasms, Complete Exome, RPD3, PLAN, Benign Neoplasm, Gene, chronic granulocytic leukaemia, Malignant, presence, RET-ELE1, CG17617, acute non lymphoblastic leukaemia, reduced, AI661194, CG8250, Prostatic Cancers, rhoGAP1A, Philadelphia-Positive Myeloid Leukemia, acute myeloid, tiny, intellectual disability, Non-Smoker, Prostate Cancers, Runx-1, study, WES, chronic myeloid, Genetic, Malignancy, D22S11, LUAD, CG12072, EG:23E12.5, Cbfa2t1h, EG:23E12.2, Myeloid Leukemia, Myelocytic Leukemias, hypertrichosis congenital generalised X-linked, DmelCG8250, E430008G22Rik, small, WGS, KARAK syndrome, Chronic Myelocytic, Dash, l(3)73Ba, rara2a, Cistrons, CG14396, development, count in organism, Chronic myelogenous leukemia, Wilson-TURNER X-linked mental retardation syndrome, NR1B1, CG40453, WARTS, chromosome Xq27.1 interchromosomal insertion syndrome, Warts, cbfa2, Oxane, acute, Wilson Turner intellectual disability syndrome (formerly), l(3)c-abl, Complete Transcriptome Sequencing, Chronic Myelogenous Leukemia, neuroaxonal dystrophy presenting with neonatal dysmorphic features, Xaml1, cml-A, RARalpha1, Prostate Neoplasm, Ddash/abl, Nr1b1, AML1T1, Wilson-TURNER X-linked intellectual disability syndrome, smMHC, lts, Aethylenoxid, cardinality, DROTKABL3, assay, mKIAA3017, c-ABL1, Pebp2, Ethylene oxide, Prostate Cancer, growth, Chronic Myeloid, RET9falseExploration of CNV’s and SNV’s in cancers with well-known genetic rearrangements: Identification of additional genetic changes in rearrangements-driven cancerSpecific cancers are well known to have specific gene rearrangements. Representative cancer is chronic myeloid leukemia (CML) which is famous for BCR/ABL gene rearrangements. By the way, also genetic rearrangements are not infrequently found in acute leukemia, and those include CBFB/MYH11 rearrangements, PML/RARA rearrangements, AML/ETO rearrangements, and BCR/ABL rearrangements. The situation is same is for lung adenocarcinoma of non-smokers and prostate cancers, and ALK and RET gene rearrangements are recently found. However, not all these rearrangements are sufficient to develop cancer, and it is suggested that some genetic aberrations are required for the development and progression of cancer in addition to these genetic rearrangements. In this study, we have a plan to explore the existence of additional genetic changes including single nucleotide variants (SNV’s) and copy number variations (CNV’s) in cancers with specific genetic rearrangements so as to define additional genetic changes that confer full oncogenic potential to cancer cells. So as to look at SNV’s and small indels, we are going to use whole exome sequencing (WES) data. And as for CNV’s, we are going to use array-CGH data. Also, to check the functionality of these genetic changes, we are going to use whole transcriptome data (WTS). In addition, in samples with whole genome sequencing (WGS ) data, we are going to explore genetic changes in intronic regions also. In fact, we sequenced 10 AML samples which are known to have specific genetic rearrangements. Analysis of these WGS, WES and WTS data are under the way. If we have a chance to access WES, array-CGH and WTS data of other cancer samples with specific genetic rearrangements, we would be able to compare additional genetic changes required for oncogenesis in cancer cells with various genetic rearrangements. We hope this result will enlighten our understanding of cancer genetics further.2017-07-26 15:39:25EGAS000010006739606EGAD00001000724EGAC00001000010