Publications


Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management.
J Mol Diagn 2018 Feb 7. Epub 2018 Feb 7.
Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address:


MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia.
J Clin Oncol 2017 Dec 25;35(35):3964-3977. Epub 2017 Oct 25.
Emilia L. Lim, Diane L. Trinh, Yussanne Ma, James Topham, Erin Pleasance, Andrew J. Mungall, Richard Moore, Yongjun Zhao, and Marco A. Marra, Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency; Marco A. Marra, University of British Columbia, Vancouver, British Columbia; Lillian Sung, The Hospital for Sick Children, Toronto, Ontario, Canada; Rhonda E. Ries, Maya Hughes, and Soheil Meshinchi, Fred Hutchinson Cancer Research Center; Rhonda E. Ries, Maya Hughes, and Soheil Meshinchi, University of Washington, Seattle, WA; Jim Wang, Robert B. Gerbing, E. Anders Kolb, Alan Gamis, and Todd A. Alonzo, Children's Oncology Group, Monrovia; Todd A. Alonzo, University of Southern California, Los Angeles, CA; Richard Aplenc, The Children's Hospital of Philadelphia, Philadelphia, PA; Malcolm Smith and Daniela S. Gerhard, Office of Cancer Genomics, National Cancer Institute, Bethesda, MD; and Robert J. Arceci, Phoenix Children's Hospital, Phoenix. AZ.


Specific muscle strength is reduced in facioscapulohumeral dystrophy: An MRI based musculoskeletal analysis.
Neuromuscul Disord 2017 Dec 12. Epub 2017 Dec 12.
Orthopaedic Research Laboratory, Radboud Institute for Health Sciences, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands; Department of Biomechanical Engineering, University of Twente, Postbus 217, 7500 AE Enschede, The Netherlands.





Whole-genome analysis reveals unexpected dynamics of mutant subclone development in a patient with JAK2-V617F-positive chronic myeloid leukemia.
Exp Hematol 2017 Sep 8;53:48-58. Epub 2017 Jun 8.
Institut National de la Santé et de la Recherche Médicale (INSERM) U935, Villejuif, France; Service d'Hématologie Biologique, Institut Federatif d'Hematologie Interpôle Paris Sud-IFHIPS (AP-HP) Kremlin Bicêtre, Paris, France; Université Paris-Sud, Faculté de Médecine Kremlin Bicêtre, and INSERM UMS 33, Villejuif, France; Human Pluripotent Stem Cell Core Facility, ESTeam Paris Sud-INGESTEM, Villejuif, France. Electronic address:

Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma.
Cancer Cell 2017 Sep;32(3):295-309.e12
Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Colket Translational Research Building, 3501 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

Evaluation of a Surrogate Contact Model in Force-Dependent Kinematic Simulations of Total Knee Replacement.
J Biomech Eng 2017 Aug;139(8)
Orthopaedic Research Laboratory, Radboud Institute for Health Sciences, Radboud University Medical Center, P. O. Box 9101, Nijmegen 6500 HB, The Netherlands;Department of Biomechanical Engineering, University of Twente, P. O. Box 217, Enschede 7500 AE, The Netherlands e-mail:





Anterior referencing of tibial slope in total knee arthroplasty considerably influences knee kinematics: a musculoskeletal simulation study.
Knee Surg Sports Traumatol Arthrosc 2017 May 12. Epub 2017 May 12.
Orthopaedic Research Laboratory, Radboud Institute for Health Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.




ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis.
Cell Stem Cell 2016 Aug 9;19(2):177-191. Epub 2016 Jun 9.
Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells.
Clin Cancer Res 2016 May 2;22(9):2226-36. Epub 2015 Dec 2.
Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada. Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.



Tracking of Normal and Malignant Progenitor Cell Cycle Transit in a Defined Niche.
Sci Rep 2016 Apr 4;6:23885. Epub 2016 Apr 4.
Divisions of Regenerative Medicine and Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA.



Putative BRAF activating fusion in a medullary thyroid cancer.
Cold Spring Harb Mol Case Stud 2016 Mar;2(2):a000729
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada;; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.
N Engl J Med 2016 Jan 4;374(2):135-45. Epub 2015 Nov 4.

Divergent clonal selection dominates medulloblastoma at recurrence.
Nature 2016 Jan 13;529(7586):351-7. Epub 2016 Jan 13.
Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.

SOX9 modulates the expression of key transcription factors required for heart valve development.
Development 2015 Dec 2;142(24):4340-50. Epub 2015 Nov 2.
Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Program in Cell and Developmental Biology, University of British Columbia, Vancouver, Canada V6T 1Z4 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4

Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal.
Proc Natl Acad Sci U S A 2015 Dec 30;112(50):15444-9. Epub 2015 Nov 30.
Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820;


Cell of origin of transformed follicular lymphoma.
Blood 2015 Oct 25;126(18):2118-27. Epub 2015 Aug 25.
Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, and.

Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers.
Cold Spring Harb Mol Case Stud 2015 Oct;1(1):a000570
British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada;; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.

Integrative genomic analysis of ghost cell odontogenic carcinoma.
Oral Oncol 2015 Sep 11;51(9):e71-5. Epub 2015 Jul 11.
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.

MEF2B mutations in non-Hodgkin lymphoma dysregulate cell migration by decreasing MEF2B target gene activation.
Nat Commun 2015 Aug 6;6:7953. Epub 2015 Aug 6.
1] Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3 [2] Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z3.

Precursor States of Brain Tumor Initiating Cell Lines Are Predictive of Survival in Xenografts and Associated with Glioblastoma Subtypes.
Stem Cell Reports 2015 Jul 18;5(1):1-9. Epub 2015 Jun 18.
Hotchkiss Brain Institute, Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB T2N 4N1, Canada; Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada. Electronic address:

Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.
BMC Genomics 2015 Jul 24;16:545. Epub 2015 Jul 24.
Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.



Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
N Engl J Med 2015 Jun 10;372(26):2481-98. Epub 2015 Jun 10.

MEN1 mutations in Hürthle cell (oncocytic) thyroid carcinoma.
J Clin Endocrinol Metab 2015 Apr 27;100(4):E611-5. Epub 2015 Jan 27.
Canada's Michael Smith Genome Sciences Centre (K.K., K.L.M., T.Z., K.T., J.E.S., A.J.M., R.A.M., M.A.M., S.J.M.J.), BC Cancer Agency, Vancouver, V5Z 4S6 Canada; Department of Otorhinolaryngology-Head and Neck Surgery (A.-M.C., J.D.C.), Mayo Clinic, Jacksonville, Florida 32224; Department of Surgery (S.M.W.), St. Paul's Hospital and University of British Columbia, Vancouver, V6Z 1Y6 Canada; Department of Laboratory Medicine and Pathology (M.R.), Mayo Clinic, Rochester, Minnesota 55905; Department of Cancer Biology (B.M.N., J.M.K., J.A.C., E.A.T., R.C.S.), Mayo Clinic, Jacksonville, Florida 32224; Department of Medical Genetics (M.A.M., S.J.M.J.), University of British Columbia, Vancouver, V6T 1Z4 Canada; Department of Medicine, Division of Endocrinology and Metabolism (R.C.S.), Mayo Clinic, Jacksonville, Florida 32224; and Department of Molecular Biology and Biochemistry (S.J.M.J.), Simon Fraser University, Burnaby, V5A 1S6 Canada.

The Drosophila TIPE family member Sigmar interacts with the Ste20-like kinase Misshapen and modulates JNK signaling, cytoskeletal remodeling and autophagy.
Biol Open 2015 Apr 2;4(5):672-84. Epub 2015 Apr 2.
The Genome Sciences Centre, BC Cancer Agency, 675 West 10 Avenue, Vancouver, BC V5Z 1L3, Canada Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada



Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.
Nature 2015 Feb 26;518(7539):422-6. Epub 2014 Nov 26.
1] Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada [3] Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada [4] Centre for Translational and Applied Genomics, BC Cancer Agency, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada.



Intermediate DNA methylation is a conserved signature of genome regulation.
Nat Commun 2015 Feb 18;6:6363. Epub 2015 Feb 18.
Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94115, USA.

Integrative analysis of 111 reference human epigenomes.
Nature 2015 Feb;518(7539):317-30
1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.
Genome Res 2014 Nov 24;24(11):1881-93. Epub 2014 Jul 24.
Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada;

Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.
Nat Commun 2014 Nov 25;5:5442. Epub 2014 Nov 25.
Department of Dermatology, University of California, San Francisco, San Francisco, California 94143, USA.

Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation.
Cell Rep 2014 Oct 25;9(1):261-71. Epub 2014 Sep 25.
Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z4H4, Canada. Electronic address:

Mutations in CIC and IDH1 cooperatively regulate 2-hydroxyglutarate levels and cell clonogenicity.
Oncotarget 2014 Sep;5(17):7960-79
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada. Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.


Quiescent sox2(+) cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma.
Cancer Cell 2014 Jul 19;26(1):33-47. Epub 2014 Jun 19.
Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery, Hospital for Sick Children (HSC), Toronto, ON M5G 1L7, Canada; Program in Developmental and Stem Cell Biology, HSC, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address:


Diagnostic value of next-generation sequencing in an unusual sphenoid tumor.
Oncologist 2014 Jun 7;19(6):623-30. Epub 2014 May 7.
Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada


Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma.
Nat Genet 2014 Apr 16;46(4):329-35. Epub 2014 Feb 16.
1] Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada. [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.


A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations.
J Mol Diagn 2013 Nov 4;15(6):796-809. Epub 2013 Oct 4.
Cancer Genetics Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.



Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.
Genome Res 2013 Sep 26;23(9):1541-53. Epub 2013 Jun 26.
Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA.



Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.
N Engl J Med 2013 05 1;368(22):2059-74. Epub 2013 May 1.




Comprehensive characterization of programmed death ligand structural rearrangements in B-cell non-Hodgkin lymphomas.
Blood 2016 09 7;128(9):1206-13. Epub 2016 Jun 7.
Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada;







The whole-genome landscape of medulloblastoma subtypes.
Nature 2017 07;547(7663):311-317
Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

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