1
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Daenekas B, Pérez E, Boniolo F, Stefan S, Benfatto S, Sill M, Sturm D, Jones DTW, Capper D, Zapatka M, Hovestadt V. Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice. Bioinformatics 2024; 40:btae029. [PMID: 38244574 PMCID: PMC10868300 DOI: 10.1093/bioinformatics/btae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
MOTIVATION Copy-number variations (CNVs) are common genetic alterations in cancer and their detection may impact tumor classification and therapeutic decisions. However, detection of clinically relevant large and focal CNVs remains challenging when sample material or resources are limited. This has motivated us to create a software tool to infer CNVs from DNA methylation arrays which are often generated as part of clinical routines and in research settings. RESULTS We present our R package, conumee 2.0, that combines tangent normalization, an adjustable genomic binning heuristic, and weighted circular binary segmentation to utilize DNA methylation arrays for CNV analysis and mitigate technical biases and batch effects. Segmentation results were validated in a lung squamous cell carcinoma dataset from TCGA (n = 367 samples) by comparison to segmentations derived from genotyping arrays (Pearson's correlation coefficient of 0.91). We further introduce a segmented block bootstrapping approach to detect focal alternations that achieved 60.9% sensitivity and 98.6% specificity for deletions affecting CDKN2A/B (60.0% and 96.9% for RB1, respectively) in a low-grade glioma cohort from TCGA (n = 239 samples). Finally, our tool provides functionality to detect and summarize CNVs across large sample cohorts. AVAILABILITY AND IMPLEMENTATION Conumee 2.0 is available under open-source license at: https://github.com/hovestadtlab/conumee2.
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Affiliation(s)
- Bjarne Daenekas
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Eilís Pérez
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Fabio Boniolo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Sabina Stefan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Salvatore Benfatto
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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2
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Vidotto T, Imada EL, Faisal F, Murali S, Mendes AA, Kaur H, Zheng S, Xu J, Schaeffer EM, Isaacs WB, Sfanos KS, Marchionni L, Lotan TL. Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer. JCI Insight 2023; 8:e162409. [PMID: 36752203 PMCID: PMC9977441 DOI: 10.1172/jci.insight.162409] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/27/2022] [Indexed: 02/09/2023] Open
Abstract
The genomic and immune landscapes of prostate cancer differ by self-identified race. However, few studies have examined the genome-wide copy number landscape and immune content of matched cohorts with genetic ancestry data and clinical outcomes. Here, we assessed prostate cancer somatic copy number alterations (sCNA) and tumor immune content of a grade-matched, surgically treated cohort of 145 self-identified Black (BL) and 145 self-identified White (WH) patients with genetic ancestry estimation. A generalized linear model adjusted with age, preoperative prostate-specific antigen (PSA), and Gleason Grade Group and filtered for germline copy number variations (gCNV) identified 143 loci where copy number varied significantly by percent African ancestry, clustering on chromosomes 6p, 10q, 11p, 12p, and 17p. Multivariable Cox regression models adjusted for age, preoperative PSA levels, and Gleason Grade Group revealed that chromosome 8q gains (including MYC) were significantly associated with biochemical recurrence and metastasis, independent of genetic ancestry. Finally, Treg density in BL and WH patients was significantly correlated with percent genome altered, and these findings were validated in the TCGA cohort. Taken together, our findings identify specific sCNA linked to genetic ancestry and outcome in primary prostate cancer and demonstrate that Treg infiltration varies by global sCNA burden in primary disease.
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Affiliation(s)
- Thiago Vidotto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eddie L. Imada
- Department of Pathology, Weill-Cornell School of Medicine, New York, New York, USA
| | - Farzana Faisal
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sanjana Murali
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adrianna A. Mendes
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harsimar Kaur
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Siqun Zheng
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University Health System, Evanston, Illinois, USA
| | - Edward M. Schaeffer
- Department of Urology, Northwestern University School of Medicine, Chicago, Illinois, USA
| | | | - Karen S. Sfanos
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Luigi Marchionni
- Department of Pathology, Weill-Cornell School of Medicine, New York, New York, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology and
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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3
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Hussmann D, Starnawska A, Kristensen L, Daugaard I, Cédile O, Nguyen VQ, Kjeldsen TE, Hansen CS, Bybjerg-Grauholm J, Kristensen T, Larsen TS, Møller MB, Nyvold CG, Hansen LL, Wojdacz TK. Methylation microarray-based detection of clinical copy-number aberrations in CLL benchmarked to standard FISH analysis. Genomics 2022; 114:110510. [PMID: 36272495 DOI: 10.1016/j.ygeno.2022.110510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 01/15/2023]
Abstract
Copy-number aberrations (CNAs) are assessed using FISH analysis in diagnostics of chronic lymphocytic leukemia (CLL), but CNAs can also be extrapolated from Illumina BeadChips developed for genome-wide methylation microarray screening. Increasing numbers of microarray data-sets are available from diagnostic samples, making it useful to assess the potential in CNA diagnostics. We benchmarked the limitations of CNA testing from two Illumina BeadChips (EPIC and 450k) and using two common packages for analysis (conumee and ChAMP) to FISH-based assessment of 11q, 13q, and 17p deletions in 202 CLL samples. Overall, the two packages predicted CNAs with similar accuracy regardless of the microarray type, but lower than FISH-based assessment. We showed that the bioinformatics analysis needs to be adjusted to the specific CNA, as no general settings were identified. Altogether, we were able to predict CNAs using methylation microarray data, however, with limited accuracy, making FISH-based assessment of deletions the superior diagnostic choice.
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Affiliation(s)
- Dianna Hussmann
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Centre for Genomics and Personalized Medicine, CGPM, Aarhus University, Aarhus, Denmark
| | - Louise Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Iben Daugaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Oriane Cédile
- Haematology-Pathology Research Laboratory, Research Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Vivi Quoc Nguyen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Tina E Kjeldsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Christine Søholm Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark; Department of Psychiatry, Mount Sinai, New York, NY, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark; Department of Clinical Development, Odense University Hospital, Odense, Denmark
| | | | - Michael Boe Møller
- Department of Pathology, Odense University Hospital, Odense, Denmark; Haematology-Pathology Research Laboratory, Research Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Charlotte Guldborg Nyvold
- Haematology-Pathology Research Laboratory, Research Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | | | - Tomasz K Wojdacz
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark; Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Szczecin, Poland.
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4
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Marttila S, Tamminen H, Rajić S, Mishra PP, Lehtimäki T, Raitakari O, Kähönen M, Kananen L, Jylhävä J, Hägg S, Delerue T, Peters A, Waldenberger M, Kleber ME, März W, Luoto R, Raitanen J, Sillanpää E, Laakkonen EK, Heikkinen A, Ollikainen M, Raitoharju E. Methylation status of VTRNA2-1/ nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Epigenomics 2022; 14:1105-1124. [PMID: 36200237 DOI: 10.2217/epi-2022-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims & methods: The aim of this study was to characterize the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues.48 datasets, consisting of more than 30 tissues and >30,000 individuals, were used. Results: nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, whereas ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle. Conclusion: The nc886 imprint may be established in the oocyte, and, after implantation, the methylation status is stable, excluding a few specific tissues.
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Affiliation(s)
- Saara Marttila
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Gerontology Research Center, Tampere University, Tampere, 33014, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku & Turku University Hospital, Turku, 20014, Finland.,Research Centre of Applied & Preventive Cardiovascular Medicine, University of Turku, Turku, 20014, Finland.,Department of Clinical Physiology & Nuclear Medicine, Turku University Hospital, Turku, 20014, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
| | - Laura Kananen
- Faculty of Medicine & Health Technology, & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520,Finland.,Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Juulia Jylhävä
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Delerue
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,Competence Cluster for Nutrition & Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, 07743, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg, 86156, Germany.,Clinical Institute of Medical & Chemical Laboratory Diagnostics, Medical University of Graz, Graz, 8010, Austria
| | - Riitta Luoto
- The Social Insurance Institute of Finland (Kela), Helsinki, 00250, Finland.,The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland
| | - Jani Raitanen
- The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland.,Faculty of Social Sciences (Health Sciences), Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Elina Sillanpää
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland.,Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Eija K Laakkonen
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
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5
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Xu K, Li S, Muskens IS, Elliott N, Myint SS, Pandey P, Hansen HM, Morimoto LM, Kang AY, Ma X, Metayer C, Mueller BA, Roberts I, Walsh K, Horvath S, Wiemels JL, de Smith AJ. Accelerated epigenetic aging in newborns with Down syndrome. Aging Cell 2022; 21:e13652. [PMID: 35661546 PMCID: PMC9282838 DOI: 10.1111/acel.13652] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/11/2022] [Accepted: 05/18/2022] [Indexed: 01/07/2023] Open
Abstract
Accelerated aging is a hallmark of Down syndrome (DS), with adults experiencing early-onset Alzheimer's disease and premature aging of the skin, hair, and immune and endocrine systems. Accelerated epigenetic aging has been found in the blood and brain tissue of adults with DS but when premature aging in DS begins remains unknown. We investigated whether accelerated aging in DS is already detectable in blood at birth. We assessed the association between age acceleration and DS using five epigenetic clocks in 346 newborns with DS and 567 newborns without DS using Illumina MethylationEPIC DNA methylation array data. We compared two epigenetic aging clocks (DNAmSkinBloodClock and pan-tissue DNAmAge) and three epigenetic gestational age clocks (Haftorn, Knight, and Bohlin) between DS and non-DS newborns using linear regression adjusting for observed age, sex, batch, deconvoluted blood cell proportions, and genetic ancestry. Targeted sequencing of GATA1 was performed in a subset of 184 newborns with DS to identify somatic mutations associated with transient abnormal myelopoiesis. DS was significantly associated with increased DNAmSkinBloodClock (effect estimate = 0.2442, p < 0.0001), with an epigenetic age acceleration of 244 days in newborns with DS after adjusting for potential confounding factors (95% confidence interval: 196-292 days). We also found evidence of epigenetic age acceleration associated with somatic GATA1 mutations among newborns with DS (p = 0.015). DS was not associated with epigenetic gestational age acceleration. We demonstrate that accelerated epigenetic aging in the blood of DS patients begins prenatally, with implications for the pathophysiology of immunosenescence and other aging-related traits in DS.
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Affiliation(s)
- Keren Xu
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Ivo S. Muskens
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Natalina Elliott
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular MedicineOxford University and BRC Blood Theme, NIHR Oxford Biomedical CentreOxfordUK
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Priyatama Pandey
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Helen M. Hansen
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Libby M. Morimoto
- School of Public HealthUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Alice Y. Kang
- School of Public HealthUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Xiaomei Ma
- Department of Chronic Disease EpidemiologyYale School of Public HealthNew HavenConnecticutUSA
| | - Catherine Metayer
- School of Public HealthUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Beth A. Mueller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, and Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Irene Roberts
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular MedicineOxford University and BRC Blood Theme, NIHR Oxford Biomedical CentreOxfordUK
| | - Kyle M. Walsh
- Department of NeurosurgeryDuke UniversityDurhamNorth CarolinaUSA
| | - Steve Horvath
- Department of Human GeneticsDavid Geffen School of Medicine, University of CaliforniaLos AngelesCaliforniaUSA
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
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6
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Blecua P, Davalos V, de Villasante I, Merkel A, Musulen E, Coll-SanMartin L, Esteller M. Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary. Brief Bioinform 2022; 23:6582004. [PMID: 35524475 PMCID: PMC9487591 DOI: 10.1093/bib/bbac161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 11/14/2022] Open
Abstract
High-throughput genomic technologies are increasingly used in personalized cancer medicine. However, computational tools to maximize the use of scarce tissues combining distinct molecular layers are needed. Here we present a refined strategy, based on the R-package 'conumee', to better predict somatic copy number alterations (SCNA) from deoxyribonucleic acid (DNA) methylation arrays. Our approach, termed hereafter as 'conumee-KCN', improves SCNA prediction by incorporating tumor purity and dynamic thresholding. We trained our algorithm using paired DNA methylation and SNP Array 6.0 data from The Cancer Genome Atlas samples and confirmed its performance in cancer cell lines. Most importantly, the application of our approach in cancers of unknown primary identified amplified potentially actionable targets that were experimentally validated by Fluorescence in situ hybridization and immunostaining, reaching 100% specificity and 93.3% sensitivity.
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Affiliation(s)
- Pedro Blecua
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Izar de Villasante
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Angelika Merkel
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Eva Musulen
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.,Department of Pathology, Hospital Universitari General de Catalunya-Grupo Quirónsalud, Sant Cugat del Vallès, Barcelona, Catalonia, Spain
| | - Laia Coll-SanMartin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain
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7
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Mariani MP, Chen JA, Zhang Z, Pike SC, Salas LA. MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions. FRONTIERS IN BIOINFORMATICS 2022; 2. [PMID: 35573871 PMCID: PMC9098103 DOI: 10.3389/fbinf.2022.859828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation-based copy number variation (CNV) calling software offers the advantages of providing both genetic (copy-number) and epigenetic (methylation) state information from a single genomic library. This method is advantageous when looking at large-scale chromosomal rearrangements such as the loss of the short arm of chromosome 3 (3p) in renal cell carcinoma and the codeletion of the short arm of chromosome 1 and the long arm of chromosome 19 (1p/19q) commonly seen in histologically defined oligodendrogliomas. Herein, we present MethylMasteR: a software framework that facilitates the standardization and customization of methylation-based CNV calling algorithms in a single R package deployed using the Docker software framework. This framework allows for the easy comparison of the performance and the large-scale CNV event identification capability of four common methylation-based CNV callers. Additionally, we incorporated our custom routine, which was among the best performing routines. We employed the Affymetrix 6.0 SNP Chip results as a gold standard against which to compare large-scale event recall. As there are disparities within the software calling algorithms themselves, no single software is likely to perform best for all samples and all combinations of parameters. The employment of a standardized software framework via creating a Docker image and its subsequent deployment as a Docker container allows researchers to efficiently compare algorithms and lends itself to the development of modified workflows such as the custom workflow we have developed. Researchers can now use the MethylMasteR software for their methylation-based CNV calling needs and follow our software deployment framework. We will continue to refine our methodology in the future with a specific focus on identifying large-scale chromosomal rearrangements in cancer methylation data.
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Affiliation(s)
- Michael P. Mariani
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
- Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, Hanover, NH, United States
| | - Jennifer A. Chen
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
| | - Ze Zhang
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
- Guarini School of Graduate and Advanced Studies, Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH, United States
| | - Steven C. Pike
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
- Guarini School of Graduate and Advanced Studies, Integrative Neuroscience at Dartmouth, Dartmouth College, Hanover, NH, United States
| | - Lucas A. Salas
- Geisel School of Medicine, Department of Epidemiology, Dartmouth College, Hanover, NH, United States
- *Correspondence: Lucas A. Salas,
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Pseudotime Analysis Reveals Exponential Trends in DNA Methylation Aging with Mortality Associated Timescales. Cells 2022; 11:cells11050767. [PMID: 35269389 PMCID: PMC8909670 DOI: 10.3390/cells11050767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
The epigenetic trajectory of DNA methylation profiles has a nonlinear relationship with time, reflecting rapid changes in DNA methylation early in life that progressively slow with age. In this study, we use pseudotime analysis to determine the functional form of these trajectories. Unlike epigenetic clocks that constrain the functional form of methylation changes with time, pseudotime analysis orders samples along a path, based on similarities in a latent dimension, to provide an unbiased trajectory. We show that pseudotime analysis can be applied to DNA methylation in human blood and brain tissue and find that it is highly correlated with the epigenetic states described by the Epigenetic Pacemaker. Moreover, we show that the pseudotime trajectory can be modeled with respect to time, using a sum of two exponentials, with coefficients that are close to the timescales of human age-associated mortality. Thus, for the first time, we can identify age-associated molecular changes that appear to track the exponential dynamics of mortality risk.
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Barrett JE, Jones A, Evans I, Reisel D, Herzog C, Chindera K, Kristiansen M, Leavy OC, Manchanda R, Bjørge L, Zikan M, Cibula D, Widschwendter M. The DNA methylome of cervical cells can predict the presence of ovarian cancer. Nat Commun 2022; 13:448. [PMID: 35105887 PMCID: PMC8807742 DOI: 10.1038/s41467-021-26615-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 10/04/2021] [Indexed: 02/03/2023] Open
Abstract
The vast majority of epithelial ovarian cancer arises from tissues that are embryologically derived from the Müllerian Duct. Here, we demonstrate that a DNA methylation signature in easy-to-access Müllerian Duct-derived cervical cells from women with and without ovarian cancer (i.e. referred to as the Women's risk IDentification for Ovarian Cancer index or WID-OC-index) is capable of identifying women with an ovarian cancer in the absence of tumour DNA with an AUC of 0.76 and women with an endometrial cancer with an AUC of 0.81. This and the observation that the cervical cell WID-OC-index mimics the epigenetic program of those cells at risk of becoming cancerous in BRCA1/2 germline mutation carriers (i.e. mammary epithelium, fallopian tube fimbriae, prostate) further suggest that the epigenetic misprogramming of cervical cells is an indicator for cancer predisposition. This concept has the potential to advance the field of risk-stratified cancer screening and prevention.
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Affiliation(s)
- James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Kantaraja Chindera
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Mark Kristiansen
- UCL Genomics, Zayed Centre for Research into Rare Disease in Children, University College London, London, WC1N 1DZ, UK
| | - Olivia C Leavy
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Department of Non-communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ranjit Manchanda
- Department of Gynaecological Oncology, Barts Health NHS Trust, Royal London Hospital, London, E1 1BB, UK
- Centre for Prevention, Detection & Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Health Services Research, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Line Bjørge
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Michal Zikan
- Hospital Na Bulovce, Prague, Czech Republic
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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