@article{fac8c483440b4c599dea2ff47e56129d,
title = "Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes",
abstract = "Cervical cancer is the most common cancer affecting sub-Saharan African women and is prevalent among HIV-positive (HIV+) individuals. No comprehensive profiling of cancer genomes, transcriptomes or epigenomes has been performed in this population thus far. We characterized 118 tumors from Ugandan patients, of whom 72 were HIV+, and performed extended mutation analysis on an additional 89 tumors. We detected human papillomavirus (HPV)-clade-specific differences in tumor DNA methylation, promoter- and enhancer-associated histone marks, gene expression and pathway dysregulation. Changes in histone modification at HPV integration events were correlated with upregulation of nearby genes and endogenous retroviruses.",
author = "Alessia Gagliardi and Porter, {Vanessa L.} and Zusheng Zong and Reanne Bowlby and Emma Titmuss and Constance Namirembe and Griner, {Nicholas B.} and Hilary Petrello and Jay Bowen and Chan, {Simon K.} and Luka Culibrk and Darragh, {Teresa M.} and Stoler, {Mark H.} and Wright, {Thomas C.} and Patee Gesuwan and Dyer, {Maureen A.} and Yussanne Ma and Mungall, {Karen L.} and Jones, {Steven J.M.} and Carolyn Nakisige and Karen Novik and Jackson Orem and Martin Origa and Gastier-Foster, {Julie M.} and Robert Yarchoan and Corey Casper and Mills, {Gordon B.} and Rader, {Janet S.} and Ojesina, {Akinyemi I.} and Gerhard, {Daniela S.} and Mungall, {Andrew J.} and Marra, {Marco A.}",
note = "Funding Information: This project has been funded in whole or in part with US federal funds from the National Cancer Institute, National Institutes of Health, under contract no. HHSN261200800001E and HHSN261201500003I. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the US government. We gratefully acknowledge the Fred Hutchinson Cancer Research Center and the Uganda Cancer Institute for overseeing sample and data collection in Uganda. We are grateful for contributions from the other members of the HTMCP Cervical Cancer Working Group at the Department of Epidemiology, University of Alabama at Birmingham, the Pancreas Centre BC and various groups at Canada{\textquoteright}s Michael Smith Genome Sciences Centre, including those from the Biospecimen, Library Construction, Sequencing, Bioinformatics, Technology Development, Quality Assurance, LIMS, Purchasing and Project Management teams. We thank the AIDS and Cancer Specimen Resource for logistical coordination and support of this project through NIH grants U01CA066535, U01CA096230 and UM1CA181255. L.C. and V.L.P. are the recipients of CIHR Frederick Banting and Charles Best Canada Graduate Scholarships GSD-164207 and GSD-152374, respectively. S.J.M.J. is the recipient of the Canada Research Chair in Computational Genomics. This research was supported by the Intramural Research Program of the NIH, National Cancer Institute (R.Y.). C.C. is supported by NIH grant P30AI027757. G.B.M. is supported by NCI grants U01CA217842 and P50CA098258. M.A.M. is the recipient of the Canada Research Chair in Genome Science. This work was supported in part by funding provided by the Canadian Institutes for Health Research (CIHR award FDN-143288) to M.A.M. A.I.O. was supported in part by the Endlichhofer Trust (OCCC 3120957) and a V Foundation grant (DVP2018-007). Publisher Copyright: {\textcopyright} 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",
year = "2020",
month = aug,
day = "1",
doi = "10.1038/s41588-020-0673-7",
language = "English (US)",
volume = "52",
pages = "800--810",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",
number = "8",
}