Professor, Department of Medical Genetics, University of British Columbia
Director, Canada’s Michael Smith Genome Sciences Centre at BC Cancer
Canada Research Chair in Genome Science
phone: 6046758168

I am Professor of Medical Genetics at UBC; UBC Canada Research Chair in Genome Science; and Director of Canada’s Michael Smith Genome Sciences Centre (GSC). I was trained as a geneticist, and have been involved in the development and application of high-throughput genomics strategies, with special emphasis on large-scale DNA sequencing and bioinformatics. I have spent much of my career working within, and leading, teams to conduct large-scale high throughput genomics projects.

A current focus of my research activities involves the development and application of “next generation” sequencing approaches to characterize cancer genomes, transcriptomes and epigenomes, with the aim of comprehensive identification of the genetic and epigenetic changes that drive cancer progression. With such data, and as co-Leader of the BC Cancer Personalized Oncogenomics Project, my objective is the development of a new generation of diagnostic, prognostic and treatment strategies to benefit cancer patients.

A second focus of my research revolves around the functional interplay between cancer genomes and epigenomes. My team has described the strikingly high frequency of mutations in transcriptional regulators, including chromatin modifiers, implying they are “cancer genes,” and that mutations in them drive cancers. The interplay between the genome and the epigenome is thus exploited by cancer cells, but exactly how, the extent to which common mechanisms exist across cancers and whether answers to such questions might reveal therapeutic opportunities, all require investigation. My team is analyzing the cancer regulatory networks impacted by epigenome dysregulation, using cell biology, genetics, genomics, bioinformatics, and functional genomics tools, and we aim to understand the selective advantages conferred to cancer cells as a consequence of such dysregulation. My objectives are: (1) to identify and characterize regulatory networks disrupted by epigenome dysregulation in cancer; (2) to assess the extent to which epigenome dysregulation converges on common pathways/networks in different malignancies; and, (3) to identify candidate therapeutic vulnerabilities resulting from epigenome dysregulation.

Selected Publications

Tessier-Cloutier B, Grewal JK, Jones MR, Pleasance E, Shen Y, Cai E, Dunham C, Hoang L, Horst B, Huntsman DG, Ionescu D, Karnezis AN, Lee AF, Lee CH, Lee TH, Twa DD, Mungall AJ, Mungall K, Naso JR, Ng T, Schaeffer DF, Sheffield BS, Skinnider B, Smith T, Williamson L, Zhong E, Regier DA, Laskin J, Marra MA, Gilks CB, Jones SJ, Yip S. The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy ofadvanced malignancies.  J Pathol Clin Res. 2022 Mar 8. doi: 10.1002/cjp2.265. Online ahead of print.

Lee SD, Song J, LeBlanc VG, Marra MA. Integrative multi-omic analysis reveals neurodevelopmental gene dysregulation in CIC-knockout and IDH1 mutant cells. J Pathol.  2022 Mar;256(3):297-309. doi: 10.1002/path.5835.

Regier DA, Chan B, Costa S, Scott DW, Steidl C, Connors JM, Karsan A, Marra MA, Kridel R, Cromwell I, Pollard S. Cost-Effectiveness of Molecularly Guided Treatment in Diffuse Large B-Cell Lymphoma (DLBCL) in Patients under 60. Cancers (Basel). 2022 Feb 12;14(4):908. doi: 10.3390/cancers14040908.

Reisle C, Williamson LM, Pleasance E, Davies A, Pellegrini B, Bleile DW, Mungall KL, Chuah E, Jones MR, Ma Y, Lewis E, Beckie I, Pham D, Matiello Pletz R, Muhammadzadeh A, Pierce BM, Li J, Stevenson R, Wong H, Bailey L, Reisle A, Douglas M, Bonakdar M, Nelson JMT, Grisdale CJ, Krzywinski M, Fisic A, Mitchell T, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM. A Platform for Oncogenomic Reporting and Interpretation. Nat Commun. 2022 Feb 9;13(1):756. doi: 10.1038/s41467-022-28348-y.

Milella M, Luchini C, Lawlor RT, Johns AL, Casolino R, Yoshino T, Biankin AV; ICGC-ARGO (incl Marra MA). ICGC-ARGO precision medicine: familial matters in pancreatic cancer. Lancet Oncol. 2022 Jan;23(1):25-26. doi: 10.1016/S1470-2045(21)00703-8.

Haile S, Nikiforuk AM, Pandoh PK, Twa DDW, Smailus DE, Nguyen J, Pleasance S, Wong A, Zhao YJ, Eisler D, Moksa M, Cao Q, Wong M, Su E, Krzywinski M, Nelson J, Mungall AJ, Tsang F, Prentice LM,  Jassem A, Manges AR, Jones SJM, Coope RJ, Prystajecky N, Marra MA, Krajden M, Hirst M. Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents. J Virol Methods. 2022 Jan;299:114339. doi: 10.1016/j.jviromet.2021.114339.

Williamson LM, Rive CM, Di Francesco D, Titmuss E, Chun HE, Brown SD, Milne K, Pleasance E, Lee AF, Yip S, Rosenbaum DG, Hasselblatt M, Johann PD, Kool M, Harvey M, Dix D, Renouf DJ, Holt RA, Nelson BH, Hirst M, Jones SJM, Laskin J, Rassekh SR, Deyell RJ, Marra MA. Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury. NPJ Precis Oncol. 2021 Dec 20;5(1):103. doi: 10.1038/s41698-021-00238-4.

Weymann D, Laskin J, Jones SJM, Roscoe R, Lim HJ, Renouf DJ, Schrader KA, Sun S, Yip S, Marra MA, Regier DA. Early stage economic analysis of research-based comprehensive genomic sequencing for advanced cancer care. J Community Genet. 2021 Nov 29:1-16. doi: 10.1007/s12687-021-00557-w. Online ahead of print.

Zhang Y, Chen F, Pleasance E, Williamson L, Grisdale CJ, Titmuss E, Laskin J, Jones SJM, Cortes-Ciriano I, Marra MA, Creighton CJ. Rearrangement-mediated cis-regulatory alterations in advanced patient tumours reveal interactions with therapy. Cell Rep. 2021 Nov 16;37(7):110023. doi: 10.1016/j.celrep.2021.110023.

Yang KC, Kalloger SE, Aird JJ, Lee MCK, Rushton C, Mungall KL, Mungall AJ, Gao D, Chow C, Xu J, Karasinska JM, Colborne S, Jones SJM, Schrader J, Morin RD, Loree JM, Marra MA, Renouf DJ, Morin GB, Schaeffer DF, Gorski SM. Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms. Cell Rep. 2021 Oct 12;37(2):109817. doi: 10.1016/j.celrep.2021.109817.

Guenter J, Abadi S, Lim H, Chia S, Woods R, Jones M, Rebic N, Renouf DJ, Laskin J, Marra M. Evaluating genomic biomarkers associated with resistance or sensitivity to chemotherapy in patients with advanced breast and colorectal cancer.  J Oncol Pharm Pract. 2021 Sep;27(6):1371-1381. doi: 10.1177/1078155220951845.

Weymann D, Pollard S, Chan B, Titmuss E, Bohm A, Laskin J, Jones SJMS, Pleasance E, Nelson J, Fok A, Lim H, Karsan A, Renouf DJ, Schrader KA, Sun S, Yip S, Schaeffer DF, Marra MA, Regier DA. Clinical and cost outcomes following genomics-informed treatment for advanced cancers. Cancer Med.  2021 Aug;10(15):5131-5140. doi: 10.1002/cam4.4076.

Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, O’Flanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA; IMAXT Consortium, McPherson A, Bouchard-Côté A, Aparicio S, Shah SP. Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Nature. 2021 Jul;595(7868):585-590. doi: 10.1038/s41586-021-03648-3.

Haile S, Corbett RD, Leblanc V, Wei L, Pleasance S, Bilobram S, Nip KM, Brown K, Trinh E, Smith J, Trinh D, Bala M, Chuah E, Coope RJ, Moore RA, Mungall AJ, Mungall K, Zhao YJ, Hirst M, Aparicio S, Birol I, Jones SJ, Marra MA. A scalable strand-specific protocol enabling full-length total RNA sequencing from single cells. Front Genet. 2021 Jun 3;12:665888. doi: 10.3389/fgene.2021.665888. eCollection 2021

Zhang B, Kim MY, Elliot G, Zhou Y, Zhao G, Li D, Lowdon RF, Gormley M, Kapidzic M, Robinson JF, McMaster M, Hong C, Mazor T, Hamilton E, Sears RL, Pehrsson EC, Marra MA, Jones SJM, Bilenky M, Hirst M, Wang T, Costello JF, Fisher SJ. Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. Dev Cell. 2021 May 3;56(9):1238-1252.e5. doi: 10.1016/j.devcel.2021.04.001.

Isaev K, Ennishi D, Hilton L, Skinnider B, Mungall KL, Mungall AJ, Bakhtiari M, Tremblay-LeMay R, Silva A, Ben-Neriah S, Boyle M, Villa D, Marra MA, Steidl C, Gascoyne RD, Morin R, Savage KJ, Scott DW, Kridel R. Molecular Attributes Underlying Central Nervous System and Systemic Relapse in Diffuse Large B-cell Lymphoma. Haematologica. 2021 May 1;106(5):1466-1471. doi: 10.3324/haematol.2020.255950.

Docking TR, Parker JDK, Jädersten M, Duns G, Chang L, Jiang J, Pilsworth JA, Swanson LA, Chan SK, Chiu R, Nip KM, Mar S, Mo A, Wang X, Martinez-Høyer S, Stubbins RJ, Mungall KL, Mungall AJ, Moore RA, Jones SJM, Birol I, Marra MA, Hogge D, Karsan A. A Clinical Transcriptome Approach to Patient Stratification and Therapy Selection in Acute Myeloid Leukemia. Nat Commun. 2021 Apr 30;12(1):2474. doi: 10.1038/s41467-021-22625-y.

Collinge BJ, Ben-Neriah S, Chong LC, Boyle M, Jiang A, Miyata-Takata T, Farinha P, Craig JW, Slack GW, Ennishi D, Mottok A, Meissner B, Chavez EA, Gerrie AS, Villa D, Freeman CL, Savage KJ, Sehn LH, Morin RD, Mungall AJ, Gascoyne RD, Marra MA, Connors JM, Steidl C, Scott DW. Impact of MYC and BCL2 structural variants in tumors of DLBCL morphology and mechanisms of false-negative MYC IHC. Blood. 2021 Apr 22;137(16):2196-2208. doi: 10.1182/blood.2020007193.

Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim SK, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng HK, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui CC, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD. The transcriptional landscape of Shh medulloblastoma. Nat Commun. 2021 Mar 19;12(1):1749. doi: 10.1038/s41467-021-21883-0.

Britton H, Levine A, Shen Y, Mungall K, Serrano J, Snuderl M, Pleasance E, Jones S, Laskin J, Marra    M, Rassekh S, Deyell R, Yip S, Cheng S, Dunham C. NTRK2 Fusion Driven Pediatric Glioblastoma: Identification of Oncogenic Drivers via Integrative Genome and Transcriptome Profiling. Clin Case Rep. 2021 Feb 10;9(3):1472-1477. doi: 10.1002/ccr3.3804.

Richards LM, Whitley OKN, MacLeod H, Cavalli FMG, Coutinho FJ, Jaramillo JE, Svergun N, Riverin M, Croucher DC, Kushida M, Yu K, Guilhamon P, Rastegar N, Ahmadi M, Bhatti JK, Bozek DA, Li N, Lee L, Che C, Luis E, Park NI, Xu Z, Ketela T, Moore RA, Marra M, Spears J, Cusimano MD, Das S, Bernstein M, Haibe-Kains B, Lupien M, Luchman HA, Weiss S, Angers S, Dirks PB, Bader GD, Pugh TJ. Gradient of developmental and injury-response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity. Nat Cancer. 2021 Jan 4; 2:157-173.

Akbari V, Garant JM, O’Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM. Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase. Genome Biol. 2021 Feb 22;22(1):68. doi: 10.1186/s13059-021-02283-5.

Coope RJN, Schlosser C, Corbett RD, Pleasance S, Tessier-Cloutier B, Pandoh P, Kirk H, Haile S, Zhao YJ, Mungall AJ, Marra MA. Whole-Slide Laser Microdissection for Tumour Enrichment. J Pathol. 2021 Feb;253(2):225-233. doi: 10.1002/path.5575.

Naso J, Topham J, Karasinska J, Lee M, Kalloger S, Wong H-L, Nelson J, Moore R, Mungall A, Jones S, Laskin J, Marra M, Renouf D, Schaeffer D. Tumor Infiltrating Neutrophils and Gland-Formation Predict Overall Survival and Molecular Subgroups in Pancreatic Ductal Adenocarcinoma. Cancer Med. 2021 Feb;10(3):1155-1165. doi: 10.1002/cam4.3695.

Tsang ES, Grisdale CJ, Pleasance ED, Topham JT, Mungall KL, Reisle CR, Choo C, Carreira M, Bowlby R, Karasinska JM, MacMillan D, Williamson LM, Chuah E, Moore RA, Mungall AJ, Zhao Y, Tessier-Cloutier B, Ng T, Sun S, Lim H, Schaeffer DF, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJ, Loree JM. Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers. Clin Cancer Res. 2021 Jan 15;27(2):522-531. doi: 10.1158/1078-0432.CCR-20-1900.

Tsang ES, Topham JT, Karasinska JM, Lee MKC, Williamson LM, Mendis S, Denroche RE, Jang GH, Kalloger SE, Moore RA, Mungall AJ, Laskin J, O’Kane GM, Knox JJ, Goodwin R, Loree JM, Gallinger S, Jones SM, Marra MA, Schaeffer DF, Renouf DJ. Delving into Early Onset Pancreatic Ductal Adenocarcinoma: How Does Age Fit In? Clin Cancer Res. 2021 Jan 1;27(1):246-254. doi: 10.1158/1078-0432.CCR-20-1042.

Topham JT, Karasinska JM, Lee MKC, Csizmok V, Williamson LM, Jang GH, Denroche RE, Tsang E, Kalloger SE, Wong H-l, O’Kane GM, Moore RA, Mungall AJ, Loree JM, Bathe O, Tang P, Goodwin R, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJM, Renouf DJ, Schaeffer DF. Subtype-discordant pancreatic ductal adenocarcinoma tumors show intermediate clinical and molecular characteristics. Clin Cancer Res. 2021 Jan 1;27(1):150-157. doi: 10.1158/1078-0432.CCR-20-2831.

Pender A, Titmuss E, Pleasance E, Fan K, Pearson H, Brown S, Grisdale C, Topham J, Shen Y, Bonakdar M, Taylor G, Williamson L, Mungall K, Chuah E, Mungall A, Moore R, Lavoie J-M, Yip S, Lim H, Renouf D, Sun S, Holt R, Jones S, Marra M, Laskin J. Genome and transcriptome biomarkers of response to immune checkpoint inhibitors in advanced solid tumours. Clin Cancer Res. 2021 Jan 1;27(1):202-212. doi: 10.1158/1078-0432.CCR-20-1163.

Weymann D, Laskin J, Jones SJM, Lim H, Renouf DJ, Roscoe R, Schrader KA, Sun S, Yip S, Marra MA, Regier DA. Matching methods in precision oncology: An introduction and illustrative example.Mol Genet Genomic Med. 2021 Jan;9(1):e1554. doi: 10.1002/mgg3.1554.

Thibodeau ML, O’Neill K, Dixon K, Reisle C, Mungall KL, Krzywinski M, Shen Y, Lim HJ, Cheng D, Tse K, Wong T, Chuah E, Fok A, Sun S, Renouf D, Schaeffer DF, Cremin C, Chia S, Young S, Pandoh P, Pleasance S, Pleasance E, Mungall AJ, Moore R, Yip S, Karsan A, Laskin J, Marra MA, Schrader KA, Jones SJM. Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing. Genet Med.  2020 Nov;22(11):1892-1897. doi: 10.1038/s41436-020-0880-8.

Wong D, Sogerer L, Lee SS, Wong V, Lum A, Marra MA, Yip S. TRIM25 promotes Capicua degradation independently of ERK in the absence of ATXN1L. BMC Biol. 2020 Oct 28;18(1):154. doi: 10.1186/s12915-020-00895-0.

De Boeck A, Ahn BY, D’Mello C, Lun X, Alsherhi M, Szulzewsky F, Shen Y, Khan L, Dang NH, Reichardt E, Goring KA, King J, Grinshtein N, Hamardzumyan D, Reilly KM, Blough MD, Cairncross JG, Yong VW, Marra MA, Jones SJM, Kaplan DR, McCoy K, Holland EC, Bose P, Chan JA, Robbins SM, Senger DL. Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression. Nat Commun. 2020 Oct 5;11(1):4997. doi: 10.1038/s41467-020-18569-4.

Lavoie J-M, Mitchell T, Lee S-E, Deol B, Chia SK, Gelmon KA, Kollmannsberger CK, Tinker AV, Jones SJM, Marra M, Laskin J, Renouf DJ. Patient Selection for a Developmental Therapeutics Program Using Whole Genome and Transcriptome Analysis.  Invest New Drugs. 2020 Oct;38(5):1601-1604. doi: 10.1007/s10637-020-00892-8.

Dixon K, Young S, Shen Y, Thibodeau ML, Fok A, Pleasance E, Zhao E, Jones M, Aubert G, Armstrong L, Virani A, Regier D, Gelmon K, Renouf D, Chia S, Bosdet I, Rassekh SR, Deyell RJ, Yip S, Fisic A, Titmuss E, Abadi S, Jones SJM, Sun S, Karsan A, Marra M, Laskin J, Lim H, Schrader KA. Establishing a framework for the clinical translation of germline findings in precision oncology. JNCI Cancer Spectr. 2020 Oct;4(5):pkaa045. doi: 10.1093/jncics/pkaa045.

Bailey MH, Meyerson WU, Dursi LJ, Wang L-B, Dong G, Liang W-W, Weerasinghe A, Li S, Kelso S, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, PCAWG Consortium. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020 Sep 21;11(1):4748. doi: 10.1038/s41467-020-18151-y.

Calvente L, Tremblay-LeMay R, Xu W, Chan FC, Hong M, Zhang T, Yhim HY, Kuruvilla J, Crump M, Kukreti V, Prica A, Regier D, Marra MA, Karsan A, Steidl C, Scott DW, Sabatini P, Kridel R. Validation of the RHL30 digital gene expression assay as a prognostic biomarker for relapsed Hodgkin lymphoma. Br J Haematol. 2020 Sep;190(6):864-868. doi: 10.1111/bjh.16777.

Topham JT, Titmuss E, Pleasance ED, Williamson LM, Karasinska JM, Culibrk L, Lee MK, Mendis S, Denroche RE, Jang GH, Kalloger SE, Wong HL, Moore RA, Mungall AJ, O’Kane GM, Knox JJ, Gallinger S, Loree JM, Mager DL, Laskin J, Marra MA, Jones SJ, Schaeffer DF, Renouf DJ. Endogenous Retrovirus Transcript Levels are Associated with Immunogenic Signatures in Multiple Metastatic Cancer Types. Mol Cancer Ther. 2020 Sep;19(9):1889-1897. doi: 10.1158/1535-7163.MCT-20-0094.

Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Tumour Subtypes and Clinical Translation, Boutros PC; PCAWG Consortium. Sex differences in oncogenic mutational processes. Nat Commun. 2020 Aug 28;11(1):4330. doi: 10.1038/s41467-020-17359-2.

Gagliardi A, Porter VL, Zong Z, Bowlby R, Titmuss E, Namirembe C, Griner NB, Petrello H, Bowen J, Chan S, Culibrk L, Darragh TM, Stoler MH, Wright TC, Gesuwan P, Dyer M, Ma Y, Mungall KL, Jones S, Nakisige C, Novik K, Orem J, Origa M, Gastier-Foster JM, Yarchoan R, Casper C,Mills GB, Rader JS, Ojesina AI, Gerhard DS, Mungall AJ, Marra MA. Analysis of Ugandan cervical carcinomas reveals human papillomavirus clade-specific epigenome and transcriptome landscapes. Nat Genet.  2020 Aug;52(8):800-810. doi: 10.1038/s41588-020-0673-7.

Pleasance E, Titmuss E, Williamson L, Kwan H, Zhao EY, Dixon K, Fan K, Culibrk L, Bowlby R, Jones MR, Shen Y, Grewal JK, Ashkani J, Wee K, Grisdale CJ, Thibodeau ML, Bozoky Z, Pearson H, Majounie E, Vira T, Shenwai R, Mungall KL, Chuah E, Davies J, Warren M, Reisle C, Bonakdar M, Taylor GA, Csizmok V, Chan SK, Zong S, Bilobram S, Muhammadzadeh A, D’Souza D, Corbett RD, MacMillan D, Carreira M, Choo C, Bleile D, Sadeghi S, Zhang W, Wong T, Cheng D, Brown SD, Holt RA, Moore RA, Mungall AJ, Zhao YJ, Nelson J, Fok A, Ma Y, Lee MKC, Lavoie J-M, Mendis S,  Karasinska JM, Deol B, Fisic A, Schaeffer DF, Yip S, Schrader K, Regier DA, Weymann D, Chia S, Gelmon K, Tinker A, Sun S, Lim H, Renouf DJ, Jones SJM, Laskin J, Marra MA. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer. 2020 Apr 13: 1:452-468. (

Chun HE, Johann PD, Milne K, Zapatka M, Buellesbach A, Ishaque N, Iskar M, Erkek S, Wei L, Tessier-Cloutier B, Lever J, Titmuss E, Topham JT, Bowlby R, Chuah E, Mungall KL, Ma Y, Mungall AJ, Moore RA, Taylor MD, Gerhard DS, Jones SJM, Korshunov A, Gessler M, Kerl K, Hasselblatt M, Frühwald MC, Perlman EJ, Nelson BH, Pfister SM, Marra MA, Kool M. Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration. Cell Rep. 2019 Nov 19; 29 (8): 2338-2354.e7.

Bolouri H, Farrar JE, Triche T Jr, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med. 2019 Mar;25(3):530. doi: 10.1038/s41591-019-0369-7.

Morrissy AS, Cavalli FM, Remke M, Ramaswamy V, Shih DJ, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DT, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJ, Das S, Malkin D, Jabado N, Marra MA, Taylor MD. Spatial heterogeneity in medulloblastoma. Nat Genet. 2017 May;49(5):780-788.

Chun H-Y, Lim EL, Heravi-Moussavi A, Saberi S, Mungall KL, Bilenky M, Carles A, Tse K, Shlafman I, Zhu K, Qian JQ, Harvey D, He An, Long W, Goya R, Ng M, LeBlanc VG, Pleasance E, Thiessen N, Wong T, Chuah E, Zhao YJ, Schein JE, Gerhard DS, Taylor MD, Mungall AJ, Moore RA,  Ma Y, Jones SJM, Perlman EJ, Hirst M, Marra MA. Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways. Cancer Cell. 2016 Mar 14; 29(3): 394-406.

Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH Jr, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD. Divergent Clonal Selection Dominates Medulloblastoma at Recurrence. Nature.  2016 Jan 21;529(7586):351-357.

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao YJ, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice L, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K,  Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan S, Griffith M, Moradian A, Cheng SWG, Morin G, Watson P, Gelmon K, Chia S, Chin S-F, Curtis C, Rueda O, Pharoah P, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello J, Meyer IM, Eaves CE, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012 Apr 4;486(7403):395-399.

Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone- modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303.

Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes A,  Griffith M, Yee J, Montgomery M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao YJ, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010 Aug 9;11(8):R82.

For Dr. Marra’s up-to-date publication list, please consult the following links


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