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Canning J, Strawbridge RJ, Miedzybrodzka Z, Marioni RE, Melbye M, Porteous DJ, Hurles ME, Sattar N, Sudlow CLM, Collins R, Padmanabhan S, Pell JP. Methods applied to neonatal dried blood spot samples for secondary research purposes: a scoping review. Crit Rev Clin Lab Sci 2024:1-24. [PMID: 38855982 DOI: 10.1080/10408363.2024.2360996] [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: 01/29/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
This scoping review aimed to synthesize the analytical techniques used and methodological limitations encountered when undertaking secondary research using residual neonatal dried blood spot (DBS) samples. Studies that used residual neonatal DBS samples for secondary research (i.e. research not related to newborn screening for inherited genetic and metabolic disorders) were identified from six electronic databases: Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Embase, Medline, PubMed and Scopus. Inclusion was restricted to studies published from 1973 and written in or translated into English that reported the storage, extraction and testing of neonatal DBS samples. Sixty-seven studies were eligible for inclusion. Included studies were predominantly methodological in nature and measured various analytes, including nucleic acids, proteins, metabolites, environmental pollutants, markers of prenatal substance use and medications. Neonatal DBS samples were stored over a range of temperatures (ambient temperature, cold storage or frozen) and durations (two weeks to 40.5 years), both of which impacted the recovery of some analytes, particularly amino acids, antibodies and environmental pollutants. The size of DBS sample used and potential contamination were also cited as methodological limitations. Residual neonatal DBS samples retained by newborn screening programs are a promising resource for secondary research purposes, with many studies reporting the successful measurement of analytes even from neonatal DBS samples stored for long periods of time in suboptimal temperatures and conditions.
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Affiliation(s)
- Jordan Canning
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
| | - Rona J Strawbridge
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
- Division of Cardiovascular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Zosia Miedzybrodzka
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, UK
- Medical Genetics Group, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Aberdeen, UK
| | - Riccardo E Marioni
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mads Melbye
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - David J Porteous
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Naveed Sattar
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Cathie L M Sudlow
- Usher Institute, University of Edinburgh, Edinburgh, UK
- Health Data Research UK, London, UK
| | - Rory Collins
- Clinical Trial Service Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sandosh Padmanabhan
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Jill P Pell
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
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Oocyte age and preconceptual alcohol use are highly correlated with epigenetic imprinting of a noncoding RNA ( nc886). Proc Natl Acad Sci U S A 2021; 118:2026580118. [PMID: 33723081 PMCID: PMC8000112 DOI: 10.1073/pnas.2026580118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting occurs before fertilization, impacts every cell of the developing child, and may be sensitive to environmental perturbations. The noncoding RNA, nc886 (also called VTRNA2-1) is the only known example of the ∼100 human genes imprinted by DNA methylation, that shows polymorphic imprinting in the population. The nc886 gene is part of an ∼1.6-kb differentially methylated region (DMR) that is methylated in the oocyte and silenced on the maternal allele in about 75% of humans worldwide. Here, we show that the presence or absence of imprinting at the nc886 DMR in an individual is consistent across different tissues, confirming that the imprint is established before cellular differentiation and is maintained into adulthood. We investigated the relationships between the frequency of imprinting in newborns and maternal age, alcohol consumption and cigarette smoking before conception in more than 1,100 mother/child pairs from South Africa. The probability of imprinting in newborns was increased in older mothers and decreased in mothers who drank alcohol before conception. On the other hand, cigarette smoking had no apparent relationship with the frequency of imprinting. These data show an epigenetic change during oocyte maturation which is potentially subject to environmental influence. Much focus has been placed on avoiding alcohol consumption during pregnancy, but our data suggest that drinking before conception may affect the epigenome of the newborn.
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Ryan CP. "Epigenetic clocks": Theory and applications in human biology. Am J Hum Biol 2020; 33:e23488. [PMID: 32845048 DOI: 10.1002/ajhb.23488] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
All humans age, but how we age-and how fast-differs considerably from person to person. This deviation between apparent age and chronological age is often referred to as "biological age" (BA) and until recently robust tools for studying BA have been scarce. "Epigenetic clocks" are starting to change this. Epigenetic clocks use predictable changes in the epigenome, usually DNA methylation, to estimate chronological age with unprecedented accuracy. More importantly, deviations between epigenetic age and chronological age predict a broad range of health outcomes and mortality risks better than chronological age alone. Thus, epigenetic clocks appear to capture fundamental molecular processes tied to BA and can serve as powerful tools for studying health, development, and aging across the lifespan. In this article, I review epigenetic clocks, especially as they relate to key theoretical and applied issues in human biology. I first provide an overview of how epigenetic clocks are constructed and what we know about them. I then discuss emerging applications of particular relevance to human biologists-those related to reproduction, life-history, stress, and the environment. I conclude with an overview of the methods necessary for implementing epigenetic clocks, including considerations of study design, sample collection, and technical considerations for processing and interpreting epigenetic clocks. The goal of this review is to highlight some of the ways that epigenetic clocks can inform questions in human biology, and vice versa, and to provide human biologists with the foundational knowledge necessary to successfully incorporate epigenetic clocks into their research.
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Affiliation(s)
- Calen P Ryan
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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Tikellis G, Dwyer T, Paltiel O, Phillips GS, Lemeshow S, Golding J, Northstone K, Boyd A, Olsen S, Ghantous A, Herceg Z, Ward MH, Håberg SE, Magnus P, Olsen J, Ström M, Mahabir S, Jones RR, Ponsonby AL, Clavel J, Charles MA, Trevathan E, Qian Z(M, Maule MM, Qiu X, Hong YC, Brandelise S, Roman E, Wake M, He JR, Linet MS. The International Childhood Cancer Cohort Consortium (I4C): A research platform of prospective cohorts for studying the aetiology of childhood cancers. Paediatr Perinat Epidemiol 2018; 32:568-583. [PMID: 30466188 PMCID: PMC11155068 DOI: 10.1111/ppe.12519] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/23/2018] [Accepted: 08/25/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND Childhood cancer is a rare but leading cause of morbidity and mortality. Established risk factors, accounting for <10% of incidence, have been identified primarily from case-control studies. However, recall, selection and other potential biases impact interpretations particularly, for modest associations. A consortium of pregnancy and birth cohorts (I4C) was established to utilise prospective, pre-diagnostic exposure assessments and biological samples. METHODS Eligibility criteria, follow-up methods and identification of paediatric cancer cases are described for cohorts currently participating or planning future participation. Also described are exposure assessments, harmonisation methods, biological samples potentially available for I4C research, the role of the I4C data and biospecimen coordinating centres and statistical approaches used in the pooled analyses. RESULTS Currently, six cohorts recruited over six decades (1950s-2000s) contribute data on 388 120 mother-child pairs. Nine new cohorts from seven countries are anticipated to contribute data on 627 500 additional projected mother-child pairs within 5 years. Harmonised data currently includes over 20 "core" variables, with notable variability in mother/child characteristics within and across cohorts, reflecting in part, secular changes in pregnancy and birth characteristics over the decades. CONCLUSIONS The I4C is the first cohort consortium to have published findings on paediatric cancer using harmonised variables across six pregnancy/birth cohorts. Projected increases in sample size, expanding sources of exposure data (eg, linkages to environmental and administrative databases), incorporation of biological measures to clarify exposures and underlying molecular mechanisms and forthcoming joint efforts to complement case-control studies offer the potential for breakthroughs in paediatric cancer aetiologic research.
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Affiliation(s)
- Gabriella Tikellis
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
| | - Terence Dwyer
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
- The George Institute for Global Health, University of Oxford, UK
| | - Ora Paltiel
- Braun School of Public Health, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Gary S. Phillips
- Center for Biostatistics, Department of Biomedical Informatics, Ohio State University, Columbus, Ohio, USA
| | - Stanley Lemeshow
- Division of Biostatistics, College of Public Health, Ohio State University, Columbus, Ohio, USA
| | - Jean Golding
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kate Northstone
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andy Boyd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sjurdur Olsen
- Centre for Fetal Programming, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Mary H. Ward
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Siri E. Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Norwat
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Norwat
| | - Jørn Olsen
- Department of Clinical Epidemiology, Aarhus University, Aarhus, Denmark
| | - Marin Ström
- Centre for Fetal Programming, Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Somdat Mahabir
- Division of Cancer Control and Population Sciences. National Cancer Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Rena R. Jones
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Anne-Louise Ponsonby
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
| | - Jacqueline Clavel
- Institut National de la Santé et de la Recherche Médicale, Centre for Research in Epidemiology and Statistics Sorbonne Paris Cité, Villejuif, France
| | - Marie Aline Charles
- Institut National de la Santé et de la Recherche Médicale, Centre for Research in Epidemiology and Statistics Sorbonne Paris Cité, Villejuif, France
| | - Edwin Trevathan
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, USA
| | - Zhengmin (Min) Qian
- College for Public Health and Social Justice, Saint Louis University, Missouri, USA
| | - Milena M. Maule
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Xiu Qiu
- Department of Woman and Child Health Care, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yun-Chul Hong
- Institute of Environmental Medicine, College of Medicine, Seoul National University, South Korea
| | | | - Eve Roman
- Epidemiology and Cancer Statistics Group, Health Sciences, York University, UK
| | - Melissa Wake
- Population Epidemiology, Murdoch Children’s Research Institute, Royal Children’s Hospital, University of Melbourne, Melbourne, Australia
| | - Jian-Rong He
- Department of Woman and Child Health Care, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, UK
| | - Martha S. Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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