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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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2
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Fernandez-De-Los-Reyes I, Gomez-Dorronsoro M, Monreal-Santesteban I, Fernandez-Fernandez A, Fraga M, Azcue P, Alonso L, Fernandez-Marlasca B, Suarez J, Cordoba-Iturriagagoitia A, Guerrero-Setas D. ZEB1 hypermethylation is associated with better prognosis in patients with colon cancer. Clin Epigenetics 2023; 15:193. [PMID: 38093305 PMCID: PMC10720242 DOI: 10.1186/s13148-023-01605-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Colon cancer (CC) is a heterogeneous disease that is categorized into four Consensus Molecular Subtypes (CMS) according to gene expression. Patients with loco-regional CC (stages II/III) lack prognostic factors, making it essential to analyze new molecular markers that can delineate more aggressive tumors. Aberrant methylation of genes that are essential in crucial mechanisms such as epithelial mesenchymal transition (EMT) contributes to tumor progression in CC. We evaluate the presence of hyper- and hypomethylation in subrogate IHC markers used for CMS classification (CDX2, FRMD6, HTR2B, ZEB1) of 144 stage II/III patients and CC cell lines by pyrosequencing. ZEB1 expression was also studied in control and shRNA-silenced CC cell lines and in paired normal tissue/tumors by quantitative PCR. The pattern of ZEB1 staining was also analyzed in methylated/unmethylated tumors by immunohistochemistry. RESULTS We describe for the first time the hypermethylation of ZEB1 gene and the hypomethylation of the FRMD6 gene in 32.6% and 50.9% of tumors, respectively. Additionally, we confirm the ZEB1 re-expression by epigenetic drugs in methylated cell lines. ZEB1 hypermethylation was more frequent in CMS1 patients and, more importantly, was a good prognostic factor related to disease-free survival (p = 0.015) and overall survival (p = 0.006) in our patient series, independently of other significant clinical parameters such as patient age, stage, lymph node involvement, and blood vessel and perineural invasion. CONCLUSIONS Aberrant methylation is present in the subrogate genes used for CMS classification. Our results are the first evidence that ZEB1 is hypermethylated in CC and that this alteration is an independent factor of good prognosis.
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Affiliation(s)
- Irene Fernandez-De-Los-Reyes
- Department of Pathology, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
- Molecular Pathology of Cancer Group, Navarrabiomed, Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Marisa Gomez-Dorronsoro
- Department of Pathology, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
- Oncogenetic and Hereditary Cancer Group, Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Iñaki Monreal-Santesteban
- Molecular Pathology of Cancer Group, Navarrabiomed, Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - Agustín Fernandez-Fernandez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), 33940, El Entrego, Spain
- Health Research Institute of Asturias (ISPA), 33011, Oviedo, Spain
- University Institute of Oncology (IUOPA), University of Oviedo, 33006, Oviedo, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Mario Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), 33940, El Entrego, Spain
- Health Research Institute of Asturias (ISPA), 33011, Oviedo, Spain
- University Institute of Oncology (IUOPA), University of Oviedo, 33006, Oviedo, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 28029, Madrid, Spain
| | - Pablo Azcue
- Department of Health Science, Public University of Navarra, Irunlarrea 3, 31008, Pamplona, Spain
| | - Laura Alonso
- Department of Pathology, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | | | - Javier Suarez
- Department of Surgery, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
| | - Alicia Cordoba-Iturriagagoitia
- Department of Pathology, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain
- Molecular Pathology of Cancer Group, Navarrabiomed, Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain
| | - David Guerrero-Setas
- Department of Pathology, Hospital Universitario de Navarra (HUN), Irunlarrea 3, 31008, Pamplona, Spain.
- Molecular Pathology of Cancer Group, Navarrabiomed, Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008, Pamplona, Spain.
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Pregnolato S, Sabir H, Luyt K, Rienecker KDA, Isles AR, Chakkarapani E. Regulation of glutamate transport and neuroinflammation in a term newborn rat model of hypoxic–ischaemic brain injury. Brain Neurosci Adv 2022; 6:23982128221097568. [PMID: 35615059 PMCID: PMC9125068 DOI: 10.1177/23982128221097568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/12/2022] [Indexed: 11/17/2022] Open
Abstract
In the newborn brain, moderate-severe hypoxia–ischaemia induces glutamate excitotoxicity and inflammation, possibly via dysregulation of candidate astrocytic glutamate transporter ( Glt1) and pro-inflammatory cytokines (e.g. Tnfα, Il1β, Il6). Epigenetic mechanisms may mediate dysregulation. Hypotheses: (1) hypoxia–ischaemia dysregulates mRNA expression of these candidate genes; (2) expression changes in Glt1 are mediated by DNA methylation changes; and (3) methylation values in brain and blood are correlated. Seven-day-old rat pups ( n = 42) were assigned to nine groups based on treatment (for each timepoint: naïve ( n = 3), sham ( n = 3), hypoxia–ischaemia ( n = 8) and timepoint for tissue collection (6, 12 and 24 h post-hypoxia). Moderate hypoxic–ischemic brain injury was induced via ligation of the left common carotid artery followed by 100 min hypoxia (8% O2, 36°C). mRNA was quantified in cortex and hippocampus for the candidate genes, myelin ( Mbp), astrocytic ( Gfap) and neuronal ( Map2) markers (qPCR). DNA methylation was measured for Glt1 in cortex and blood (bisulphite pyrosequencing). Hypoxia–ischaemia induced pro-inflammatory cytokine upregulation in both brain regions at 6 h. This was accompanied by gene expression changes potentially indicating onset of astrogliosis and myelin injury. There were no significant changes in expression or promoter DNA methylation of Glt1. This pilot study supports accumulating evidence that hypoxia–ischaemia causes neuroinflammation in the newborn brain and prioritises further expression and DNA methylation analyses focusing on this pathway. Epigenetic blood biomarkers may facilitate identification of high-risk newborns at birth, maximising chances of neuroprotective interventions.
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Affiliation(s)
- Silvia Pregnolato
- Department of Neonatal Neurology, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hemmen Sabir
- Department of Neonatology and Pediatric Intensive Care, Children’s Hospital, University of Bonn, Bonn, Germany
- Department of Pediatrics I/Neonatology, University Hospital Essen, University Duisburg Essen, Essen, Germany
| | - Karen Luyt
- Department of Neonatal Neurology, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kira DA Rienecker
- Department of Physical Therapy and Rehabilitation Science, University of California San Francisco, San Francisco, CA, USA
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Anthony R Isles
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
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Guan X, Ohuchi T, Hashiyada M, Funayama M. Age-related DNA methylation analysis for forensic age estimation using post-mortem blood samples from Japanese individuals. Leg Med (Tokyo) 2021; 53:101917. [PMID: 34126371 DOI: 10.1016/j.legalmed.2021.101917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 01/21/2023]
Abstract
As one of external visible characteristics (EVCs) in forensic phenotyping, age estimation is essential to providing additional information about a sample donor. With the development of epigenetics, age-related DNA methylation may be used as a reliable predictor of age estimation. With the aim of building a feasible age estimation model for Japanese individuals, 53 CpG sites distributed between 11 candidate genes were selected from previous studies. The DNA methylation level of each target CpG site was identified and measured on a massive parallel platform (synthesis by sequencing, Illumina, California, United States) from 60 forensic blood samples during the initial training phase. Multiple linear regression and quantile regression analyses were later performed to build linear and quantile age estimation models, respectively. Four CpG sites on four genes- ASPA, ELOVL2, ITGA2B, and PDE4C -, were found to be highly correlated with chronological age in DNA samples from Japanese individuals (|R| > 0.75). Subsequently, an independent validation dataset (n = 30) was used to verify and evaluate the performance of the two models. Comparison of mean absolute deviation (MAD) with other indicators showed that both models provide accurate age predictions (MAD: linear = 6.493 years; quantile = 6.243 years). The quantile model, however, can provide the changeable prediction intervals that grow wider with increasing age, and this tendency is consistent with the natural aging process in humans. Hence, the quantile model is recommended in this study.
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Affiliation(s)
- X Guan
- Tohoku University, Graduate School of Medicine, Department of Forensic Medicine, Japan.
| | - T Ohuchi
- Tohoku University, Graduate School of Medicine, Department of Forensic Medicine, Japan
| | - M Hashiyada
- Department of Legal Medicine, Kansai Medical University, Japan
| | - M Funayama
- Tohoku University, Graduate School of Medicine, Department of Forensic Medicine, Japan
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Woźniak A, Heidegger A, Piniewska-Róg D, Pośpiech E, Xavier C, Pisarek A, Kartasińska E, Boroń M, Freire-Aradas A, Wojtas M, de la Puente M, Niederstätter H, Płoski R, Spólnicka M, Kayser M, Phillips C, Parson W, Branicki W. Development of the VISAGE enhanced tool and statistical models for epigenetic age estimation in blood, buccal cells and bones. Aging (Albany NY) 2021; 13:6459-6484. [PMID: 33707346 PMCID: PMC7993733 DOI: 10.18632/aging.202783] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/16/2021] [Indexed: 01/07/2023]
Abstract
DNA methylation is known as a biomarker for age with applications in forensics. Here we describe the VISAGE (VISible Attributes through GEnomics) Consortium's enhanced tool for epigenetic age estimation in somatic tissues. The tool is based on eight DNA methylation markers (44 CpGs), bisulfite multiplex PCR followed by sequencing on the MiSeq FGx platform, and three statistical prediction models for blood, buccal cells and bones. The model for blood is based on six CpGs from ELOVL2, MIR29B2CHG, KLF14, FHL2, TRIM59 and PDE4C, and predicts age with a mean absolute error (MAE) of 3.2 years, while the model for buccal cells includes five CpGs from PDE4C, MIR29B2CHG, ELOVL2, KLF14 and EDARADD and predicts age with MAE of 3.7 years, and the model for bones has six CpGs from ELOVL2, KLF14, PDE4C and ASPA and predicts age with MAE of 3.4 years. The VISAGE enhanced tool for age estimation in somatic tissues enables reliable collection of DNA methylation data from small amounts of DNA using a sensitive multiplex MPS assay that provides accurate estimation of age in blood, buccal swabs, and bones using the statistical model tailored to each tissue.
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Affiliation(s)
- Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Antonia Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Danuta Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Wojtas
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Maria de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Rafał Płoski
- Department Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | | | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Wojciech Branicki
- Central Forensic Laboratory of the Police, Warsaw, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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6
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Development and optimization of the VISAGE basic prototype tool for forensic age estimation. Forensic Sci Int Genet 2020; 48:102322. [PMID: 32574993 DOI: 10.1016/j.fsigen.2020.102322] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/22/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023]
Abstract
The VISAGE (VISible Attributes through GEnomics) consortium aims to develop, optimize and validate prototype tools to broaden the use of DNA intelligence methods in forensic routine laboratories. This includes age estimation based on the quantification of DNA methylation at specific CpG sites. Here, we present the VISAGE basic prototype tool for age estimation targeting 32 CpGs from five genes ELOVL2, MIR29B2CHG (herein, MIR29B2C), FHL2, TRIM59 and KLF14. The assay interrogates these well described age markers by multiplex PCR for bisulfite converted DNA and massively parallel sequencing on a MiSeq FGx instrument. We describe protocol optimizations including tests on five bisulfite conversion kits and an evaluation of the assay's reproducibility and sensitivity with artificially methylated DNA standards. We observed robust quantification of methylation levels with a mean standard deviation of 1.4 % across ratios. Sensitivity tests showed no increase of variability down to 20 ng DNA input into bisulfite conversion with a median difference below 1.6 % between technical replicates.
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7
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Menschikowski M, Jandeck C, Friedemann M, Nacke B, Hantsche S, Tiebel O, Sukocheva O, Hagelgans A. Identification of rare levels of methylated tumor DNA fragments using an optimized bias based pre-amplification-digital droplet PCR (OBBPA-ddPCR). Oncotarget 2018; 9:36137-36150. [PMID: 30546833 PMCID: PMC6281424 DOI: 10.18632/oncotarget.26315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/24/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The analysis of aberrant DNA methylations is used for the diagnosis of cancer as significant changes in the gene methylation pattern are often detected during early carcinogenesis. In this study, we evaluated the performance of a two-step method that combines pre-amplification with ddPCR technique. RESULTS By using ddPCR, the dependence of amplification efficiency for methylated and unmethylated DNA fragments on the relevant MgCl2 concentration and the annealing temperature was established in addition to the primer design. We found that the efficiency can be adjusted toward methylated sequences by using primers covering one to four CpG sites under appropriately selected MgCl2 concentration and annealing temperature. Applying a PCR bias between 85% and 95%, five copies of methylated tumor DNA fragments were detected against a background of 700,000 copies of unmethylated DNA fragments with a high signal-to-noise ratio. The analysis of serum samples from patients with prostate cancer showed a significantly improved performance of the new method in comparison with the MS-HRM technique, ddPCR alone, or ddPCR in combination with an unbiased pre-amplification using methylation-independent primers. CONCLUSIONS We define this method as an optimized bias-based pre-amplification-digital droplet PCR (OBBPA-ddPCR) technique. This novel method is recommended for the early detection of cancer-specific DNA methylation biomarkers in the form of a liquid biopsy.
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Affiliation(s)
- Mario Menschikowski
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Carsten Jandeck
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Markus Friedemann
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Brit Nacke
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Saskia Hantsche
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Oliver Tiebel
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
| | - Olga Sukocheva
- 2 School of Health Sciences, Flinders University of South Australia, Adelaide, Australia
| | - Albert Hagelgans
- 1 Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany
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Menschikowski M, Jandeck C, Friedemann M, Richter S, Thiem D, Lange BS, Suttorp M. Identification and Quantification of Heterogeneously-methylated DNA Fragments Using Epiallele-sensitive Droplet Digital Polymerase Chain Reaction (EAST-ddPCR). Cancer Genomics Proteomics 2018; 15:299-312. [PMID: 29976635 DOI: 10.21873/cgp.20088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/28/2018] [Accepted: 04/23/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND/AIM DNA methylation plays an important role in the initiation and propagation of carcinogenesis; however, the role of heterogeneously methylated epialleles is currently not well studied, also due to the lack of sensitive, unbiased and high throughput methods. Here, a newly developed droplet digital PCR (ddPCR)-based method was evaluated regarding its ability to quantify such heterogeneously methylated epialleles with sufficient analytical sensitivity and specificity. MATERIALS AND METHODS Genomic DNA from blood leukocytes and bone marrow aspirate of an 8-year old male with B-cell acute lymphoblastic leukemia (B-ALL) and from normal and malignant prostate cell lines were analysed using ddPCR. RESULTS By using these DNA samples, the specificity of an applied set of fluorescence-labeled probes was demonstrated as a proof of concept. CONCLUSION All individual heterogeneously-methylated epialleles were quantifiable by a set of fluorescence-labeled probes with complementary sequences to epialleles in a closed-tube and high-throughput manner. The new method named epiallele-sensitive droplet digital PCR (EAST-ddPCR) may give new insights in the generation and regulation of epialleles and may help in finding new biomarkers for the diagnosis of benign und malignant diseases.
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Affiliation(s)
- Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Carsten Jandeck
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Markus Friedemann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Dana Thiem
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Björn Sönke Lange
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Meinolf Suttorp
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
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9
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Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR, Reik W. Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data. Genome Biol 2018; 19:33. [PMID: 29544553 PMCID: PMC5856372 DOI: 10.1186/s13059-018-1408-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 02/14/2018] [Indexed: 12/20/2022] Open
Abstract
Background Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. Results We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. Conclusions We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets. Electronic supplementary material The online version of this article (10.1186/s13059-018-1408-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nelly Olova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Present address: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Rebecca V Berrens
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. .,Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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