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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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Dewar LJ, Alcaide M, Fornika D, D’Amato L, Shafaatalab S, Stevens CM, Balachandra T, Phillips SM, Sanatani S, Morin RD, Tibbits GF. Investigating the Genetic Causes of Sudden Unexpected Death in Children Through Targeted Next-Generation Sequencing Analysis. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.116.001738. [DOI: 10.1161/circgenetics.116.001738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 04/25/2017] [Indexed: 12/27/2022]
Abstract
Background—
Inherited arrhythmia syndromes are responsible for a significant portion of autopsy-negative sudden unexpected death (SUD) cases, but molecular autopsy used to identify potentially causal variants is not routinely included in SUD investigations. We collaborated with a medical examiner's office to assist in finding a diagnosis for their autopsy-negative child SUD cases.
Methods and Results—
191 child SUD cases (<5 years of age) were selected for analyses. Our next generation sequencing panel incorporated 38 inherited arrhythmia syndrome candidate genes and another 33 genes not previously investigated for variants that may underlie SUDY pathophysiology. Overall, we identified 11 potentially causal disease-associated variants in 12 cases, for an overall yield of 6.3%. We also identified 31 variants of uncertain significance in 36 cases and 16 novel variants predicted to be pathogenic in silico in 15 cases. The disease-associated variants were reported to the medical examiner to notify surviving relatives and recommend clinical assessment.
Conclusions—
We have identified variants that may assist in the diagnosis of at least 6.3% of autopsy-negative child SUD cases and reduce risk of future SUD in surviving relatives. We recommend a cautious approach to variant interpretation. We also suggest inclusion of cardiomyopathy genes as well as other candidate SUD genes in molecular autopsy analyses.
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Affiliation(s)
- Laura J. Dewar
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Miguel Alcaide
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Daniel Fornika
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Luisa D’Amato
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Sanam Shafaatalab
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Charles M. Stevens
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Thambirajah Balachandra
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Susan M. Phillips
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Shubhayan Sanatani
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Ryan D. Morin
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Glen F. Tibbits
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
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Alcaide M, Yu S, Bushell K, Fornika D, Nielsen JS, Nelson BH, Mann KK, Assouline S, Johnson NA, Morin RD. Multiplex Droplet Digital PCR Quantification of Recurrent Somatic Mutations in Diffuse Large B-Cell and Follicular Lymphoma. Clin Chem 2016; 62:1238-47. [PMID: 27440511 DOI: 10.1373/clinchem.2016.255315] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/23/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND A plethora of options to detect mutations in tumor-derived DNA currently exist but each suffers limitations in analytical sensitivity, cost, or scalability. Droplet digital PCR (ddPCR) is an appealing technology for detecting the presence of specific mutations based on a priori knowledge and can be applied to tumor biopsies, including formalin-fixed paraffin embedded (FFPE) tissues. More recently, ddPCR has gained popularity in its utility in quantifying circulating tumor DNA. METHODS We have developed a suite of novel ddPCR assays for detecting recurrent mutations that are prevalent in common B-cell non-Hodgkin lymphomas (NHLs), including diffuse large B-cell lymphoma, follicular lymphoma, and lymphoplasmacytic lymphoma. These assays allowed the differentiation and counting of mutant and wild-type molecules using one single hydrolysis probe. We also implemented multiplexing that allowed the simultaneous detection of distinct mutations and an "inverted" ddPCR assay design, based on employing probes matching wild-type alleles, capable of detecting the presence of multiple single nucleotide polymorphisms. RESULTS The assays successfully detected and quantified somatic mutations commonly affecting enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) (Y641) and signal transducer and activator of transcription 6 (STAT6) (D419) hotspots in fresh tumor, FFPE, and liquid biopsies. The "inverted" ddPCR approach effectively reported any single nucleotide variant affecting either of these 2 hotspots as well. Finally, we could effectively multiplex hydrolysis probes targeting 2 additional lymphoma-related hotspots: myeloid differentiation primary response 88 (MYD88; L265P) and cyclin D3 (CCND3; I290R). CONCLUSIONS Our suite of ddPCR assays provides sufficient analytical sensitivity and specificity for either the invasive or noninvasive detection of multiple recurrent somatic mutations in B-cell NHLs.
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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
| | - 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
| | - Julie S Nielsen
- Deeley Research Centre, BC Cancer Agency, Victoria, BC, Canada
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer Agency, Victoria, BC, Canada
| | - Koren K Mann
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Sarit Assouline
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nathalie A Johnson
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.
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4
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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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McNamara S, Morin R, Couëtoux du Tertre M, McCloskey R, Johnston R, Fornika D, Samson B, Lespérance B, Alcindor T, Ko YJ, Dalfen R, St-Hilaire E, Sideris L, Couture F, Prenen H, Tejpar S, Burkes R, Constantin A, Camlioglu E, Aguilar A, Gologan A, Têtu B, Greenwood CM, Hoffert C, Qureshi S, Diaz Z, Marques M, Witcher M, Gagnon-Kugler T, Kavan P, Batist G. Abstract 3888: Molecular profiling of sequential biopsies in patients with metastatic colorectal cancer identifies genomic alterations that evolve during first-line therapy and could have therapeutic implications: A prospective study to identify molecular mechanisms of clinical resistance (QCROC-01: NCT00984048). Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Therapeutic resistance remains a major obstacle in metastatic colorectal cancer (mCRC) and biomarkers to guide treatment are essential to improving survival and quality of life in mCRC patients. A biopsy-driven prospective study was designed to identify biomarkers and mechanisms of resistance to a standard first-line therapy in patients with mCRC which could be useful in guiding treatment selection (QCROC-01; NCT00984048). We also hoped to recognize molecular changes over time, or resulting from the selection pressure of treatment, which could have implications for subsequent therapy.
This study is ongoing and approved at thirteen sites with one-hundred patients enrolled so far. Patients with mCRC receiving FOLFOX (5-fluorouracil, leucovorin and oxaliplatin) with bevacizumab consented to three needle core tumour biopsies at pre-treatment and at the time of resistance. The rate of both patient and physician acceptance of biopsies has steadily risen with time and experience. Serial bloods were also collected for proteomic analysis and circulating tumor DNA. Twenty-five biopsy samples were profiled using exome sequencing (tumor and germ line), RNAseq, low pass genome sequencing and miRNA analysis. Differential gene expression analysis revealed signatures associated with clinical response and resistance when comparing tumours obtained pre- and post-treatment. We detect changes in variant allele fraction including both depletion and enrichment of individual somatic mutations over the course of treatment, the latter of which may indicate subclonal and acquired “driver” mutations that confer therapeutic resistance. A small number of genes show recurrent evidence for changes in clonal enrichment at the time of relapse across multiple patients. These could also represent therapeutic targets for subsequent therapy for these patients, and as such, represent new treatment opportunities. Our findings provide insights into tumor evolution during first-line chemotherapy of mCRC that may hold clues to optimize current first-line therapeutic decision making and identifies potential target pathways for second-line stratification of patients. This study is part of the Canadian Colorectal Cancer Consortium which is a multi-site collaboration funded by the Terry Fox Research Institute and le fonds de recherche du québec - santé.
Citation Format: Suzan McNamara, Ryan Morin, Mathilde Couëtoux du Tertre, Rosemary McCloskey, Rebecca Johnston, Daniel Fornika, Benoit Samson, Bernard Lespérance, Thierry Alcindor, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sideris, Felix Couture, Hans Prenen, Sabine Tejpar, Ronald Burkes, André Constantin, Errol Camlioglu, Adriana Aguilar, Adrian Gologan, Benoit Têtu, Celia M. Greenwood, Cyrla Hoffert, Samia Qureshi, Zuanel Diaz, Maud Marques, Micheal Witcher, Thérèse Gagnon-Kugler, Petr Kavan, Gerald Batist. Molecular profiling of sequential biopsies in patients with metastatic colorectal cancer identifies genomic alterations that evolve during first-line therapy and could have therapeutic implications: A prospective study to identify molecular mechanisms of clinical resistance (QCROC-01: NCT00984048). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3888. doi:10.1158/1538-7445.AM2015-3888
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Affiliation(s)
- Suzan McNamara
- 1Quebec Clinical Research Organization in Cancer, Montreal, Quebec, Canada
| | - Ryan Morin
- 2Simon Fraser University, Burnaby, British Columbia, Canada
| | | | | | - Rebecca Johnston
- 3University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Fornika
- 2Simon Fraser University, Burnaby, British Columbia, Canada
| | - Benoit Samson
- 4CSSS Champlain - Charles-Le Moyne, Greenfield Park, Quebec, Canada
| | | | | | - Yoo-Joung Ko
- 7Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | | | - Eve St-Hilaire
- 9Hôpital Georges L. Dumont, Moncton, New Brunswick, Canada
| | - Lucas Sideris
- 10Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | | | - Hans Prenen
- 12University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | | | | | - André Constantin
- 15Department of Radiology, Jewish General Hospital, Montreal, Quebec, Canada
| | - Errol Camlioglu
- 15Department of Radiology, Jewish General Hospital, Montreal, Quebec, Canada
| | - Adriana Aguilar
- 16Jewish General Hospital, Segal Cancer Center, Montreal, Quebec, Canada
| | - Adrian Gologan
- 16Jewish General Hospital, Segal Cancer Center, Montreal, Quebec, Canada
| | - Benoit Têtu
- 17Hôpital du Saint-Sacrement, Quebec, Quebec, Canada
| | - Celia M. Greenwood
- 16Jewish General Hospital, Segal Cancer Center, Montreal, Quebec, Canada
| | - Cyrla Hoffert
- 1Quebec Clinical Research Organization in Cancer, Montreal, Quebec, Canada
| | - Samia Qureshi
- 1Quebec Clinical Research Organization in Cancer, Montreal, Quebec, Canada
| | - Zuanel Diaz
- 1Quebec Clinical Research Organization in Cancer, Montreal, Quebec, Canada
| | - Maud Marques
- 16Jewish General Hospital, Segal Cancer Center, Montreal, Quebec, Canada
| | - Micheal Witcher
- 16Jewish General Hospital, Segal Cancer Center, Montreal, Quebec, Canada
| | | | - Petr Kavan
- 16Jewish General Hospital, Segal Cancer Center, Montreal, Quebec, Canada
| | - Gerald Batist
- 18Quebec Clinical Research Organization in Cancer, Jewish General Hospital, Segal Cancer Center, Montreal, Quebec, Canada
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Moore RA, Ogilvie G, Fornika D, Moravan V, Brisson M, Amirabbasi-Beik M, Kollar A, Burgess T, Hsu R, Towers L, Lo J, Matisic J, Brooks-Wilson A. Prevalence and type distribution of human papillomavirus in 5,000 British Columbia women--implications for vaccination. Cancer Causes Control 2009; 20:1387-96. [PMID: 19475481 PMCID: PMC2746887 DOI: 10.1007/s10552-009-9365-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [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: 06/09/2008] [Accepted: 05/06/2009] [Indexed: 11/29/2022]
Abstract
Background Human papilloma virus (HPV) prevalence studies performed in different regions and population groups across Canada would inform public health decisions regarding implementation of anti-HPV vaccines. Methods A total of 8,700 liquid-based specimens from 8,660 women aged 13–86 from throughout British Columbia were collected. DNA was isolated from 4,980 of these samples and assessed for HPV prevalence and type distribution. HPV was detected by PCR analysis using tagged GP5+/6+ consensus primers to amplify the L1 region of HPV; typing was done by bi-directional sequencing of PCR products. Results Overall HPV prevalence was 16.8% (age adjusted 15.5%). Prevalence of high-risk HPV was 13.9, and 10.7% of samples contained HPV16. HPV prevalence was highest in the youngest group of women (<20 years). One-third of HPV positive samples contained more than one HPV type. Percentages of low-grade (LGIL) and high-grade intraepithelial lesions (HGIL) containing high-risk HPV are 52.3 and 79.4%, respectively. Conclusions Overall HPV prevalence in this study is within the range of estimates from other studies. The prevalence of HPV16 is higher than what is found in other Canadian and international studies. HPV16 and HPV18 compose a majority of the high-risk virus in this study. Use of current HPV vaccines could considerably reduce HPV-related conditions including cervical cancer and procedures such as colposcopy. Electronic supplementary material The online version of this article (doi:10.1007/s10552-009-9365-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 675 West 10th Ave., Vancouver, BC, V5Z 1L3, Canada
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