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Aberg KA, Chan RF, van den Oord EJCG. MBD-seq - realities of a misunderstood method for high-quality methylome-wide association studies. Epigenetics 2019; 15:431-438. [PMID: 31739727 DOI: 10.1080/15592294.2019.1695339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The majority of methylome-wide association studies (MWAS) have been performed using commercially available array-based technologies such as the Infinium Human Methylation 450K and the Infinium MethylationEPIC arrays (Illumina). While these arrays offer a convenient and relatively robust assessment of the probed sites they only allow interrogation of 2-4% of all CpG sites in the human genome. Methyl-binding domain sequencing (MBD-seq) is an alternative approach for MWAS that provides near-complete coverage of the methylome at similar costs as the array-based technologies. However, despite publication of multiple positive evaluations, the use of MBD-seq for MWAS is often fiercely criticized. Here we discuss key features of the method and debunk misconceptions using empirical data. We conclude that MBD-seq represents an excellent approach for large-scale MWAS and that increased utilization is likely to result in more discoveries, advance biological knowledge, and expedite the clinical translation of methylome-wide research findings.
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Affiliation(s)
- Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Robin F Chan
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
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Konwar C, Del Gobbo G, Yuan V, Robinson WP. Considerations when processing and interpreting genomics data of the placenta. Placenta 2019; 84:57-62. [PMID: 30642669 PMCID: PMC6612459 DOI: 10.1016/j.placenta.2019.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/28/2018] [Accepted: 01/04/2019] [Indexed: 12/27/2022]
Abstract
The application of genomic approaches to placental research has opened exciting new avenues to help us understand basic biological properties of the placenta, improve prenatal screening/diagnosis, and measure effects of in utero exposures on child health outcomes. In the last decade, such large-scale genomic data (including epigenomics and transcriptomics) have become more easily accessible to researchers from many disciplines due to the increasing ease of obtaining such data and the rapidly evolving computational tools available for analysis. While the potential of large-scale studies has been widely promoted, less attention has been given to some of the challenges associated with processing and interpreting such data. We hereby share some of our experiences in assessing data quality, reproducibility, and interpretation in the context of genome-wide studies of the placenta, with the aim to improve future studies. There is rarely a single "best" approach, as that can depend on the study question and sample cohort. However, being consistent, thoroughly assessing potential confounders in the data, and communicating key variables in the methods section of the manuscript are critically important to help researchers to collaborate and build on each other's work.
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Affiliation(s)
- Chaini Konwar
- BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, 4500, Oak Street, Vancouver, BC V6H3N1, Canada.
| | - Giulia Del Gobbo
- BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, 4500, Oak Street, Vancouver, BC V6H3N1, Canada.
| | - Victor Yuan
- BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, 4500, Oak Street, Vancouver, BC V6H3N1, Canada.
| | - Wendy P Robinson
- BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, 4500, Oak Street, Vancouver, BC V6H3N1, Canada.
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Yuan V, Price EM, Del Gobbo G, Mostafavi S, Cox B, Binder AM, Michels KB, Marsit C, Robinson WP. Accurate ethnicity prediction from placental DNA methylation data. Epigenetics Chromatin 2019; 12:51. [PMID: 31399127 PMCID: PMC6688210 DOI: 10.1186/s13072-019-0296-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background The influence of genetics on variation in DNA methylation (DNAme) is well documented. Yet confounding from population stratification is often unaccounted for in DNAme association studies. Existing approaches to address confounding by population stratification using DNAme data may not generalize to populations or tissues outside those in which they were developed. To aid future placental DNAme studies in assessing population stratification, we developed an ethnicity classifier, PlaNET (Placental DNAme Elastic Net Ethnicity Tool), using five cohorts with Infinium Human Methylation 450k BeadChip array (HM450k) data from placental samples that is also compatible with the newer EPIC platform. Results Data from 509 placental samples were used to develop PlaNET and show that it accurately predicts (accuracy = 0.938, kappa = 0.823) major classes of self-reported ethnicity/race (African: n = 58, Asian: n = 53, Caucasian: n = 389), and produces ethnicity probabilities that are highly correlated with genetic ancestry inferred from genome-wide SNP arrays (> 2.5 million SNP) and ancestry informative markers (n = 50 SNPs). PlaNET’s ethnicity classification relies on 1860 HM450K microarray sites, and over half of these were linked to nearby genetic polymorphisms (n = 955). Our placental-optimized method outperforms existing approaches in assessing population stratification in placental samples from individuals of Asian, African, and Caucasian ethnicities. Conclusion PlaNET provides an improved approach to address population stratification in placental DNAme association studies. The method can be applied to predict ethnicity as a discrete or continuous variable and will be especially useful when self-reported ethnicity information is missing and genotyping markers are unavailable. Electronic supplementary material The online version of this article (10.1186/s13072-019-0296-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Victor Yuan
- Department of Medical Genetics, University of British Columbia, C201-4500 Oak Street, Vancouver, BC, V6H 3N1, Canada.,BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - E Magda Price
- Department of Medical Genetics, University of British Columbia, C201-4500 Oak Street, Vancouver, BC, V6H 3N1, Canada.,BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Giulia Del Gobbo
- Department of Medical Genetics, University of British Columbia, C201-4500 Oak Street, Vancouver, BC, V6H 3N1, Canada.,BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Sara Mostafavi
- Department of Medical Genetics, University of British Columbia, C201-4500 Oak Street, Vancouver, BC, V6H 3N1, Canada.,BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Statistics, University of British Columbia, 3182 Earth Sciences Building, 2207 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Brian Cox
- Department of Physiology, University of Toronto, Medical Sciences Building, 3rd Floor, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Alexandra M Binder
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
| | - Karin B Michels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
| | - Carmen Marsit
- Department of Environmental Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, C201-4500 Oak Street, Vancouver, BC, V6H 3N1, Canada. .,BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.
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Han LKM, Verhoeven JE, Tyrka AR, Penninx BWJH, Wolkowitz OM, Månsson KNT, Lindqvist D, Boks MP, Révész D, Mellon SH, Picard M. Accelerating research on biological aging and mental health: Current challenges and future directions. Psychoneuroendocrinology 2019; 106:293-311. [PMID: 31154264 PMCID: PMC6589133 DOI: 10.1016/j.psyneuen.2019.04.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/22/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Aging is associated with complex biological changes that can be accelerated, slowed, or even temporarily reversed by biological and non-biological factors. This article focuses on the link between biological aging, psychological stressors, and mental illness. Rather than comprehensively reviewing this rapidly expanding field, we highlight challenges in this area of research and propose potential strategies to accelerate progress in this field. This effort requires the interaction of scientists across disciplines - including biology, psychiatry, psychology, and epidemiology; and across levels of analysis that emphasize different outcome measures - functional capacity, physiological, cellular, and molecular. Dialogues across disciplines and levels of analysis naturally lead to new opportunities for discovery but also to stimulating challenges. Some important challenges consist of 1) establishing the best objective and predictive biological age indicators or combinations of indicators, 2) identifying the basis for inter-individual differences in the rate of biological aging, and 3) examining to what extent interventions can delay, halt or temporarily reverse aging trajectories. Discovering how psychological states influence biological aging, and vice versa, has the potential to create novel and exciting opportunities for healthcare and possibly yield insights into the fundamental mechanisms that drive human aging.
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Affiliation(s)
- Laura K M Han
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Public Health Research Institute, Oldenaller 1, the Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Josine E Verhoeven
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Public Health Research Institute, Oldenaller 1, the Netherlands
| | - Audrey R Tyrka
- Butler Hospital and the Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Brenda W J H Penninx
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Public Health Research Institute, Oldenaller 1, the Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam Neuroscience, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Owen M Wolkowitz
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Kristoffer N T Månsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Psychology, Stockholm University, Stockholm, Sweden; Department of Psychology, Uppsala University, Uppsala, Sweden
| | - Daniel Lindqvist
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden; Department of Psychiatry, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; Psychiatric Clinic, Lund, Division of Psychiatry, Lund, Sweden
| | - Marco P Boks
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, the Netherlands
| | - Dóra Révész
- Center of Research on Psychology in Somatic diseases (CoRPS), Department of Medical and Clinical Psychology, Tilburg University, Tilburg, the Netherlands
| | - Synthia H Mellon
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, School of Medicine, San Francisco, CA, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, NY, USA; Columbia Aging Center, Columbia University, New York, NY, USA.
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Lee Y, Choufani S, Weksberg R, Wilson SL, Yuan V, Burt A, Marsit C, Lu AT, Ritz B, Bohlin J, Gjessing HK, Harris JR, Magnus P, Binder AM, Robinson WP, Jugessur A, Horvath S. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging (Albany NY) 2019; 11:4238-4253. [PMID: 31235674 PMCID: PMC6628997 DOI: 10.18632/aging.102049] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
The human pan-tissue epigenetic clock is widely used for estimating age across the entire lifespan, but it does not lend itself well to estimating gestational age (GA) based on placental DNAm methylation (DNAm) data. We replicate previous findings demonstrating a strong correlation between GA and genome-wide DNAm changes. Using substantially more DNAm arrays (n=1,102 in the training set) than a previous study, we present three new placental epigenetic clocks: 1) a robust placental clock (RPC) which is unaffected by common pregnancy complications (e.g., gestational diabetes, preeclampsia), and 2) a control placental clock (CPC) constructed using placental samples from pregnancies without known placental pathology, and 3) a refined RPC for uncomplicated term pregnancies. These placental clocks are highly accurate estimators of GA based on placental tissue; e.g., predicted GA based on RPC is highly correlated with actual GA (r>0.95 in test data, median error less than one week). We show that epigenetic clocks derived from cord blood or other tissues do not accurately estimate GA in placental samples. While fundamentally different from Horvath's pan-tissue epigenetic clock, placental clocks closely track fetal age during development and may have interesting applications.
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Affiliation(s)
- Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Samantha L. Wilson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Victor Yuan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Amber Burt
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Carmen Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beate Ritz
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K. Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jennifer R. Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexandra M. Binder
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Wendy P. Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
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Unbiased data analytic strategies to improve biomarker discovery in precision medicine. Drug Discov Today 2019; 24:1735-1748. [PMID: 31158511 DOI: 10.1016/j.drudis.2019.05.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/23/2019] [Accepted: 05/28/2019] [Indexed: 12/25/2022]
Abstract
Omics technologies promised improved biomarker discovery for precision medicine. The foremost problem of discovered biomarkers is irreproducibility between patient cohorts. From a data analytics perspective, the main reason for these failures is bias in statistical approaches and overfitting resulting from batch effects and confounding factors. The keys to reproducible biomarker discovery are: proper study design, unbiased data preprocessing and quality control analyses, and a knowledgeable application of statistics and machine learning algorithms. In this review, we discuss study design and analysis considerations and suggest standards from an expert point-of-view to promote unbiased decision-making in biomarker discovery in precision medicine.
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Del Gobbo GF, Price EM, Hanna CW, Robinson WP. No evidence for association of MTHFR 677C>T and 1298A>C variants with placental DNA methylation. Clin Epigenetics 2018; 10:34. [PMID: 29564022 PMCID: PMC5851070 DOI: 10.1186/s13148-018-0468-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/01/2018] [Indexed: 01/30/2023] Open
Abstract
Background 5,10-Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in one-carbon metabolism that ensures the availability of methyl groups for methylation reactions. Two single-nucleotide polymorphisms (SNPs) in the MTHFR gene, 677C>T and 1298A>C, result in a thermolabile enzyme with reduced function. These variants, in both the maternal and/or fetal genes, have been associated with pregnancy complications including miscarriage, neural tube defects (NTDs), and preeclampsia (PE), perhaps due to altered capacity for DNA methylation (DNAm). In this study, we assessed the association between MTHFR 677TT and 1298CC genotypes and risk of NTDs, PE, or normotensive intrauterine growth restriction (nIUGR). Additionally, we assessed whether these high-risk genotypes are associated with altered DNAm in the placenta. Results In 303 placentas screened for this study, we observed no significant association between the occurrence of NTDs (N = 55), PE (early-onset: N = 28, late-onset: N = 20), or nIUGR (N = 21) and placental (fetal) MTHFR 677TT or 1298CC genotypes compared to healthy pregnancies (N = 179), though a trend of increased 677TT genotype in PE/IUGR together was observed (OR 2.53, p = 0.048). DNAm was profiled in 10 high-risk 677 (677TT + 1298AA), 10 high-risk 1298 (677CC + 1298CC), and 10 reference (677CC + 1298AA) genotype placentas. Linear modeling identified no significantly differentially methylated sites between high-risk 677 or 1298 and reference placentas at a false discovery rate < 0.05 and Δβ ≥ 0.05 using the Illumina Infinium HumanMethylation450 BeadChip. Using a differentially methylated region analysis or separating cytosine-guanine dinucleotides (CpGs) by CpG density to reduce multiple comparisons also did not identify differential methylation. Additionally, there was no consistent evidence for altered methylation of repetitive DNA between high-risk and reference placentas. Conclusions We conclude that large-scale, genome-wide disruption in DNAm does not occur in placentas with the high-risk MTHFR 677TT or 1298CC genotypes. Furthermore, there was no evidence for an association of the 1298CC genotype and only a tendency to higher 677TT in pregnancy complications of PE/IUGR. This may be due to small sample sizes or folate repletion in our Canadian population attenuating effects of the high-risk MTHFR variants. However, given our results and the conflicting results in the literature, investigations into alternative mechanisms that may explain the link between MTHFR variants and pregnancy complications, or in populations at risk of folate deficiencies, are warranted. Electronic supplementary material The online version of this article (10.1186/s13148-018-0468-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giulia F Del Gobbo
- 1BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada.,2Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, BC V6H 3N1 Canada
| | - E Magda Price
- 1BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada.,2Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, BC V6H 3N1 Canada
| | - Courtney W Hanna
- 3Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK.,4Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG UK
| | - Wendy P Robinson
- 1BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada.,2Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, BC V6H 3N1 Canada.,5Child and Family Research Institute, Room 2082, 950 W 28th Avenue, Vancouver, BC V5Z 4H4 Canada
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