1
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Kurgan G, Turk R, Li H, Roberts N, Rettig GR, Jacobi AM, Tso L, Sturgeon M, Mertens M, Noten R, Florus K, Behlke MA, Wang Y, McNeill MS. CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing. Mol Ther Methods Clin Dev 2021; 21:478-491. [PMID: 33981780 PMCID: PMC8082044 DOI: 10.1016/j.omtm.2021.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/26/2022]
Abstract
CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair fingerprints that result from non-homologous end joining (NHEJ) after double-stranded breaks (DSBs) were introduced by Cas9 or Cas12a for >500 paired treatment/control experiments. We found that building biological understanding of the repair into a novel analysis tool (CRISPAltRations) improved the quality of the results. We validated our software using simulated, targeted amplicon sequencing data (11 guide RNAs [gRNAs] and 603 on- and off-target locations) and demonstrated that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR-associated indels and homology-directed repair (HDR) events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user interface (GUI) and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a user interface (UI), we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.
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Affiliation(s)
- Gavin Kurgan
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215
| | | | | | | | - Lauren Tso
- Integrated DNA Technologies, Coralville, IA 52241, USA
| | | | | | | | | | | | - Yu Wang
- Integrated DNA Technologies, Coralville, IA 52241, USA
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2
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Anazawa T, Matsunaga H, Yamamoto S, Inaba R. Highly sensitive mutation quantification by high-dynamic-range capillary-array electrophoresis (HiDy CE). LAB ON A CHIP 2020; 20:1083-1091. [PMID: 32108835 DOI: 10.1039/c9lc00853e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A simple and robust ultra-small four-color-fluorescence detection system was developed by integrating its components, namely, a four-capillary array, an injection-molded-plastic four-lens array, a four-dichroic-mirror array, and a CMOS sensor, as one device. The developed system was applied to a high-dynamic-range capillary-array electrophoresis (HiDy CE) to quantify a rare EGFR mutant (MT) of exon 19 deletion in a large excess of EGFR wild type (WT). Samples with serially diluted MT and constant-concentration WT were co-amplified by competitive PCR and subjected to HiDy CE. The MT peak in each electropherogram was then compared to the WT peak. As a result, MT was quantified with high-sensitivity (LOD of 0.004% MT/WT) and four-orders-of-magnitude dynamic range (0.01-100% MT/WT) by HiDy CE. Moreover, compared with existing methods, HiDy CE achieves higher speed, higher sample throughput, and lower consumable cost per sample. It has therefore great potential to be used in clinical practice.
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Affiliation(s)
- Takashi Anazawa
- Research & Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan.
| | - Hiroko Matsunaga
- Research & Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan. and Present address: Research Organization for Nano and Life Innovation, Waseda University, 513 Waseda-tsurumaki-cho, Shinjuku, Tokyo 162-0041, Japan
| | - Shuhei Yamamoto
- Science & Medical Systems Business Group, Hitachi High-Technologies Corporation, 882 Ichige, Hitachinaka, Ibaraki 312-8504, Japan
| | - Ryoji Inaba
- Science & Medical Systems Business Group, Hitachi High-Technologies Corporation, 882 Ichige, Hitachinaka, Ibaraki 312-8504, Japan
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3
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Oota S. Somatic mutations - Evolution within the individual. Methods 2019; 176:91-98. [PMID: 31711929 DOI: 10.1016/j.ymeth.2019.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023] Open
Abstract
With the rapid advancement of sequencing technologies over the last two decades, it is becoming feasible to detect rare variants from somatic tissue samples. Studying such somatic mutations can provide deep insights into various senescence-related diseases, including cancer, inflammation, and sporadic psychiatric disorders. While it is still a difficult task to identify true somatic mutations, relentless efforts to combine experimental and computational methods have made it possible to obtain reliable data. Furthermore, state-of-the-art machine learning approaches have drastically improved the efficiency and sensitivity of these methods. Meanwhile, we can regard somatic mutations as a counterpart of germline mutations, and it is possible to apply well-formulated mathematical frameworks developed for population genetics and molecular evolution to analyze this 'somatic evolution'. For example, retrospective cell lineage tracing is a promising technique to elucidate the mechanism of pre-diseases using single-cell RNA-sequencing (scRNA-seq) data.
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Affiliation(s)
- Satoshi Oota
- Image Processing Research Team, Center for Advanced Photonics, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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4
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Raimondi F, Inoue A, Kadji FMN, Shuai N, Gonzalez JC, Singh G, de la Vega AA, Sotillo R, Fischer B, Aoki J, Gutkind JS, Russell RB. Rare, functional, somatic variants in gene families linked to cancer genes: GPCR signaling as a paradigm. Oncogene 2019; 38:6491-6506. [PMID: 31337866 PMCID: PMC6756116 DOI: 10.1038/s41388-019-0895-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
Abstract
Oncodriver genes are usually identified when mutations recur in multiple tumours. Different drivers often converge in the activation or repression of key cancer-relevant pathways. However, as many pathways contain multiple members of the same gene family, individual mutations might be overlooked, as each family member would necessarily have a lower mutation frequency and thus not identified as significant in any one-gene-at-a-time analysis. Here, we looked for mutated, functional sequence positions in gene families that were mutually exclusive (in patients) with another gene in the same pathway, which identified both known and new candidate oncodrivers. For instance, many inactivating mutations in multiple G-protein (particularly Gi/o) coupled receptors, are mutually exclusive with Gαs oncogenic activating mutations, both of which ultimately enhance cAMP signalling. By integrating transcriptomics and interaction data, we show that the Gs pathway is upregulated in multiple cancer types, even those lacking known GNAS activating mutations. This suggests that cancer cells may develop alternative strategies to activate adenylate cyclase signalling in multiple cancer types. Our study provides a mechanistic interpretation for several rare somatic mutations in multi-gene oncodrivers, and offers possible explanations for known and potential off-label cancer treatments, suggesting new therapeutic opportunities.
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Affiliation(s)
- Francesco Raimondi
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Asuka Inoue
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, 980-8578, Miyagi, Japan
- Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Francois M N Kadji
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, 980-8578, Miyagi, Japan
- Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Ni Shuai
- Computational Genome Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Juan-Carlos Gonzalez
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Gurdeep Singh
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120, Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), 69120, Heidelberg, Germany
| | - Bernd Fischer
- Computational Genome Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Junken Aoki
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, 980-8578, Miyagi, Japan
- Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, 100-0004, Japan
| | - J Silvio Gutkind
- Moores Cancer Center, University of San Diego, San Diego, La Jolla, CA 92093, USA
| | - Robert B Russell
- BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
- Heidelberg University Biochemistry Centre (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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Abstract
In the context of oncology, liquid biopsies consist of harvesting cancer biomarkers, such as circulating tumor cells, tumor-derived cell-free DNA, and extracellular vesicles, from bodily fluids. These biomarkers provide a source of clinically actionable molecular information that can enable precision medicine. Herein, we review technologies for the molecular profiling of liquid biopsy markers with special emphasis on the analysis of low abundant markers from mixed populations.
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Affiliation(s)
- Camila D. M. Campos
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
| | - Joshua M. Jackson
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
| | - Małgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
- Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047
- BioEngineering Program, The University of Kansas, Lawrence, KS 66047
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66047
- Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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6
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Muller E, Goardon N, Brault B, Rousselin A, Paimparay G, Legros A, Fouillet R, Bruet O, Tranchant A, Domin F, San C, Quesnelle C, Frebourg T, Ricou A, Krieger S, Vaur D, Castera L. OutLyzer: software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Oncotarget 2018; 7:79485-79493. [PMID: 27825131 PMCID: PMC5346729 DOI: 10.18632/oncotarget.13103] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023] Open
Abstract
Highlighting tumoral mutations is a key step in oncology for personalizing care. Considering the genetic heterogeneity in a tumor, software used for detecting mutations should clearly distinguish real tumor events of interest that could be predictive markers for personalized medicine from false positives. OutLyzer is a new variant-caller designed for the specific and sensitive detection of mutations for research and diagnostic purposes. It is based on statistic and local evaluation of sequencing background noise to highlight potential true positive variants. 130 previously genotyped patients were sequenced after enrichment by capturing the exons of 22 genes. Sequencing data were analyzed by HaplotypeCaller, LofreqStar, Varscan2 and OutLyzer. OutLyzer had the best sensitivity and specificity with a fixed limit of detection for all tools of 1% for SNVs and 2% for Indels. OutLyzer is a useful tool for detecting mutations of interest in tumors including low allele-frequency mutations, and could be adopted in standard practice for delivering targeted therapies in cancer treatment.
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Affiliation(s)
- Etienne Muller
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France.,Inserm U1079, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Rouen, France
| | - Nicolas Goardon
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Baptiste Brault
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Antoine Rousselin
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Germain Paimparay
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Angelina Legros
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Robin Fouillet
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Olivia Bruet
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Aurore Tranchant
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Florian Domin
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Chankannira San
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Céline Quesnelle
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Thierry Frebourg
- Inserm U1079, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Rouen, France.,Genetic Department, Rouen University Hospital, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Rouen, France.,Rouen University, France
| | - Agathe Ricou
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France
| | - Sophie Krieger
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France.,Inserm U1079, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Rouen, France.,Caen University, France
| | - Dominique Vaur
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France.,Inserm U1079, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Rouen, France
| | - Laurent Castera
- Department of Cancer Biology and Genetics, CCC François Baclesse, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Caen, France.,Inserm U1079, Genomic and Personalized Medicine in Cancer and Neurological Disorders Unit, Rouen, France
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7
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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] [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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