EGAGenomicsN/Ahttps://ega-archive.org/datasets/EGAD000010006665EGA dataset EGAD00001000666EGAMutation is a fundamental process in tumorigenesis. However, the degree to which the rate of somatic mutation varies across the human genome and the mechanistic basis underlying this variation remain to be fully elucidated. Here, we performed a cross-cancer comparison of 402 whole genomes comprising a diverse set of childhood and adult tumors, including both solid and hematopoietic malignancies. Surprisingly, we found that the inactive X chromosome of many female cancer genomes accumulates on average twice and up to four times as many somatic mutations per megabase, as compared to the individual autosomes. Whole-genome sequencing of clonally expanded hematopoietic stem/progenitor cells (HSPCs) from healthy individuals and a premalignant myelodysplastic syndrome (MDS) sample revealed no X chromosome hypermutation. Our data suggest that hypermutation of the inactive X chromosome is an early and frequent feature of tumorigenesis resulting from DNA replication stress in aberrantly proliferating cells.Hypermutation of the inactive X chromosome is a frequent event in cancer.Jäger Natalie N, Schlesner Matthias M, Jones David T W DT, Raffel Simon S, Mallm Jan-Philipp JP, Junge Kristin M KM, Weichenhan Dieter D, Bauer Tobias T, Ishaque Naveed N, Kool Marcel M, Northcott Paul A PA, Korshunov Andrey A, Drews Ruben M RM, Koster Jan J, Versteeg Rogier R, Richter Julia J, Hummel Michael M, Mack Stephen C SC, Taylor Michael D MD, Witt Hendrik H, Swartman Benedict B, Schulte-Bockholt Dietrich D, Sultan Marc M, Yaspo Marie-Laure ML, Lehrach Hans H, Hutter Barbara B, Brors Benedikt B, Wolf Stephan S, Plass Christoph C, Siebert Reiner R, Trumpp Andreas A, Rippe Karsten K, Lehmann Irina I, Lichter Peter P, Pfister Stefan M SM, Eils Roland Rphapii, SET, IPP2A2, HLA-DR-associated protein II, i2pp2a., ensemble, DI-2, TAF-I, I-2Dm, ipp2a2, igaad, StF-IT-1, 2pp2a, CG4299, CG10574, PHAPII, group, DmelCG4299, I-2PP1, 5730420M11Rik, IGAAD, set, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, 2PP2A, DmelCG10574, taf-ibeta, I-2PP2A, Dm I-2, I2PP2A, dSET, dSet, TAF-Ibeta, AA407739primary cancer, frequent, Malignant Neoplasm, Malignancy, Neoplasms, Benign Neoplasm, Benign Neoplasms, X Chromosomes, Cancers, X, Tumor, Malignant, malignant tumor, Chromosomes, Neoplasias, high frequency, MT, Benign, Chromosome, malignant neoplasm, Neoplasm, Malignancies, Neoplasia, Cancer, Tumors, Malignant Neoplasms.hematopoietic precursor cell, Granulocyte, Ass-1, Hepatocyte-Stimulating Factor, Colony-stimulating factor 2, cell surface glycoprotein MAC-1 subunit alpha, Visible Light, CG17348, dmTAF[[II]]230, B Cell Stimulatory Factor 2, Cultural, B1, Ly-4, Interferon beta-2, SCO5, B4, Hybridoma growth factor, 3, SCO1, B8, CG1451, mst075, cel, N'-bis(aminoiminomethyl)-, L, FLT, Tissue, Granulocyte Colony Stimulating Factor, RP-A, nucleic acid library preparation, Kitl, CG9148, W, Granulocyte Colony-Stimulating, D17Mit170, Mast cell growth factor, B Cell Differentiation Factor 2, interleukin-6 receptor ligand, g, autoimmune disease of retina, scientific observation, l, Red, Colony-Stimulating Factor, Bs, Hematopoietin 2, cfu, interleukin-3 receptor ligand, AA589576, Eosinophil differentiation factor, NCAM, dTAF[[II]]230, CG10758, BFL, UNQ391/PRO726, BCGF-II, Light, HSC, Tl3, HSF, Tl2, female, Expanded, APC2, BSF2, APC1, Propidium Diiodide, LIGHT, E-APC dAPC2, Cultures, 1270, Emrk2, apc1, B-cell differentiation factor I, Propidium, apc2, Phenanthridinium, Donors, Estreptomicina Normon, Methyl Cellulose, Membrane-spanning 4-domains subfamily A member 1, Histamine Producing Cell Stimulating Factor, pbt, Methocel, B Cell Growth Factor II, Cultural Beliefs, Granulocyte-Macrophage, Stem cell factor, Iodide, expanded, Ex, CD11b/CD18, Dm APC2, Dm APC1, stem cell factor, MSK39, Taf250, GS, differentiation antigen CD19, Cells, ds DNA, leukocyte adhesion receptor MO1, Pluripoietin, DNA, Organ Donors, Gb, Celevac, Burst-Promoting Factor, D-Axin, Clo, Cellulose, DNS, e-apc, FRT, (Deoxyribonucleotide)n, AA960661, SLF, B-cell hybridoma growth factor, number, Tpo2, Tpo1, B-Cell Growth Factor-II, DP3, DP2, litre, hematopoietic progenitor cell, Deoxyribonucleic Acid, Metilcelulosa, B-lymphocyte antigen CD20, Growth Factor, P Cell Stimulating Factor, CTL differentiation factor, MAL, dTAF[[II]]250, cell, Cellulose methyl, Complete Genome Sequencing, homopolymer, Tpo, Double Stranded, Cultural Relativisms, pk18, Hsc73, MBR, Hsc70, Sequencing, Hsc71, dTAF250, Con, Tpo4, Rpa-70, Tpo3, Csfg, PTBR, T10, (Deoxyribonucleotide)m, anon-EST:Posey14, DRL, LN, measuring, ITGAM, proto-oncogene c-Kit, cou, female human body, FLT-1, DNAn+1, Progenitor Cells, Neutrophil adherence receptor, CG4114, i164, Factor, Cultural Backgrounds, CD258, ML, dTAF230, Lr, Cytokine, T-cell differentiation antigen L3T4, IFN-beta-2, chemical analysis, BPA, ami, Cell-Stimulating Factor, XKrk1, Ml, AU020952, Taf[[II]]250, Rpa, Yellow Marrow, library construction, medullary bone, HVEM-L, Myeloid Growth, Mast-Cell, Multipotential Colony Stimulating Factor, DAxin, l(2)01270, Reticuloendothelial System, rpa, Cellulone, B Cell Differentiation Factor, Photoradiations, C-Kit, MGF, DmelCG7926, B-Cell Stimulatory Factor 2, Desoxyribonukleinsaeure, Methylcellulose, Relativism, DNA Replication Factor A, Cd11b, Differentiation-Inducing Protein, Replication Factor A Single-Stranded DNA-Binding Protein, B-Cell Stimulatory Factor-2, D-APC1, D-APC2, T-cell surface antigen T4/Leu-3, Il-5, Il-3, Il-6, apc, Csfmu, contrasted, PPP1R46, tissue culture, MPLLG, d-axin, IL-5, IL-3, medulla ossea, AA408052, IL-6, GSK3beta, LEU-16, Mpllg, Vascular permeability factor receptor, prevention and control, cADPr hydrolase 1, multicellular organismal biosynthetic process, CD20, methylcellulose, S7, single-organism biosynthetic process, Mast-Cell Colony-Stimulating Factor, Propidium Iodide, SF, mAPC, CD19, IBP, CD14, SO, T1, Red Marrow, Cd20, TNFSF14, Hsp73, dmrpa1, Eosinophil Mast Cell Growth Factor, Soluble KIT ligand, Bladder pain syndrome, Cd38-rs1, Sl, So, CR-3 alpha chain, Ssb-70, NIM-R5 antigen, lin, lio, B Cell Stimulatory Factor-2, Cytotoxic T-lymphocyte inducer, Tr-kit, beta-2, Double-Stranded, CD38, TAFII-250, Blood Serum, TAF250/230, CD34, (Deoxyribonucleotide)n+m, 5031405K23Rik, TAFII250, Complete Genome, Stem Cell, T-Cell, KIT, dAPC2, dAPC1, tyrosine-protein kinase Kit, BEST:CK02682, absence of, SHEP7, Painful Bladder Syndrome, mast cell growth factor, T-cell surface glycoprotein CD4, RF-A, p32, Stem, 0442/30, MGI-IG, Colony Forming Units, AW124434, Colony-stimulating factor, Csfgm, CG17603, TAF[[II]], Plasmacytoma, CD56, Kitlg, Semen, KL-1, 2'-phospho-ADP-ribosyl cyclase|2'-phospho-cyclic-ADP-ribose transferase, RPA1, Multipotential, enlarged, NCAM-1, Differentiation antigen CD19, l(2)ey, SLEB6, anaphase promoting complex, Ovum, Cd56, CVID3, Bladder Pain Syndrome, CVID5, NCAM-C, ADPRC 1, KIT binding, experimental, Progenitor Cell, SCF receptor activity, B-Cell, hematopoietic progenitor cell antigen CD34, RPA 70 kDa, dTAFII250, axn, B-Cell Differentiation Factor, MKCSF, Monocyte differentiation antigen CD14, Deoxyribonucleic acids, gDNA, lymphocyte antigen 44, Leukocyte adhesion receptor MO1, Histamine-Producing Cell-Stimulating Factor, Homo sapiens, dmTAF1, Marrow, 2'-phospho-cyclic-ADP-ribose transferase, Strepto Hefa, Low, Tyrosine-protein kinase FRT, D-APC, Progenitor, CSF-GM, dAPC, TAF250, Fdc, methods, MAC-1, D-Streptamine, experimental section, Bp35, B-cell surface antigen CD20, Lenograstim, Estreptomicina CEPA, CD11 antigen-like family member B, 10^[-6], Cellulose methylate, great, dRP-A, IL6, IL5, RPA70, TAF, DmelCG6193, HHT1, Controlled, 2'-phospho-ADP-ribosyl cyclase, 2.4.99.20, Controlling, TAF[[II]]250, EDF, MGI-2, DmRPA, E-APC, Gm-csf, l(3)84Ab, dAXIN, T-cell replacing factor, count in organism, SCFR binding, hemopoietic progenitor cell, Sargramostim, p230, AW557552, membrane-bound form, ds-DNA, MGDF, MS4A2, MS4A1, Radiations, IFN-beta 2, MAC1A, c-KIT, with urinary tract Abnormality and cryptorchidism, TAF[[II]]230, CC1, 70kDa, Colony Stimulating Factor, Fms-like tyrosine kinase 1, sample population, retina autoimmune disease, cytotoxic T-lymphocyte inducer, DmelCG17603, Ms4a2, progenitor cell, CD4, Eosinophil Differentiation Factor, Eosinophil-Mast Cell Growth-Factor, CD8, Serums, TAF1, Myeloid Differentiation-Inducing Protein, CDF, lobular intraepithelial neoplasia, Myeloid, hemopoietic stem cell, GCSF, Histamine-Producing, prevention, B Cell, KL receptor activity, fold, monocyte differentiation antigen CD14, Gsfsow3, O-2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl-(1-2)-O-5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl-(1-4)-N, average, ethnicity, DmelCG9633, thymus nucleic acid, Erythrocyte Burst Promoting Factor, TFIID TAF250, Cellothyl, P-Cell Stimulating Factor, Multipotential colony-stimulating factor, Dacryolarmes, myeloid cell-specific leucine-rich glycoprotein, C17orf33, AI047805, Strepto-Hefa, blutbildende Stammzelle, sample, Tissue Donor, stem cell factor receptor ligand, Granulocyte Macrophage, preventive therapy, Transplant Donor, Radiation, din, Hematopoietic growth factor, BZRP, Transplant, TAF200, Semen Donors, MGI-IGM, Penicillin, antibodies, d-APC, PBS, PBR, Apc1, PBT, Cultural Background, rp-a, hssb, G-CSF, apc 1, Streptomycine Panpharma, Differentiation Factor-2, CK20, desoxyribose nucleic acid, END, MAC1, VEGFR1, HVEML, T-cell surface antigen Leu-12, alpha-D-Glucopyranoside, MCGF, CD4mut, cellulose methyl ether, human, Semen Donor, experimental procedures, Atmospheres, Ncam, Painful bladder syndrome, T Cell Replacing Factor, TAF230, krk1, BPBS, big, MULTI-CSF, Slf, GM-CSF, Strepto Fatol, abdominal muscles, Human, Ly113, DmelCG17348, large, DmelCG4114, AIR, urinary form, Yellow, Man, Backgrounds, Complete, Whole Genome, Differentiation Factor, CD38H, Hybridoma Growth Factor, DRP-A, TPO, nucleic acid library construction, Deoxyribonucleic acid, Multipotential Colony-Stimulating Factor, CG7926, Transplant Donors, dAPC2/E-APC, Diiodide, Whole, blz, Customs, lobular neoplasia, Antibiotics, E-NCAM, TR2, Ovum Donor, Leukocyte surface antigen Leu-16, Streptomycin Grünenthal, Drl, Organ, rpa70, whole blood, TRF, CD11b, Leu2, BG:DS00004.13, Cell, AW495831, Mdu, Colony-Stimulating Factor 2 Alpha, CR3, medulla ossium, eosinophil differentiation factor, mda, B-lymphocyte surface antigen B1, KIT ligand receptor activity, B-lymphocyte surface antigen B4, TAF[[II]]250/230, BSF-2, Donor, eagle-Barrett syndrome, d-APC2, Cyclic ADP-ribose hydrolase 1, RPA, Peripheral Blood, P-cell-stimulating factor, med, prophylaxis, interleukin-5 receptor ligand, N-CAM, Interleukin HP-1, HSC cell, CSF, Tyrosine-protein kinase receptor FLT, CD117, mDRC, TC-GM-CSF, F730045J24Rik, N-CAM-1, control, Tumor-Cell Human GM Colony-Stimulating Factor, Ssm, Mgf, CD11B, Single Strand Binding Protein RP A, Bra, xkl-1, Relativisms, APC, Citrucel, VEGFR-1, Single-Strand Binding Protein RP-A, Cultural Relativism, colony forming unit spleen, determination, Daxin, I-19, Blood, Cologel, CK-20, Xkl-1, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase, Serum, methylated cellulose, brl, Hspa10, CG11121, B-cell stimulatory factor 2, lio/drl, L3T4, RPA 70, Background, Replacing Factor, old, Gsfsco1, Streptomycin Sulfate, methyl ether, replication protein A, CSF-2, Mother Cells, Min, Gsfsco5, SOW3, Penicillin Antibiotics, me75, Man (Taxonomy), reference sample, CFU-S, RNAse protection assay, free, Tumor Cell Human GM Colony Stimulating Factor, preventive measures, ASS, cyclosome, LIN, Double-Stranded DNA, Granulocyte Macrophage Colony Stimulating Factor, deoxyribonucleic acids, DNAn, T-Cell-Replacing Factor, 8-diamino-5-(3-(diethylmethylammonio)propyl)-6-phenyl-, DmelCG1451, dApc2, l(3)S044230, T-cell surface antigen T4|Leu-3, KRT21, DP2.5, Modern, Genome Sequencing, beta-D-fructofuranosyl, sKITLG, PSF, Interferon beta 2, xapc, Colony-Forming Unit, THCYT1, Streptomycin Sulphate, 2410008N15Rik, kl1-A, Erythrocyte Burst-Promoting Factor, Mother Cell, Visible Radiations, AU040960, Differentiation Factor 2, Visible Radiation, Ly-44, medulla of bone, Filgrastim, kit, Hematopoietin-2, DmelCG9148, IFNB2, SR3-5, Lymphocyte antigen 44, Plasmacytoma Growth Factor, PBMCs, Eosinophil, Erythrocyte, Myeloid Growth Factor, CG9633, Ly-40, Interferon, Ovum Donors, Bone, CR3A, CIB8, Methylcellulosum, d230, human being, D-SSB, RpA70, Colony-Forming Units, FPH2, Methyl, EfW1, presence, HGF, scfr, DmelCG11121, Strepto-Fatol, Taf230, Gmcsf, PBMC, Hepatocyte Stimulating Factor, DAPC, CG6193, DCB-45, BTPS2, SCFR, repa1, HCGF, GMCSF, rf-a, dApc, Taf200, somda, Mac-1a, neutrophil adherence receptor, Interleukin 6, Interleukin 5, Mother, Taf1p, Interleukin 3, Visible, Molgramostin, 2.7.10.1, Replication Factor A Single Stranded DNA Binding Protein, PBMCs., 3.2.2.6, MO1A, culture, Mac-1, B-cell differentiation antigen Ly-44, dAxin, leukocyte surface antigen Leu-16, Mast Cell, Colony Forming Unit, D-RPA70, Edg, DBI, Gm-CSf, Myeloid Differentiation Inducing Protein, Mgdf, cyclic ADP-ribose hydrolase 1, NCAMC, Burst Promoting Factor, PKBS, E461, Myeloid cell-specific leucine-rich glycoprotein, axin, TFIID, B-Cell Differentiation Factor-2, K20, B-cell growth factor II, Organ Donor, Streptomycin Sulfate (2:3) Salt, T-Cell Replacing Factor, Photoradiation, TAF[II]250, NCAM1, Replication Factor A, LTg, c-kit, Hybridoma, Estreptomicina Clariana, Cell surface glycoprotein MAC-1 subunit alpha, Modern Man, c-Kit ligand, Muciplasma, assay, SCF, ORW1, Females, ADP-ribosyl cyclase 1, CK02682Mds1-Evi1, IPP2A2, degree (angle), Dmel_CG31829, adult stage, X Chromosomes, Jbo, Tumor, dCul3, brl, Mutations, 5730420M11Rik, Mds1, Scanning Transmission Electron Microscopy, Autonomous Replication, primary stem, Fs(3)Hor, SF3b155, adult, average, DMcul-3, SET, DmelCG2684, Dysmyelopoietic Syndrome, Genomes, TAF-I, X, LIS1, NTef2, Autonomous, PAFAHA, LIS2, DmelCG4299, MDCR, IGAAD, set, high frequency, Human Genomes, DmelCG10574, malignant neoplasm, sample, lis2, Malignancies, mdcr, myelodysplastic syndrome, Tumors, phapii, l(2)06430, pafah1b1-b, anatomical protrusion, StF-IT-1, CUL-3, female, Expanded, gft/dCul-3, br34, Fs(3)Sz11, Electron Microscopy, Hematopoetic Myelodysplasia, Benign, 1270, Adults, PRPF10, l35Cd, HLA-DR-associated protein II, DmelCG42616, cul-3, DI-2, I-2Dm, susceptibility to, Cullin3, expanded, Ex, Benign Neoplasms, SAP155, CG4299, whole genome, Myelodysplastic, CG11861, platelet-activating factor acetylhydrolase IB subunit alpha, early, Malignant Neoplasms, I-2PP1, TAF-IBETA, Replications, Syndromes, Znfpr1b1, Chromosome, enlarged, primary axis, 14-3-3E, spine, Myelodysplasias, Horka, STEM, CG2684, l(2)ey, Fs(3)Horka, Autonomous Replications, TAF-Ibeta, DNA, i2pp2a, big, HEL2, Myelodysplasia, Neoplasms, BOPS, Benign Neoplasm, stalk, cul3, Malignant, Cullin 3, Chromosomes, PHAPII, l(2)br34, protrusion, Human, large, DmelCG4114, pafah, Core Genome, Dysmyelopoietic Syndromes, CG31829, Cell., DmF2, DNA Replications, lod, CUL3, Hematopoetic Myelodysplasias, Malignancy, guftagu, Accessory Genome, ipp2a2, 2pp2a, Evi1, D630039M04Rik, CG10574, culm, Evi-1, Myelodysplastic Syndromes, Neoplasias, 2PP2A, taf-ibeta, great, Syndrome, dSET, dSet, gft, Cul3, Cancer, Myelodysplastic Syndrome, Malignant Neoplasm, female human body, axis, igaad, CG4114, KIAA1546, Scanning Transmission, Pangenome, Cell, MDS, Mds, Hematopoetic, group, PRP10, MT, Human Genome, I-2PP2A, Dm I-2, KCIP-1, I2PP2A, Neoplasm, Hsh155, Replication, mds, primary cancer, frequent, ensemble, BG:DS07851.2, arc degree, Cancers, dCul-3, PAFAH, Lds, malignant tumor, sample population, l(2)01270, dSET/TAF-Ibeta, CG42616, 2610030F17Rik, Pan-genome, Dmel_CG11861, l(2)35Cd, Prdm3, AA407739, Neoplasia, Females, DysmyelopoieticfalseWGSeq_HealthyHuman_DATA_SET_xmas_MB_2013_07_10 - samplesHSC73_clone: Bone marrow mononuclear cells from the healthy 73 years old female were thawed and labeled with Alexa-Fluor 488-conjugated anti-CD34 (581, Biolegend), Alexa-Fluor 700-conjugated anti-CD38 (HIT2, eBioscience), a cocktail of APC-conjugated lineage antibodies consisting of anti-CD4 (RPA-T4), anti-CD8 (RPA-T8), anti-CD11b (ICRF44), anti-CD20 (2H7), anti-CD56 (B159, all BD Biosciences), anti-CD14 (61D3), anti-CD19 (HIB19) and anti-CD235a (HIR2, all eBiocience) and 1 micro-gram/ml propidium iodide (Sigma). Using a BD FACSAria cell sorter, single Lin-CD34+CD38-PI- cells were individually sorted into low-adhesion 96-well tissue culture plates (Corning) containing 100micro-litre of StemSpan Serum-Free Expansion Medium (Stemcell technologies) supplemented with 100ng/ml of human SCF and FLT-3L, 50ng/ml of human TPO, 20ng/ml of human IL-3, IL-6 and G-CSF (all cytokines from Peprotech) and 50U/ml of penicillin and 50μg/ml of streptomycin (Sigma). Cells were incubated at 37 degrees C in a humidified atmosphere with 5% CO2 in air. After 5 days in culture, another 100micro litres of cytokine-containing medium were added. 13 days after seeding, clones B6 and G2 had expanded to approx. 105 cells and were selected for whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) after tagmentation-based library preparation (see Extended Experimental Procedures) for clone B6 and standard library preparation for clone G2. For germline-control ~106 unsorted bone marrow mononuclear cells from the same donor were used for sequencing. An average of 30-fold sequence coverage for each the clones and the matching control were obtained. L4clone: A progenitor cell clone was raised from a peripheral blood sample of the 39 year old healthy female. Frozen peripheral blood mononuclear cells (PBMCs) were isolated from 2 ml heparinised peripheral blood via Ficoll Paque density centrifugation. A methylcellulose assay was performed as described earlier (Weisse et al., 2012). In brief, non-adherent mononuclear cells were incubated in the presence of the recombinant human cytokines IL-3, IL-5 and GM-CSF (R&D systems) over 14 days to induce colony formation. Colonies were detected under an inverted light microscope, and plucked by a pipette when colonies had approximately 10,000 cells/CFU. Each colony was washed three times in PBS and finally frozen as a cell pellet in -80 degrees C. Genomic DNA was isolated using the QIAamp DNA micro kit according to the instructions of the manufacturer (Qiagen, Hilden, Germany). Whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) was performed for colony 4 after tagmentation-based library preparation and resulted in 15-fold sequence coverage for each the colony and the matching whole blood.2020-07-16 15:33:08EGAD00001000666960624139898EGAC00001000010EGAS00001000565