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1. Estimating the health care burden of prescription opioid abuse in five European countries

Author

Shei A, Hirst M, Kirson NY, Enloe CJ, Birnbaum HG, and Dunlop WCN

Subjects
Medicine (General), R5-920, Therapeutics. Pharmacology, RM1-950
Abstract

Amie Shei,1 Matthew Hirst,2 Noam Y Kirson,1 Caroline J Enloe,1 Howard G Birnbaum,1 William C N Dunlop21Analysis Group, Inc., Boston, MA, USA; 2Mundipharma International Limited, Cambridge, UK Background: Opioid abuse, including abuse of prescription opioids (“RxOs”) and illicit substances like heroin, is a serious public health issue in Europe. Currently, there is limited data on the magnitude of RxO abuse in Europe, despite increasing public and scientific interest in the issue. The purpose of this study was to use the best-available data to derive comparable estimates of the health care burden of RxO abuse in France, Germany, Italy, Spain, and the United Kingdom (EU5). Methods: Published data on the prevalence of problem opioid use and the share of opioid abuse patients reporting misuse of non-heroin opioids were used to estimate the prevalence of RxO abuse in the EU5 countries. The costs of RxO abuse were calculated by applying published estimates of the incremental health care costs of opioid abuse to country-specific estimates of the costs of chronic pain conditions. These estimates were input into an economic model that quantified the health care burden of RxO abuse in each of the EU5 countries. Sensitivity analyses examined key assumptions. Results: Based on best-available current data, prevalence estimates of RxO abuse ranged from 0.7 to 13.7 per 10,000 individuals across the EU5 countries. Estimates of the incremental health care costs of RxO abuse ranged from €900 to €2,551 per patient per year. The annual health care cost burden of RxO abuse ranged from €6,264 to €279,927 per 100,000 individuals across the EU5 countries. Conclusion: This study suggests that RxO abuse imposes a cost burden on health systems in the five largest European countries. The extent of RxO abuse in Europe should be monitored given the potential for change over time. Continued efforts should be made to collect reliable data on the prevalence and costs of RxO abuse in Europe to facilitate an accurate characterization of the extent of this potentially growing problem. Keywords: prescription opioids, abuse, prevalence, health care costs

Published
2015

3. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

Author

Mack, SC, Witt, H, Piro, RM, Gu, L, Zuyderduyn, S, Stütz, AM, Wang, X, Gallo, M, Garzia, L, Zayne, K, Zhang, X, Ramaswamy, V, Jäger, N, Jones, DTW, Sill, M, Pugh, TJ, Ryzhova, M, Wani, KM, Shih, DJH, Head, R, Remke, M, Bailey, SD, Zichner, T, Faria, CC, Barszczyk, M, Stark, S, Seker-Cin, H, Hutter, S, Johann, P, Bender, S, Hovestadt, V, Tzaridis, T, Dubuc, AM, Northcott, PA, Peacock, J, Bertrand, KC, Agnihotri, S, Cavalli, FMG, Clarke, I, Nethery-Brokx, K, Creasy, CL, Verma, SK, Koster, J, Wu, X, Yao, Y, Milde, T, Sin-Chan, P, Zuccaro, J, Lau, L, Pereira, S, Castelo-Branco, P, Hirst, M, Marra, MA, Roberts, SS, Fults, D, Massimi, L, Cho, YJ, Van Meter, T, Grajkowska, W, Lach, B, Kulozik, AE, von Deimling, A, Witt, O, Scherer, SW, Fan, X, Muraszko, KM, Kool, M, Pomeroy, SL, Gupta, N, Phillips, J, Huang, A, Tabori, U, Hawkins, C, Malkin, D, Kongkham, PN, Weiss, WA, Jabado, N, Rutka, JT, Bouffet, E, Korbel, JO, Lupien, M, Aldape, KD, Bader, GD, Eils, R, Lichter, P, Dirks, PB, Pfister, SM, Korshunov, A, and Taylor, MD

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Pediatric, Human Genome, Rare Diseases, Animals, Brain Neoplasms, CpG Islands, DNA Methylation, Embryonic Stem Cells, Ependymoma, Epigenesis, Genetic, Epigenomics, Female, Gene Expression Regulation, Neoplastic, Gene Silencing, Histones, Humans, Infant, Mice, Mice, Inbred NOD, Mice, SCID, Mutation, Phenotype, Polycomb Repressive Complex 2, Prognosis, Rhombencephalon, Xenograft Model Antitumor Assays, General Science & Technology
Abstract

Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype. Transcriptional silencing driven by CpG methylation converges exclusively on targets of the Polycomb repressive complex 2 which represses expression of differentiation genes through trimethylation of H3K27. CpG island methylator phenotype-positive hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically deregulated but genetically bland.

Published
2014

4. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells

Author

Ramalho-Santos, Miguel, Laird, Diana, Blaschke, K, Ebata, KT, Karimi, MM, Zepeda-Martínez, JA, Goyal, P, Mahapatra, S, Tam, A, Laird, DJ, Hirst, M, and Rao, A

Abstract

DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germ line, and may be mediated by Tet (ten eleven translocat

Published
2013

9. Additional file 1 of Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs

Author

Lorzadeh, A., Hammond, C., Wang, F., Knapp, D. J. H. F., Wong, J. CH., Zhu, J. Y. A., Cao, Q., Heravi-Moussavi, A., Carles, A., Wong, M., Sharafian, Z., Steif, J., Moksa, M., Bilenky, M., Lavoie, P. M., Eaves, C. J., and Hirst, M.

Subjects
macromolecular substances
Abstract

Additional file 1: Fig. S1 to 8. Fig S1 - Sorting strategy for hematopoietic populations profiled in this study. Fig S2 - Progenitor populations possess unique expression profiles. Fig S3 - H3K27me3 promoter density signatures are conserved across progenitor populations. Fig S4 - H3K27me3 LOCKs lost during myeloid differentiation are associated with LADs in CD34+ progenitor cells. Fig S5 - BMI1 loss reduces genome-wide levels of H3K27me3. Fig S6 - Enhancers dynamics in erythroid precursor, monocyte and differentiated lymphoid cells. Fig S7 - Lineage-specific enhancers are marked by H3K27ac in hematopoietic progenitor subsets. Fig S8 - Lineage specific enhancers harbor lineage specific TF binding site are marked with H3K27ac in progenitor population.

Published
2022
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29. Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs

Author

Lorzadeh, A., primary, Hammond, C., additional, Wang, F., additional, Knapp, D.J.H.F., additional, Wong, J.CH., additional, Zhu, J.Y.A, additional, Cao, Q., additional, Heravi-Moussavi, A., additional, Carles, A., additional, Wong, M., additional, Sharafian, Z., additional, Moksa, M., additional, Bilenky, M., additional, Lavoie, P.M., additional, Eaves, C.J., additional, and Hirst, M., additional

Published
2019
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33. The Rights of Participating Victims to Appeal and Participate in the Appeal Against Interlocutory Decisions and Trial Judgments

Author

Tibori-Szabó, K., Hirst, M., and Strafrecht (FdR)

Subjects
Tribunal, Acquittal, law, Political science, Appeal, CLARITY, Interlocutory, Conviction, Criminal court, Entitlement, law.invention
Abstract

Appeals against decisions at international criminal courts can generally be classified into appeals against interlocutory decisions (rulings made by a court before rendering a judgment in the case) and appeals against judgments, of acquittal, conviction, sentencing and reparations. All three courts analysed in this chapter—the Extraordinary Chambers in the Courts of Cambodia (ECCC), the International Criminal Court (ICC) and the Special Tribunal for Lebanon (STL)—provide victims participating in the proceedings with varying degrees of entitlements in respect to such appeals. This chapter provides an overview of these rights. First, it addresses the rights of participating victims to lodge interlocutory appeals in their own right. Then it looks at the extent to which victims can participate in the interlocutory appeals of the (other) parties and the procedure that must be followed. On this basis, it provides a comparative table of the different approaches adopted by the three courts as regards victims’ rights in interlocutory appeals. Secondly, the chapter reviews the rights of participating victims to appeal judgments on acquittals, conviction, sentencing and reparations as well as their entitlement to participate in such appeals. The comparative conclusions as to the rights of participating victims in appeals against judgments are also organised into a table for better clarity. Finally, the chapter highlights the key points to be remembered in relation to victims’ rights in interlocutory and final appeals.

Published
2017
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34. Victim Participation in International Criminal Justice: Practitioner's Guide

Author

Tibori-Szabó, K., Hirst, M., and Strafrecht (FdR)

Abstract

This book is a guide to the law and practice of victims’ roles before the International Criminal Court, the Extraordinary Chambers in the Courts of Cambodia and the Special Tribunal for Lebanon. The various chapters focus on the provisions relevant to victim participation at these courts and the case law interpreting and applying those provisions. The book thus informs the reader on the principal ways in which the relevant practice is developing, the distinct avenues taken in the application of similar provisions as well as the ensuing advantages and challenges. Unlike other volumes focusing on relevant academic literature, this volume is written mainly by practitioners and is addressed to those lawyers, legal advisers and victimologists who work or wish to work in the field of victim participation in international criminal justice.

Published
2017

37. Tests For Cancer

Author

Jennings, R. C., Brocklehurst, D., Hirst, M., and Ziros, A.

Published
1969

40. P003 Implementation of High Throughput Parallel Sequencing in a Diagnostic Setting: Multiplexed Amplicon Sequencing of the Breast Cancer Genes BRCA1 and 2

Author

Zogopoulos G, Tomi Pastinen, Sivanandan K, Vaca F, Kinoshita T, Johannes B, Leguis E, Jansen-van der Weide M, Learn L, Godlewski D, Ed Saunders, Montserrat Rué, Vaisman A, de Bock G, Ángel Segura, Sabbaghian N, Mohammad Amin Kerachian, Pelletier S, Metcalfe K, Lilge L, Stockle E, Cheng S, Burger C, Woike A, Michelle Guy, Ragone A, Y. J. Bignon, Bronkhorst Y, Patricia N. Tonin, Lima M, Mieke Kriege, Karsan A, Zweemer R, Prady C, Beattie M, Panchal S, Kathleen Claes, van Zon P, Diane Provencher, Ummels A, Kang I, Shumak R, Arcusa Â, Yosr Hamdi, Alonso Mc, Dolman L, Houssami N, Olivier Delattre, Yannick Bidet, Claude Houdayer, Mercedes Durán, Ganschow P, Isabel Chirivella, Domingo S, Rebsamen M, Giustina Simone, Orland Diez, Chapman J, An tSaoir C, Jeanna McCuaig, Blayney J, Bosdet I, Treacy R, Esther Darder, Ando J, Luc Dehaspe, García-Casado Z, Duffy J, Harkin D, Z Kote-Jarai, Kasamatsu T, Ulf Kristoffersson, Membrez, Priston M, Noreau-Heisz D, Trivedi A, Begoña Graña, Ghadirian P, Ashuryk O, Consol López, Wenzel L, Vogel R, Joseph G, Poll A, Kennedy R, Patton S, Pérez C, Mónica Cornet, Panighetti A, Cassart P, Burke K, Mes-Masson A, Llacuachaqui M, Marc Tischkowitz, Wong N, Arcand S, Kotsopoulos J, Meschino W, Hall A, Marles S, Docking R, Haroun I, Marie Plante, Rachel Laframboise, Daniel Sinnett, Luce J, Sekiguchi I, Edenir Inêz Palmero, de Winter J, Christopher J. Lord, Hamel N, Pruski-Clark J, Lee D, Rusnak A, Carson N, Marta Santamariña, Knoppers B, Oakhill K, Bruce R. Rosen, Pierre O. Chappuis, Bruce Poppe, Stanislaw C, Catts Z, Brood M, van der Wall E, Yip C, Christine Walsh, Hoodfar E, Pressman A, Andrulis I, Alicia Barroso, D. Leongamornlert, Gillian Mitchell, Akira Hirasawa, Shen Z, Sameer Parpia, Horgan M, van Echtelt J, Chun K, Lubinski J, Rebecca Sutphen, Terespolsky D, Richard D, McDyer F, Floquet A, Lambo R, Bathurst L, Brown G, Kidd M, Nicolas Sevenet, Mourits M, Vencken P, Tatiana Popova, Garcia N, Armel S, van Amstel H, Valentini A, Ellen Warner, Hofland N, Hanna D, Kim J, Osann K, Enmore M, Loranger K, Sulivan I, J. Oliveira, Meijers H, Jansen R, Edmundo Carvalho Mauad, Kirkpatrick R, Danilo V Viana, Ian G. Campbell, Mil S, E J Sawyer, J. Balmaña, Samra Turajlic, Graham G, Alonso C, Inanc Birol, Sinclair F, van Tuil M, Pascual Bolufer, Micheli R, Andrew R. Green, Junyent N, Whittaker J, Monnerat C, Rhéaume J, Livingston D, Chan S, L. Ramadan, Lee R, Katarzyna Durda, De Leeneer K, Grados C, Côté C, Kyle B. Matchett, Robert Winqvist, Bonner D, Brunella Pilato, Mohd Taib N, Judy Garber, Kleiderman E, Murakami S, Sharifi N, Kimberley Hill, Desbiens C, Robert Royer, Jasperson K, Hsieh S, De Summa S, Dominique Stoppa-Lyonnet, de Lima J, Stuart McIntosh, Shakeri M, Wendy Kohlmann, Albert-Green A, de Hullu J, Pasick R, Avard D, Pathania S, van der Groep P, Laura Fachal, Bruno Zeitouni, Susan M. Domchek, Davey S, Richard Marais, Powell C, Hans J. J. P. Gille, Greenberg R, Kamata H, Cina, Gaarenstroom K, Lakhal Chaieb M, Kavanagh L, Gaelle Benais-Pont, Sun P, Jansen L, Matthew Parker, Barjhoux L, Russ H, Simon J. Furney, Willems A, Robb L, David E. Goldgar, Young S, Natalia Campacci, Mark G. Thomas, Doug Easton, Klugman S, Barrault M, Calvo N, Adriana C. Flora, Littell R, Narod S, Fragoso, N. Bosch, Finch A, Paul M. Wilkerson, Teo S, Tomasz Huzarski, Manuel Salto-Tellez, Moseley M, Davis S, Olga M. Sinilnikova, Iturbe A, Joan Brunet, Tierney M, Tsai E, Navarro de Souza A, Leclerc M, Lorenzo Manti, Gutiérrez-Enríquez S, Milewski B, Simon S. McDade, Kaplan C, Buckley N, Eva Esteban-Cardeñosa, Richter S, Shimizu C, Li J, Elena Castro, Iwanka Kozarewa, Harley I, Atocha Romero, Carlos E. Andrade, Carole Verny-Pierre, Barouk E, Vian D, Montserrat Baiget, Chan J, Sandra Bonache, Andrew Y Shuen, van der Merwe N, Kaklewski K, Mohar A, Tamura C, Heale E, Rooyadeh M, van Asperen C, Gemma Llort, Alan Mackay, Denroche R, Seelaus C, Zbuk K, McCluggage W, van der Luijt R, Maaike P.G. Vreeswijk, Edelweiss M, Crossan G, Arseneau J, Ambus I, Verheul H, Rodrigo Augusto Depieri Michelli, Juul T. Wijnen, Gross-Lester J, Britta Weigelt, Pedro Pérez-Segura, Richard A. Moore, Cornelissen C, Larouche G, McAlpine J, Daniel Nava Rodrigues, Trim L, Furnival J, Elser C, Muszyńka M, Adriana Lasa, Tuya Pal, Greuter. M, Ng K, Dorval M, Bresee C, Reimnitz G, Gaëtan MacGrogan, Perry Maxwell, Barnadas A, Hwang E, Powell B, Knapke S, Griskevicius. L, Alvarez R, Mester J, Anne-Bine Skytte, Eladio Velasco, Vidal S, Australie K, Leunen K, Ben-Yishay M, Van Houdt J, Phuah S, Amy E Taylor, Pinto R, Fonseca T, Champine M, Gammon A, Hollema H, Menko F, Feng B, David Olmos, Chong G, Tomasz Byrski, Patrick J. Morrison, Gregoire J, André Lopes Carvalho, Don B. Plewes, Rabeneck L, Carrol J, Alan Ashworth, Terlinge A, A Jakubowska, Odette Mariani, Setareh Moghadasi, Reitsma W, Rothenmund H, Herrera L, Anna Tenés, Angel Izquierdo, Asunción Torres, Stawicka M, Goh C, Hirst M, Drummond J, Osorio A, Ostrovsky R, Jeffrey N. Weitzel, Gareth W. Irwin, Fehniger J, Sugano K, Spriggs E, Dęniak T, Volenik A, Thorne H, Piccinin C, Amie Blanco, Jinno H, Robert A. Holt, Stephen B. Fox, Julia J. Gorski, Gilpin C, Herschorn S, Vega A, E. Page, Hamet P, McKenna D, Fabrice Bonnet, Yoshida T, Kienan I. Savage, Petzel S, Elizabeth Bancroft, Schneider S, Warwick L, Stewart S, William D. Foulkes, Colizza K, Bell K, Demsky R, Malgorzata Tymrakiewicz, Caldés T, Fons G, Bowen D, Côté S, Clouston D, Kitagawa Y, Gordon Glendon, Jenny Lester, Kinney A, Nelson E, Silke Hollants, Macrae L, Cajal T, Andrew J. Mungall, Ferrell B, Creighton B, Bressler L, Uy P, Makishima K, Haffaf Z, Ramūnas Janavičius, Einstein G, Zakalik D, Chiarelli A, Cantu D, Croce S, Kalloger S, Lin F, Ian O. Ellis, Benedito Mauro Rossi, R A Wilkinson, Mulligan J, Murphy J, Vadaparampil S, Smith E, Slangen B, Loiselle C, Iqbal J, Palma L, Cooper K, Jorge S. Reis-Filho, Chen. L, Quinten Waisfisz, Haneda E, Banks P, Vermeulen K, Visser B, Montalbán G, McCabe N, Honeyford J, Naseri S, Ng J, Ali A, Sandrine Viala, Mensa I, Kamarainen O, Guerra C, Mazzola E, David A. Schwartz, Marjanka K. Schmidt, Simon R, Fergus J. Couch, Margreet G. E. M. Ausems, Anne Vincent-Salomon, Olinski R, Zewald R, Moreno R, Semple J, McPherson J, Lamers E, Kharbanda A, Kessler L, Biemans D, Au A, Bordeleau L, Jean Feunteun, Mar Infante, Mullan P, Rudaitis, Molenda A, Rachael Natrajan, Pawar, Boman B, Kok T, Andrew A. Brown, Geller M, Monfared N, Bart J, Murata P, Crawford N, Butterfield Y, Bargalló J, Katherine L. Tucker, Cook-Wiens G, Rhodes A, Elodie Manié, Rubio E, Oram L, Shandiz F, Hayden R, Crawford B, Parmigiani G, Harkin P, Müller C, Grant M, Maryou B. Lambros, Thong M, Grzegorz Sukiennicki, Wouts J, Haddock P, Ramon y Cajal T, Kenneth C. Anderson, Michel Longy, Batiste W, Carroll J, Matte C, Hojyo T, Zhao Y, Caroline Seynaeve, Wai P, Simard J, Hurley K, Bolton D, Karlan B, Javier Benítez, Miriam Masas, Tołczko-Grabarek A, de Dueñas E, Geneviève Michils, Moncoutier, Nancy Uhrhammer, MacDonald D, Keyserlingk J, Osher D, Gilks C, Christopher T. Elliott, Scharf L, Gabram-Mendola S, Grondin K, Dohany L, van Diest P, Joris Vermeesch, Jan C. Oosterwijk, M’Baïlara K, DePuit M, Jacek Gronwald, Stefania Tommasi, de la Hoya M, Bouchard K, Black L, Lui M, Soucy P, Rosalind A. Eeles, Gert Matthijs, Graham T, Andrea Eisen, Bacha O, Alvaro N.A. Monteiro, Yoon S, Caron T, Smith D, Marc-Henri Stern, Hampson E, Kurz R, Gaasbeek W, Mundt E, Angela Velasco, Quinn J, Jocelyne Chiquette, Marquez T, Adam B. Murphy, Bakker J, Neus Gadea, Anita Grigoriadis, Aoki D, Dean S, Looi L, Paradiso A, Agostina Stradella, K. Govindasami, Lovell N, Eva Tomiak, Siesling S, Belanger M, Feilotter H, Knight J, Emmanuel Barillot, Huang M, Raquel Andrés, Kang P, Somerman C, Gackowski D, Rimel B, Nakamura S, McClellan K, Barrros E, Henriette Roed Nielsen, Rui Manuel Reis, Greening S, Ayme A, Carmen Guillen, de Vries E, and Katarzyna Jaworska

Subjects
Oncology, Education and Communication, medicine.medical_specialty, endocrine system diseases, medicine.diagnostic_test, business.industry, Psycho-Oncology, medicine.disease, Meeting Abstracts, Transcriptome, Basic Research, Clinical Management, Germline mutation, Breast cancer, Applied Research, Internal medicine, Mutation (genetic algorithm), medicine, Genetic Counselling, Human genome, skin and connective tissue diseases, business, Ovarian cancer, Comparative genomic hybridization, Fluorescence in situ hybridization
Abstract

Background: Germline mutation screening of BRCA1 and BRCA2 genes is performed in suspected familial breast cancer cases, but a causative mutation is found in only 30% of patients. The development of additional methods to identify good candidates for BRCA1 and BRCA2 analysis would therefore increase the efficacy of diagnostic mutation screening. With this in mind, we developed a study to determine molecular signatures of BRCA1—or BRCA2—mutated breast cancers. Materials and Methods: Array-cgh (comparative genomic hybridization) and transcriptomic analysis were performed on a series of 103 familial breast cancers. The series included 7 breast cancers with a BRCA1 mutation and 5 breast cancers with a BRCA2 mutation. The remaining 91 cases were obtained from 73 families selected on the basis of at least 3 affected first-degree relatives or at least 2 affected first-degree relatives with breast cancer at an average age of 45 years. Array-cgh analyses were performed on a 4407 BAC-array (CIT-V8) manufactured by IntegraGen. Transcriptomic analyses were performed using an Affymetrix Human Genome U133 Plus 2.0 chip. Results: Using supervised clustering analyses we identified two transcriptomic signatures: one for BRCA1-mutated breast cancers consisting of 600 probe sets and another for BRCA2-mutated breast cancers also consisting of 600 probes sets. We also defined cgh-array signatures, based on the presence of specific genomic rearrangements, one for BRCA1-mutated breast cancers and one for BRCA2-mutated breast cancers. Conclusions: This study identified molecular signatures of breast cancers with BRCA1 or BRCA2 germline mutations. Genes present in these signatures could be exploited to find new markers for such breast cancers. We also identified specific genomic rearrangements in these breast cancers, which could be screened for in a diagnostic setting using fluorescence in situ hybridization, thus improving patient selection for BRCA1 and BRCA2 molecular genetic analysis.

Published
2009
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42. Molecular and biological analysis of human hematopoietic stem cells at single-cell resolution

Author

Eaves, Connie, primary, Knapp, D.J.H.F., additional, Hammond, C.A., additional, Hui, A., additional, van Loenhout, M., additional, Pellacani, D., additional, Wang, F., additional, Miller, P.H., additional, Lorzadeh, A., additional, Aghaeepour, N., additional, Moksa, M., additional, Vaninsberghe, M., additional, Rabu, G.M., additional, Beer, P.A., additional, Humphries, R.K., additional, Bendall, S., additional, Nolan, G.P., additional, Hansen, C., additional, and Hirst, M., additional

Published
2017
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44. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

Author

Harris, R, Wang, T, Coarfa, C, Nagarajan, R, Hong, C, Downey, S, Johnson, B, Fouse, S, Delaney, A, Zhao, Y, Olshen, A, Ballinger, T, Zhou, X, Forsberg, K, Gu, J, Echipare, L, O'Geen, H, Lister, R, Pelizzola, M, Xi, Y, Epstein, C, Bernstein, B, Hawkins, R, Ren, B, Chung, W, Gu, H, Bock, C, Gnirke, A, Zhang, M, Haussler, D, Ecker, J, Li, W, Farnham, P, Waterland, R, Meissner, A, Marra, M, Hirst, M, Milosavljevic, A, Costello, J, Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF, Harris, R, Wang, T, Coarfa, C, Nagarajan, R, Hong, C, Downey, S, Johnson, B, Fouse, S, Delaney, A, Zhao, Y, Olshen, A, Ballinger, T, Zhou, X, Forsberg, K, Gu, J, Echipare, L, O'Geen, H, Lister, R, Pelizzola, M, Xi, Y, Epstein, C, Bernstein, B, Hawkins, R, Ren, B, Chung, W, Gu, H, Bock, C, Gnirke, A, Zhang, M, Haussler, D, Ecker, J, Li, W, Farnham, P, Waterland, R, Meissner, A, Marra, M, Hirst, M, Milosavljevic, A, Costello, J, Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, and Costello JF

Abstract

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression.

Published
2010

45. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

Author

Stunnenberg, H.G., Hirst, M., Netea, M.G., et al., Stunnenberg, H.G., Hirst, M., Netea, M.G., and et al.

Abstract

Item does not contain fulltext, The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC) highlight the coordinated achievements of IHEC teams to gather and interpret comprehensive epigenomic datasets to gain insights in the epigenetic control of cell states relevant for human health and disease. PAPERCLIP.

Published
2016

47. Interpretative reflections on Nomzi's story

Author

Edwards, DJA, Hirst, M, and Booi, BN

Abstract

In this, the second of two papers, three interpretative investigations are undertaken of Nomzi's story (presented in the first paper) of her troubled childhood, her dreams of ancestors calling her to become an igqirha (isiXhosa traditional healer), her training by experienced healers, various rituals that were performed at different stages of her life, and her eventual graduation as an igqirha at the age of 61. The narrative cannot be understood apart from the framework of the isiXhosa traditional understanding of intwaso, the initiatory illness, the role of the ancestors, and the manner in which clairvoyant abilities of divination and healing are developed under their guidance. Nomzi's account, however, reflects a considerable modification of the tradition, several features of which she does not seem to understand herself. From a clinical psychological perspective, Nomzi's behavioural disturbances in childhood, as well as her lifelong suspiciousness and paranoia, can be understood as a consequence of an unstable childhood in which there was no secure attachment, nor any adult guidance on emotional regulation of the kind needed to form the basis of a stable adult personality. From the perspective of transpersonal psychology, it seems likely that Nomzi was endowed with a degree of natural clairvoyance, but her development as a healer was impaired by displacement of her paranoid ideation into the role of witch-finder, and her chronic social alienation.

Published
2014

50. Epigenome data release: a participant-centered approach to privacy protection

Author

Dyke, S.O.M., Cheung, W.A., Joly, Y., Ammerpohl, O., Lutsik, P., Rothstein, M.A., Caron, M., Busche, S., Bourque, G., Ronnblom, L., Flicek, P., Beck, S., Hirst, M., Stunnenberg, H., Siebert, R., Walter, J., Pastinen, T., Dyke, S.O.M., Cheung, W.A., Joly, Y., Ammerpohl, O., Lutsik, P., Rothstein, M.A., Caron, M., Busche, S., Bourque, G., Ronnblom, L., Flicek, P., Beck, S., Hirst, M., Stunnenberg, H., Siebert, R., Walter, J., and Pastinen, T.

Abstract

Contains fulltext : 149175.pdf (publisher's version ) (Open Access)

Published
2015

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