1
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Dreval K, Hilton LK, Cruz M, Shaalan H, Ben-Neriah S, Boyle M, Collinge B, Coyle KM, Duns G, Farinha P, Grande BM, Meissner B, Pararajalingam P, Rushton CK, Slack GW, Wong J, Mungall AJ, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns. Blood 2023; 142:561-573. [PMID: 37084389 PMCID: PMC10644066 DOI: 10.1182/blood.2022018719] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/23/2023] Open
Abstract
Follicular lymphoma (FL) accounts for ∼20% of all new lymphoma cases. Increases in cytological grade are a feature of the clinical progression of this malignancy, and eventual histologic transformation (HT) to the aggressive diffuse large B-cell lymphoma (DLBCL) occurs in up to 15% of patients. Clinical or genetic features to predict the risk and timing of HT have not been described comprehensively. In this study, we analyzed whole-genome sequencing data from 423 patients to compare the protein coding and noncoding mutation landscapes of untransformed FL, transformed FL, and de novo DLBCL. This revealed 2 genetically distinct subgroups of FL, which we have named DLBCL-like (dFL) and constrained FL (cFL). Each subgroup has distinguishing mutational patterns, aberrant somatic hypermutation rates, and biological and clinical characteristics. We implemented a machine learning-derived classification approach to stratify patients with FL into cFL and dFL subgroups based on their genomic features. Using separate validation cohorts, we demonstrate that cFL status, whether assigned with this full classifier or a single-gene approximation, is associated with a reduced rate of HT. This implies distinct biological features of cFL that constrain its evolution, and we highlight the potential for this classification to predict HT from genetic features present at diagnosis.
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Affiliation(s)
- Kostiantyn Dreval
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Laura K. Hilton
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Manuela Cruz
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Haya Shaalan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Brett Collinge
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Krysta M. Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Gerben Duns
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | | | - Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher K. Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Graham W. Slack
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Jasper Wong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | | | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Ryan D. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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2
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Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood 2023; 141:904-916. [PMID: 36201743 PMCID: PMC10023728 DOI: 10.1182/blood.2022016534] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022] Open
Abstract
Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), leaving its relationship to adult BL (aBL) and other adult lymphomas not fully explored. We sought to more thoroughly identify the somatic changes that underlie lymphomagenesis in aBL and any molecular features that associate with clinical disparities within and between pBL and aBL. Through comprehensive whole-genome sequencing of 230 BL and 295 diffuse large B-cell lymphoma (DLBCL) tumors, we identified additional significantly mutated genes, including more genetic features that associate with tumor Epstein-Barr virus status, and unraveled new distinct subgroupings within BL and DLBCL with 3 predominantly comprising BLs: DGG-BL (DDX3X, GNA13, and GNAI2), IC-BL (ID3 and CCND3), and Q53-BL (quiet TP53). Each BL subgroup is characterized by combinations of common driver and noncoding mutations caused by aberrant somatic hypermutation. The largest subgroups of BL cases, IC-BL and DGG-BL, are further characterized by distinct biological and gene expression differences. IC-BL and DGG-BL and their prototypical genetic features (ID3 and TP53) had significant associations with patient outcomes that were different among aBL and pBL cohorts. These findings highlight shared pathogenesis between aBL and pBL, and establish genetic subtypes within BL that serve to delineate tumors with distinct molecular features, providing a new framework for epidemiologic, diagnostic, and therapeutic strategies.
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Affiliation(s)
- Nicole Thomas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura K. Hilton
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Jeremy S. Abramson
- Center for Lymphoma, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Richard F. Ambinder
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stefan Barta
- University of Pennsylvania Hospital, Philadelphia, PA
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Jeffrey Bethony
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC
| | | | - Jay Bowen
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
| | - Anthony C. Bryan
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY
| | - Corey Casper
- Infectious Disease Research Institute, Seattle, WA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Manuela Cruz
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Dirk P. Dittmer
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Maureen A. Dyer
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Julie M. Gastier-Foster
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
- Departments of Pathology and Pediatrics, The Ohio State University, Columbus, OH
| | - Alina S. Gerrie
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | - Timothy Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Nicholas B. Griner
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas G. Gross
- Center for Global Health, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Nancy L. Harris
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - John D. Irvin
- Foundation for Burkitt Lymphoma Research, Geneva, Switzerland
| | - Elaine S. Jaffe
- Laboratory of Pathology, Clinical Center, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - David Henry
- University of Pennsylvania Hospital, Philadelphia, PA
| | - Rebecca Huppi
- Office of HIV/AIDS Malignancies, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Fabio E. Leal
- Programa de Oncovirologia, Instituto Nacional de Cancer Jose de Alencar, Rio de Janeiro, Brazil
| | - Michael S. Lee
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Sam M. Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Ronald Mitsuyasu
- Center for Clinical AIDS Research and Education, University of California Los Angeles, Los Angeles, CA
| | - Vivian Morris
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | | | - Mostafa Nokta
- Office of HIV/AIDS Malignancies, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Ariela Noy
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | | | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Hilary Petrello
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
| | - Stefania Pittaluga
- Laboratory of Pathology, Clinical Center, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - James D. Phelan
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Juan Carlos Ramos
- Department of Medicine, Division of Hematology, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Lee Ratner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Steven J. Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Paul G. Rubinstein
- Section of Hematology/Oncology, John H. Stroger Jr Hospital of Cook County, Chicago, IL
| | - Gerhard Sissolak
- Tygerberg Academic Hospital and Stellenbosch University, Cape Town, South Africa
| | - Graham Slack
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Shaghayegh Soudi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H. Swerdlow
- Division of Hematopathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Alexandra Traverse-Glehen
- Hospices Civils de Lyon, Université Lyon 1, Service d'Anatomie Pathologique, Hopital Lyon Sud France
| | - Wyndham H. Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jasper Wong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Robert Yarchoan
- Office of HIV/AIDS Malignancies, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jean C. ZenKlusen
- The Cancer Genome Atlas, Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Louis M. Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Ryan D. Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
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3
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Jiang A, Hilton LK, Tang J, Rushton CK, Grande BM, Scott DW, Morin RD. PRPS-ST: A protocol-agnostic self-training method for gene expression-based classification of blood cancers. Blood Cancer Discov 2020; 1:244-257. [PMID: 33392514 DOI: 10.1158/2643-3230.bcd-20-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gene expression classifiers are gaining increasing popularity for stratifying tumors into subgroups with distinct biological features. A fundamental limitation shared by current classifiers is the requirement for comparable training and testing data sets. Here, we describe a self-training implementation of our probability ratio-based classification prediction score method (PRPS-ST), which facilitates the porting of existing classification models to other gene expression data sets. In comparison to gold standards, we demonstrate favorable performance of PRPS-ST in gene expression-based classification of DLBCL and B-ALL using a diverse variety of gene expression data types and pre-processing methods, including in classifications with a high degree of class imbalance. Tumors classified by our method were significantly enriched for prototypical genetic features of their respective subgroups. Interestingly, this included cases that were unclassifiable by established methods, implying the potential enhanced sensitivity of PRPS-ST.
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Affiliation(s)
- Aixiang Jiang
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Laura K Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Jeffrey Tang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
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4
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Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood 2020; 136:572-584. [PMID: 32160292 PMCID: PMC7440974 DOI: 10.1182/blood.2019002385] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/20/2020] [Indexed: 12/11/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established, and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we resequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent noncoding mutations surrounding a single exon of the HNRNPH1gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent noncoding mutations in disrupting an autoregulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly imply a role for aberrant regulation of messenger RNA processing in MCL pathobiology.
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Affiliation(s)
- Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nicole Thomas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Barbara Meissner
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Merrill Boyle
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Quratulain Qureshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Graham W Slack
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - Constantine S Tam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Rishu Agarwal
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Randy D Gascoyne
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Christian Steidl
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Joseph Connors
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Diego Villa
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Marra
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - David W Scott
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
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5
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Webster TH, Couse M, Grande BM, Karlins E, Phung TN, Richmond PA, Whitford W, Wilson MA. Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data. Gigascience 2020; 8:5530326. [PMID: 31289836 PMCID: PMC6615978 DOI: 10.1093/gigascience/giz074] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/04/2018] [Accepted: 06/03/2019] [Indexed: 11/25/2022] Open
Abstract
Background Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. Similar sequence content can confound the mapping of short next-generation sequencing reads to a reference genome. It is therefore possible that the presence of both sex chromosomes in a reference genome can cause technical artifacts in genomic data and affect downstream analyses and applications. Understanding this problem is critical for medical genomics and population genomic inference. Results Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We find that sequence homology affects read mapping on the sex chromosomes and this has downstream effects on variant calling. However, we show that XYalign can correct mismapping, resulting in more accurate variant calling. We also show how metrics output by XYalign can be used to identify XX and XY individuals across diverse sequencing experiments, including low- and high-coverage whole-genome sequencing, and exome sequencing. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other uses including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3). Conclusions Sex chromsome sequence homology causes the mismapping of short reads, which in turn affects downstream analyses. XYalign provides a reproducible framework to correct mismapping and improve variant calling on the sex chromsomes.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Department of Anthropology, University of Utah, 260 S Central Drive, Carolyn and Kem Gardner Commons, Suite 4625, Salt Lake City, UT 84112, USA
| | - Madeline Couse
- University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.,BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, MSC 9776, Bethesda, MD 20892, USA
| | - Tanya N Phung
- Interdepartmental Program in Bioinformatics, UCLA, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Phillip A Richmond
- BC Children's Hospital Research Institute, 950 W 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V52 4H4, Canada
| | - Whitney Whitford
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.,Centre for Brain Research, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85281, USA.,Center for Evolution and Medicine, Arizona State University, 401 E. Tyler Mall, Tempe, AZ 85287, USA
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6
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Haile S, Corbett RD, Bilobram S, Mungall K, Grande BM, Kirk H, Pandoh P, MacLeod T, McDonald H, Bala M, Coope RJ, Moore RA, Mungall AJ, Zhao Y, Morin RD, Jones SJ, Marra MA. Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA. PLoS One 2019; 14:e0224578. [PMID: 31671154 PMCID: PMC6822755 DOI: 10.1371/journal.pone.0224578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 12/19/2022] Open
Abstract
Next generation RNA-sequencing (RNA-seq) is a flexible approach that can be applied to a range of applications including global quantification of transcript expression, the characterization of RNA structure such as splicing patterns and profiling of expressed mutations. Many RNA-seq protocols require up to microgram levels of total RNA input amounts to generate high quality data, and thus remain impractical for the limited starting material amounts typically obtained from rare cell populations, such as those from early developmental stages or from laser micro-dissected clinical samples. Here, we present an assessment of the contemporary ribosomal RNA depletion-based protocols, and identify those that are suitable for inputs as low as 1–10 ng of intact total RNA and 100–500 ng of partially degraded RNA from formalin-fixed paraffin-embedded tissues.
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Affiliation(s)
- Simon Haile
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard D. Corbett
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Steve Bilobram
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Karen Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Bruno M. Grande
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Tina MacLeod
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Helen McDonald
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Miruna Bala
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Robin J. Coope
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard A. Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Steven J. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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7
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Khakabimamaghani S, Kelkar YD, Grande BM, Morin RD, Ester M, Ziemek D. SUBSTRA: Supervised Bayesian Patient Stratification. Bioinformatics 2019; 35:3263-3272. [DOI: 10.1093/bioinformatics/btz112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Motivation
Patient stratification methods are key to the vision of precision medicine. Here, we consider transcriptional data to segment the patient population into subsets relevant to a given phenotype. Whereas most existing patient stratification methods focus either on predictive performance or interpretable features, we developed a method striking a balance between these two important goals.
Results
We introduce a Bayesian method called SUBSTRA that uses regularized biclustering to identify patient subtypes and interpretable subtype-specific transcript clusters. The method iteratively re-weights feature importance to optimize phenotype prediction performance by producing more phenotype-relevant patient subtypes. We investigate the performance of SUBSTRA in finding relevant features using simulated data and successfully benchmark it against state-of-the-art unsupervised stratification methods and supervised alternatives. Moreover, SUBSTRA achieves predictive performance competitive with the supervised benchmark methods and provides interpretable transcriptional features in diverse biological settings, such as drug response prediction, cancer diagnosis, or kidney transplant rejection.
Availability and implementation
The R code of SUBSTRA is available at https://github.com/sahandk/SUBSTRA.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Yogeshwar D Kelkar
- Computational Systems Immunology, Pfizer Worldwide R&D, Cambridge, MA, USA
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ryan D Morin
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Martin Ester
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel Ziemek
- Computational Systems Immunology, Pfizer Worldwide R&D, Berlin, Germany
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8
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Negri GL, Grande BM, Delaidelli A, El-Naggar A, Cochrane D, Lau CC, Triche TJ, Moore RA, Jones SJ, Montpetit A, Marra MA, Malkin D, Morin RD, Sorensen PH. Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma. J Pathol 2019; 249:319-331. [PMID: 31236944 DOI: 10.1002/path.5319] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/23/2019] [Accepted: 06/20/2019] [Indexed: 01/14/2023]
Abstract
Despite being the most common childhood bone tumor, the genomic characterization of osteosarcoma remains incomplete. In particular, very few osteosarcoma metastases have been sequenced to date, critical to better understand mechanisms of progression and evolution in this tumor. We performed an integrated whole genome and exome sequencing analysis of paired primary and metastatic pediatric osteosarcoma specimens to identify recurrent genomic alterations. Sequencing of 13 osteosarcoma patients including 13 primary, 10 metastatic, and 3 locally recurring tumors revealed a highly heterogeneous mutational landscape, including cases of hypermutation and microsatellite instability positivity, but with virtually no recurrent alterations except for mutations involving the tumor suppressor genes RB1 and TP53. At the germline level, we detected alterations in multiple cancer related genes in the majority of the cohort, including those potentially disrupting DNA damage response pathways. Metastases retained only a minimal number of short variants from their corresponding primary tumors, while copy number alterations showed higher conservation. One recurrently amplified gene, KDR, was highly expressed in advanced cases and associated with poor prognosis. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Amal El-Naggar
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Shebeen El-Kom, Egypt
| | - Dawn Cochrane
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Ching C Lau
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Timothy J Triche
- Department of Pathology and Laboratory Medicine, Childrens Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Alexandre Montpetit
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - David Malkin
- Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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9
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Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood 2019; 133:1313-1324. [PMID: 30617194 PMCID: PMC6428665 DOI: 10.1182/blood-2018-09-871418] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022] Open
Abstract
Although generally curable with intensive chemotherapy in resource-rich settings, Burkitt lymphoma (BL) remains a deadly disease in older patients and in sub-Saharan Africa. Epstein-Barr virus (EBV) positivity is a feature in more than 90% of cases in malaria-endemic regions, and up to 30% elsewhere. However, the molecular features of BL have not been comprehensively evaluated when taking into account tumor EBV status or geographic origin. Through an integrative analysis of whole-genome and transcriptome data, we show a striking genome-wide increase in aberrant somatic hypermutation in EBV-positive tumors, supporting a link between EBV and activation-induced cytidine deaminase (AICDA) activity. In addition to identifying novel candidate BL genes such as SIN3A, USP7, and CHD8, we demonstrate that EBV-positive tumors had significantly fewer driver mutations, especially among genes with roles in apoptosis. We also found immunoglobulin variable region genes that were disproportionally used to encode clonal B-cell receptors (BCRs) in the tumors. These include IGHV4-34, known to produce autoreactive antibodies, and IGKV3-20, a feature described in other B-cell malignancies but not yet in BL. Our results suggest that tumor EBV status defines a specific BL phenotype irrespective of geographic origin, with particular molecular properties and distinct pathogenic mechanisms. The novel mutation patterns identified here imply rational use of DNA-damaging chemotherapy in some patients with BL and targeted agents such as the CDK4/6 inhibitor palbociclib in others, whereas the importance of BCR signaling in BL strengthens the potential benefit of inhibitors for PI3K, Syk, and Src family kinases among these patients.
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Affiliation(s)
- Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Aixiang Jiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas B Griner
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jeremy S Abramson
- Center for Lymphoma, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH
| | | | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH
| | - Corey Casper
- Infectious Disease Research Institute, Seattle, WA
| | - John Kim Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Tanja M Davidsen
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Maureen A Dyer
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Columbus, OH
- Departments of Pathology and Pediatrics, The Ohio State University, Columbus, OH
| | - Patee Gesuwan
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Thomas G Gross
- Center for Global Health, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Nancy Lee Harris
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Yiwen He
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - John D Irvin
- Foundation for Burkitt Lymphoma Research, Geneva, Switzerland
| | - Elaine S Jaffe
- Laboratory of Pathology, Clinical Center, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steven J M Jones
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Nicole Knoetze
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Fabio E Leal
- Programa de Oncovirologia, Instituto Nacional de Câncer José de Alencar, Rio de Janeiro, Brazil
| | | | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | | | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Karen Novik
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ariela Noy
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | | | | | | | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD; and
| | - Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - John T Sandlund
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Roland Schmitz
- Lymphoid Malignancies Branch, Center for Cancer Research and
| | | | | | - George W Wright
- Biometric Research Program, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research and
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10
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Ennishi D, Jiang A, Boyle M, Collinge B, Grande BM, Ben-Neriah S, Rushton C, Tang J, Thomas N, Slack GW, Farinha P, Takata K, Miyata-Takata T, Craig J, Mottok A, Meissner B, Saberi S, Bashashati A, Villa D, Savage KJ, Sehn LH, Kridel R, Mungall AJ, Marra MA, Shah SP, Steidl C, Connors JM, Gascoyne RD, Morin RD, Scott DW. Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma. J Clin Oncol 2018; 37:190-201. [PMID: 30523716 DOI: 10.1200/jco.18.01583] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PURPOSE High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) has a poor outcome after standard chemoimmunotherapy. We sought to understand the biologic underpinnings of HGBL-DH/TH with BCL2 rearrangements (HGBL-DH/TH- BCL2) and diffuse large B-cell lymphoma (DLBCL) morphology through examination of gene expression. PATIENTS AND METHODS We analyzed RNA sequencing data from 157 de novo germinal center B-cell-like (GCB)-DLBCLs, including 25 with HGBL-DH/TH- BCL2, to define a gene expression signature that distinguishes HGBL-DH/TH- BCL2 from other GCB-DLBCLs. To assess the genetic, molecular, and phenotypic features associated with this signature, we analyzed targeted resequencing, whole-exome sequencing, RNA sequencing, and immunohistochemistry data. RESULTS We developed a 104-gene double-hit signature (DHITsig) that assigned 27% of GCB-DLBCLs to the DHITsig-positive group, with only one half harboring MYC and BCL2 rearrangements (HGBL-DH/TH- BCL2). DHITsig-positive patients had inferior outcomes after rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone immunochemotherapy compared with DHITsig-negative patients (5-year time to progression rate, 57% and 81%, respectively; P < .001), irrespective of HGBL-DH/TH- BCL2 status. The prognostic value of DHITsig was confirmed in an independent validation cohort. DHITsig-positive tumors are biologically characterized by a putative non-light zone germinal center cell of origin and a distinct mutational landscape that comprises genes associated with chromatin modification. A new NanoString assay (DLBCL90) recapitulated the prognostic significance and RNA sequencing assignments. Validating the association with HGBL-DH/TH- BCL2, 11 of 25 DHITsig-positive-transformed follicular lymphomas were classified as HGBL-DH/TH- BCL2 compared with zero of 50 in the DHITsig-negative group. Furthermore, the DHITsig was shared with the majority of B-cell lymphomas with high-grade morphology tested. CONCLUSION We have defined a clinically and biologically distinct subgroup of tumors within GCB-DLBCL characterized by a gene expression signature of HGBL-DH/TH- BCL2. This knowledge has been translated into an assay applicable to routinely available biopsy samples, which enables exploration of its utility to guide patient management.
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Affiliation(s)
- Daisuke Ennishi
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Aixiang Jiang
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada.,2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Merrill Boyle
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Brett Collinge
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Bruno M Grande
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Susana Ben-Neriah
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | | | - Jeffrey Tang
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Nicole Thomas
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Graham W Slack
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Pedro Farinha
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Katsuyoshi Takata
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Tomoko Miyata-Takata
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Jeffrey Craig
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Anja Mottok
- 3 Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Barbara Meissner
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- 4 Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ali Bashashati
- 4 Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Diego Villa
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Kerry J Savage
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Laurie H Sehn
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Robert Kridel
- 5 Princess Margaret Cancer Center-University Health Network, Toronto, Ontario, Canada
| | - Andrew J Mungall
- 6 Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- 6 Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- 4 Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Christian Steidl
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Joseph M Connors
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Randy D Gascoyne
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - David W Scott
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
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11
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Wong HL, Zhao EY, Jones MR, Reisle CR, Eirew P, Pleasance E, Grande BM, Karasinska JM, Kalloger SE, Lim HJ, Shen Y, Yip S, Morin RD, Laskin J, Marra MA, Jones SJ, Schrader KA, Schaeffer DF, Renouf DJ. Temporal Dynamics of Genomic Alterations in a BRCA1 Germline-Mutated Pancreatic Cancer With Low Genomic Instability Burden but Exceptional Response to Fluorouracil, Oxaliplatin, Leucovorin, and Irinotecan. JCO Precis Oncol 2018; 2:PO.18.00057. [PMID: 32913994 PMCID: PMC7446469 DOI: 10.1200/po.18.00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Hui-li Wong
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Eric Y. Zhao
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Martin R. Jones
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Caralyn R. Reisle
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Bruno M. Grande
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Joanna M. Karasinska
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steve E. Kalloger
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Howard J. Lim
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J.M. Jones
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Kasmintan A. Schrader
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - David F. Schaeffer
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Daniel J. Renouf
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
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12
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Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP. Kronos: a workflow assembler for genome analytics and informatics. Gigascience 2018; 6:1-10. [PMID: 28655203 PMCID: PMC5569921 DOI: 10.1093/gigascience/gix042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/07/2017] [Indexed: 11/25/2022] Open
Abstract
Background: The field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into “best practices” for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise. Results: We present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows. Conclusions: The Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos.
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Affiliation(s)
- M Jafar Taghiyar
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Jamie Rosner
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada
| | - Diljot Grewal
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, BC, Canada
| | - Radhouane Aniba
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Jasleen Grewal
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, BC, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research (OICR), 661 University Avenue, M5G 0A3 Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, M5G 1L7 Toronto, ON, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, BC, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
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13
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Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience 2018; 6:1-13. [PMID: 28327945 PMCID: PMC5437943 DOI: 10.1093/gigascience/gix015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/06/2017] [Indexed: 01/15/2023] Open
Abstract
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker.
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Affiliation(s)
- Marco A Albuquerque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Elie J Ritch
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Selin Jessa
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
| | - Jasleen K Grewal
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sohrab P Shah
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
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14
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Wever CM, Geoffrion D, Grande BM, Yu S, Alcaide M, Lemaire M, Riazalhosseini Y, Hébert J, Gavino C, Vinh DC, Petrogiannis-Haliotis T, Dmitrienko S, Mann KK, Morin RD, Johnson NA. The genomic landscape of two Burkitt lymphoma cases and derived cell lines: comparison between primary and relapse samples. Leuk Lymphoma 2018; 59:2159-2174. [PMID: 29295643 DOI: 10.1080/10428194.2017.1413186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Relapse occurs in 10-40% of Burkitt lymphoma (BL) patients that have completed intensive chemotherapy regimens and is typically fatal. While treatment-naive BL has been characterized, the genomic landscape of BL at the time of relapse (rBL) has never been reported. Here, we present a genomic characterization of two rBL patients. The diagnostic samples had mutations common in BL, including MYC and CCND3. Additional mutations were detected at relapse, affecting important pathways such as NFκB (IKBKB) and MEK/ERK (NRAS) signaling, glutamine metabolism (SIRT4), and RNA processing (ZFP36L2). Genes implicated in drug resistance were also mutated at relapse (TP53, BAX, ALDH3A1, APAF1, FANCI). This concurrent genomic profiling of samples obtained at diagnosis and relapse has revealed mutations not previously reported in this disease. The patient-derived cell lines will be made available and, along with their detailed genetics, will be a valuable resource to examine the role of specific mutations in therapeutic resistance.
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Affiliation(s)
- Claudia M Wever
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | | | - Bruno M Grande
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Stephen Yu
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Miguel Alcaide
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Maryse Lemaire
- b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Yasser Riazalhosseini
- e Department of Human Genetics , McGill University , Montreal , Canada.,f McGill University and Genome Quebec Innovation Centre , Montreal , Canada
| | - Josée Hébert
- g Department of Medicine, Faculty of Medicine , Université de Montréal , Montreal , Canada.,h Research Centre and Division of Hematology-Oncology Maisonneuve-Rosemont Hospital , The Québec Leukemia Cell Bank , Montreal , Canada
| | - Christina Gavino
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | - Donald C Vinh
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | | | | | - Koren K Mann
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Ryan D Morin
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Nathalie A Johnson
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
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15
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Alcaide M, Yu S, Davidson J, Albuquerque M, Bushell K, Fornika D, Arthur S, Grande BM, McNamara S, Tertre MCD, Batist G, Huntsman DG, Cavallone L, Aguilar A, Basik M, Johnson NA, Deyell RJ, Rassekh SR, Morin RD. Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits. Sci Rep 2017; 7:10574. [PMID: 28874686 PMCID: PMC5585219 DOI: 10.1038/s41598-017-10269-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Abstract
Ultrasensitive methods for rare allele detection are critical to leverage the full potential offered by liquid biopsies. Here, we describe a novel molecular barcoding method for the precise detection and quantification of circulating tumor DNA (ctDNA). The major benefits of our design include straightforward and cost-effective production of barcoded adapters to tag individual DNA molecules before PCR and sequencing, and better control over cross-contamination between experiments. We validated our approach in a cohort of 24 patients with a broad spectrum of cancer diagnoses by targeting and quantifying single-nucleotide variants (SNVs), indels and genomic rearrangements in plasma samples. By using personalized panels targeting a priori known mutations, we demonstrate comprehensive error-suppression capabilities for SNVs and detection thresholds for ctDNA below 0.1%. We also show that our semi-degenerate barcoded adapters hold promise for noninvasive genotyping in the absence of tumor biopsies and monitoring of minimal residual disease in longitudinal plasma samples. The benefits demonstrated here include broad applicability, flexibility, affordability and reproducibility in the research and clinical settings.
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Affiliation(s)
- Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Stephen Yu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Jordan Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco Albuquerque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kevin Bushell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel Fornika
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Suzan McNamara
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - Mathilde Couetoux du Tertre
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - Gerald Batist
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine and Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Luca Cavallone
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Adriana Aguilar
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark Basik
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nathalie A Johnson
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Rebecca J Deyell
- Division of Oncology, Hematology and Bone Marrow Transplant, British Columbia Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - S Rod Rassekh
- Division of Oncology, Hematology and Bone Marrow Transplant, British Columbia Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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16
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Morin RD, Assouline S, Alcaide M, Mohajeri A, Johnston RL, Chong L, Grewal J, Yu S, Fornika D, Bushell K, Nielsen TH, Petrogiannis-Haliotis T, Crump M, Tosikyan A, Grande BM, MacDonald D, Rousseau C, Bayat M, Sesques P, Froment R, Albuquerque M, Monczak Y, Oros KK, Greenwood C, Riazalhosseini Y, Arseneault M, Camlioglu E, Constantin A, Pan-Hammarstrom Q, Peng R, Mann KK, Johnson NA. Genetic Landscapes of Relapsed and Refractory Diffuse Large B-Cell Lymphomas. Clin Cancer Res 2016; 22:2290-300. [PMID: 26647218 DOI: 10.1158/1078-0432.ccr-15-2123] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 11/17/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Relapsed or refractory diffuse large B-cell lymphoma (rrDLBCL) is fatal in 90% of patients, and yet little is known about its biology. EXPERIMENTAL DESIGN Using exome sequencing, we characterized the mutation profiles of 38 rrDLBCL biopsies obtained at the time of progression after immunochemotherapy. To identify genes that may be associated with relapse, we compared the mutation frequency in samples obtained at relapse to an unrelated cohort of 138 diagnostic DLBCLs and separately amplified specific mutations in their matched diagnostic samples to identify clonal expansions. RESULTS On the basis of a higher frequency at relapse and evidence for clonal selection, TP53, FOXO1, MLL3 (KMT2C), CCND3, NFKBIZ, and STAT6 emerged as top candidate genes implicated in therapeutic resistance. We observed individual examples of clonal expansions affecting genes whose mutations had not been previously associated with DLBCL including two regulators of NF-κB: NFKBIE and NFKBIZ We detected mutations that may be affect sensitivity to novel therapeutics, such as MYD88 and CD79B mutations, in 31% and 23% of patients with activated B-cell-type of rrDLBCL, respectively. We also identified recurrent STAT6 mutations affecting D419 in 36% of patients with the germinal center B (GCB) cell rrDLBCL. These were associated with activated JAK/STAT signaling, increased phospho-STAT6 protein expression and increased expression of STAT6 target genes. CONCLUSIONS This work improves our understanding of therapeutic resistance in rrDLBCL and has identified novel therapeutic opportunities especially for the high-risk patients with GCB-type rrDLBCL. Clin Cancer Res; 22(9); 2290-300. ©2015 AACR.
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Affiliation(s)
- Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Sarit Assouline
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada. McGill University, Montreal, Quebec, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Arezoo Mohajeri
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Lauren Chong
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Jasleen Grewal
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Stephen Yu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Daniel Fornika
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kevin Bushell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Torsten Holm Nielsen
- Department of Internal Medicine, Copenhagen University Hospital, Roskilde, Denmark
| | | | - Michael Crump
- Princess Margaret Hospital, Toronto, Ontario, Canada
| | | | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - David MacDonald
- Department of Medicine, University of Dalhousie, Halifax, Nova Scotia, Canada
| | - Caroline Rousseau
- Quebec Clinical Research Organization in Cancer, Montreal, Quebec, Canada
| | | | - Pierre Sesques
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Remi Froment
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Marco Albuquerque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yury Monczak
- Department of Pathology, Jewish General Hospital, Montreal, Quebec, Canada
| | | | - Celia Greenwood
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada. Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada. Department of Oncology, McGill University, Montreal, Quebec, Canada
| | | | | | - Errol Camlioglu
- Department of Radiology, Jewish General Hospital, Montreal, McGill University, Quebec, Canada
| | - André Constantin
- Department of Radiology, Jewish General Hospital, Montreal, McGill University, Quebec, Canada
| | - Qiang Pan-Hammarstrom
- Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital, Huddinge, Sweden. Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China
| | - Roujun Peng
- Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital, Huddinge, Sweden. Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China
| | - Koren K Mann
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada. McGill University, Montreal, Quebec, Canada
| | - Nathalie A Johnson
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada. McGill University, Montreal, Quebec, Canada.
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