1
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Eralp B, Sefer E. Reference-free inferring of transcriptomic events in cancer cells on single-cell data. BMC Cancer 2024; 24:607. [PMID: 38769480 PMCID: PMC11107047 DOI: 10.1186/s12885-024-12331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Cancerous cells' identity is determined via a mixture of multiple factors such as genomic variations, epigenetics, and the regulatory variations that are involved in transcription. The differences in transcriptome expression as well as abnormal structures in peptides determine phenotypical differences. Thus, bulk RNA-seq and more recent single-cell RNA-seq data (scRNA-seq) are important to identify pathogenic differences. In this case, we rely on k-mer decomposition of sequences to identify pathogenic variations in detail which does not need a reference, so it outperforms more traditional Next-Generation Sequencing (NGS) analysis techniques depending on the alignment of the sequences to a reference. RESULTS Via our alignment-free analysis, over esophageal and glioblastoma cancer patients, high-frequency variations over multiple different locations (repeats, intergenic regions, exons, introns) as well as multiple different forms (fusion, polyadenylation, splicing, etc.) could be discovered. Additionally, we have analyzed the importance of less-focused events systematically in a classic transcriptome analysis pipeline where these events are considered as indicators for tumor prognosis, tumor prediction, tumor neoantigen inference, as well as their connection with respect to the immune microenvironment. CONCLUSIONS Our results suggest that esophageal cancer (ESCA) and glioblastoma processes can be explained via pathogenic microbial RNA, repeated sequences, novel splicing variants, and long intergenic non-coding RNAs (lincRNAs). We expect our application of reference-free process and analysis to be helpful in tumor and normal samples differential scRNA-seq analysis, which in turn offers a more comprehensive scheme for major cancer-associated events.
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Affiliation(s)
- Batuhan Eralp
- Department of Computer Science, Ozyegin University, Istanbul, Turkey
| | - Emre Sefer
- Department of Computer Science, Ozyegin University, Istanbul, Turkey.
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2
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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3
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Cmero M, Schmidt B, Majewski IJ, Ekert PG, Oshlack A, Davidson NM. MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data. Genome Biol 2021; 22:296. [PMID: 34686194 PMCID: PMC8532352 DOI: 10.1186/s13059-021-02507-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting > 85% of variants while no other method is able to achieve this. We posit that MINTIE will be able to identify new disease variants across a range of disease types.
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Affiliation(s)
- Marek Cmero
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Parkville, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Breon Schmidt
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Parkville, Australia.,School of BioSciences, University of Melbourne, Parkville, Australia
| | - Ian J Majewski
- Walter and Eliza Hall Institute, Parkville, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Paul G Ekert
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Parkville, Australia.,Children's Cancer Institute, UNSW, Sydney, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Alicia Oshlack
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia. .,School of BioSciences, University of Melbourne, Parkville, Australia.
| | - Nadia M Davidson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, Australia. .,School of BioSciences, University of Melbourne, Parkville, Australia.
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4
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Docking TR, Parker JDK, Jädersten M, Duns G, Chang L, Jiang J, Pilsworth JA, Swanson LA, Chan SK, Chiu R, Nip KM, Mar S, Mo A, Wang X, Martinez-Høyer S, Stubbins RJ, Mungall KL, Mungall AJ, Moore RA, Jones SJM, Birol İ, Marra MA, Hogge D, Karsan A. A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. Nat Commun 2021; 12:2474. [PMID: 33931648 PMCID: PMC8087683 DOI: 10.1038/s41467-021-22625-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/17/2021] [Indexed: 02/08/2023] Open
Abstract
As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we develop and validate a clinical transcriptome-based assay for stratification of acute myeloid leukemia (AML). Comparison of ribonucleic acid sequencing (RNA-Seq) to whole genome and exome sequencing reveals that a standalone RNA-Seq assay offers the greatest diagnostic return, enabling identification of expressed gene fusions, single nucleotide and short insertion/deletion variants, and whole-transcriptome expression information. Expression data from 154 AML patients are used to develop a novel AML prognostic score, which is strongly associated with patient outcomes across 620 patients from three independent cohorts, and 42 patients from a prospective cohort. When combined with molecular risk guidelines, the risk score allows for the re-stratification of 22.1 to 25.3% of AML patients from three independent cohorts into correct risk groups. Within the adverse-risk subgroup, we identify a subset of patients characterized by dysregulated integrin signaling and RUNX1 or TP53 mutation. We show that these patients may benefit from therapy with inhibitors of focal adhesion kinase, encoded by PTK2, demonstrating additional utility of transcriptome-based testing for therapy selection in myeloid malignancy.
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Affiliation(s)
- T Roderick Docking
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jeremy D K Parker
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Martin Jädersten
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Gerben Duns
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Linda Chang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jihong Jiang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jessica A Pilsworth
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Lucas A Swanson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Simon K Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Samantha Mar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Angela Mo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Xuan Wang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Ryan J Stubbins
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - İnanç Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Donna Hogge
- Leukemia Bone Marrow Transplant Program of BC, Vancouver General Hospital, Vancouver, BC, Canada
| | - Aly Karsan
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, BC, Canada. .,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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5
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Chiu R, Nip KM, Birol I. Fusion-Bloom: fusion detection in assembled transcriptomes. Bioinformatics 2020; 36:2256-2257. [PMID: 31790154 PMCID: PMC7141844 DOI: 10.1093/bioinformatics/btz902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/13/2019] [Accepted: 11/27/2019] [Indexed: 11/13/2022] Open
Abstract
Summary Presence or absence of gene fusions is one of the most important diagnostic markers in many cancer types. Consequently, fusion detection methods using various genomics data types, such as RNA sequencing (RNA-seq) are valuable tools for research and clinical applications. While information-rich RNA-seq data have proven to be instrumental in discovery of a number of hallmark fusion events, bioinformatics tools to detect fusions still have room for improvement. Here, we present Fusion-Bloom, a fusion detection method that leverages recent developments in de novo transcriptome assembly and assembly-based structural variant calling technologies (RNA-Bloom and PAVFinder, respectively). We benchmarked Fusion-Bloom against the performance of five other state-of-the-art fusion detection tools using multiple datasets. Overall, we observed Fusion-Bloom to display a good balance between detection sensitivity and specificity. We expect the tool to find applications in translational research and clinical genomics pipelines. Availability and implementation Fusion-Bloom is implemented as a UNIX Make utility, available at https://github.com/bcgsc/pavfinder and released under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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6
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Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters. Proc Natl Acad Sci U S A 2020; 117:16961-16968. [PMID: 32641514 PMCID: PMC7382288 DOI: 10.1073/pnas.1903436117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alignment-free classification tools have enabled high-throughput processing of sequencing data in many bioinformatics analysis pipelines primarily due to their computational efficiency. Originally k-mer based, such tools often lack sensitivity when faced with sequencing errors and polymorphisms. In response, some tools have been augmented with spaced seeds, which are capable of tolerating mismatches. However, spaced seeds have seen little practical use in classification because they bring increased computational and memory costs compared to methods that use k-mers. These limitations have also caused the design and length of practical spaced seeds to be constrained, since storing spaced seeds can be costly. To address these challenges, we have designed a probabilistic data structure called a multiindex Bloom Filter (miBF), which can store multiple spaced seed sequences with a low memory cost that remains static regardless of seed length or seed design. We formalize how to minimize the false-positive rate of miBFs when classifying sequences from multiple targets or references. Available within BioBloom Tools, we illustrate the utility of miBF in two use cases: read-binning for targeted assembly, and taxonomic read assignment. In our benchmarks, an analysis pipeline based on miBF shows higher sensitivity and specificity for read-binning than sequence alignment-based methods, also executing in less time. Similarly, for taxonomic classification, miBF enables higher sensitivity than a conventional spaced seed-based approach, while using half the memory and an order of magnitude less computational time.
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7
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Thibodeau ML, Zhao EY, Reisle C, Ch'ng C, Wong HL, Shen Y, Jones MR, Lim HJ, Young S, Cremin C, Pleasance E, Zhang W, Holt R, Eirew P, Karasinska J, Kalloger SE, Taylor G, Majounie E, Bonakdar M, Zong Z, Bleile D, Chiu R, Birol I, Gelmon K, Lohrisch C, Mungall KL, Mungall AJ, Moore R, Ma YP, Fok A, Yip S, Karsan A, Huntsman D, Schaeffer DF, Laskin J, Marra MA, Renouf DJ, Jones SJM, Schrader KA. Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003681. [PMID: 30833417 PMCID: PMC6549570 DOI: 10.1101/mcs.a003681] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/17/2019] [Indexed: 12/21/2022] Open
Abstract
We report a case of early-onset pancreatic ductal adenocarcinoma in a patient harboring biallelic MUTYH germline mutations, whose tumor featured somatic mutational signatures consistent with defective MUTYH-mediated base excision repair and the associated driver KRAS transversion mutation p.Gly12Cys. Analysis of an additional 730 advanced cancer cases (N = 731) was undertaken to determine whether the mutational signatures were also present in tumors from germline MUTYH heterozygote carriers or if instead the signatures were only seen in those with biallelic loss of function. We identified two patients with breast cancer each carrying a pathogenic germline MUTYH variant with a somatic MUTYH copy loss leading to the germline variant being homozygous in the tumor and demonstrating the same somatic signatures. Our results suggest that monoallelic inactivation of MUTYH is not sufficient for C:G>A:T transversion signatures previously linked to MUTYH deficiency to arise (N = 9), but that biallelic complete loss of MUTYH function can cause such signatures to arise even in tumors not classically seen in MUTYH-associated polyposis (N = 3). Although defective MUTYH is not the only determinant of these signatures, MUTYH germline variants may be present in a subset of patients with tumors demonstrating elevated somatic signatures possibly suggestive of MUTYH deficiency (e.g., COSMIC Signature 18, SigProfiler SBS18/SBS36, SignatureAnalyzer SBS18/SBS36).
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada
| | - Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Hui-Li Wong
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Sean Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Cancer Genetics and Genomics Laboratory, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Carol Cremin
- Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Wei Zhang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Robert Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | | | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,The Canadian Centre for Applied Research in Cancer Control, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Greg Taylor
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Elisa Majounie
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Dustin Bleile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Inanc Birol
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Karen Gelmon
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Caroline Lohrisch
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Yussanne P Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada
| | - Stephen Yip
- Cancer Genetics and Genomics Laboratory, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - David Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
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