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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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Stingone JA, Triantafillou S, Larsen A, Kitt JP, Shaw GM, Marsillach J. Interdisciplinary data science to advance environmental health research and improve birth outcomes. ENVIRONMENTAL RESEARCH 2021; 197:111019. [PMID: 33737076 PMCID: PMC8187296 DOI: 10.1016/j.envres.2021.111019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 03/10/2021] [Indexed: 05/30/2023]
Abstract
Rates of preterm birth and low birthweight continue to rise in the United States and pose a significant public health problem. Although a variety of environmental exposures are known to contribute to these and other adverse birth outcomes, there has been a limited success in developing policies to prevent these outcomes. A better characterization of the complexities between multiple exposures and their biological responses can provide the evidence needed to inform public health policy and strengthen preventative population-level interventions. In order to achieve this, we encourage the establishment of an interdisciplinary data science framework that integrates epidemiology, toxicology and bioinformatics with biomarker-based research to better define how population-level exposures contribute to these adverse birth outcomes. The proposed interdisciplinary research framework would 1) facilitate data-driven analyses using existing data from health registries and environmental monitoring programs; 2) develop novel algorithms with the ability to predict which exposures are driving, in this case, adverse birth outcomes in the context of simultaneous exposures; and 3) refine biomarker-based research, ultimately leading to new policies and interventions to reduce the incidence of adverse birth outcomes.
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Affiliation(s)
- Jeanette A Stingone
- Department of Epidemiology, Columbia University's Mailman School of Public Health, 722 West 168th St, Room 1608, New York, NY, 10032, USA.
| | - Sofia Triantafillou
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexandra Larsen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Jay P Kitt
- Departments of Chemistry and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Judit Marsillach
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
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Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, Wiemels J, Marini NJ. Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk. Epigenetics 2019; 14:198-213. [PMID: 30870065 PMCID: PMC6557558 DOI: 10.1080/15592294.2019.1581591] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common human birth defect whose etiologies remain largely unknown. Several studies have demonstrated that periconceptional supplementation of folic acid can reduce risk of CL/P in offspring. In this study, we tested the hypothesis that the preventive effect of folic acid is manifested through epigenetic modifications by determining whether DNA methylation changes are associated with CL/P. To more readily observe the potential effects of maternal folate on the offspring epigenome, we focused on births prior to mandatory dietary folate fortification in the United States (i.e. birth year 1997 or earlier). Genomic DNA methylation levels were assessed from archived newborn bloodspots in a 182-member case-control study using the Illumina® Human Beadchip 450K array. CL/P cases displayed striking epigenome-wide hypomethylation relative to controls: 63% of CpGs interrogated had lower methylation levels in case newborns, a trend which held up in racially stratified sub-groups. 28 CpG sites reached epigenome-wide significance and all were case-hypomethylated. The most significant CL/P-associated differentially methylated region encompassed the VTRNA2-1 gene, which was also hypomethylated in cases (FWER p = 0.014). This region has been previously characterized as a nutritionally-responsive, metastable epiallele and CL/P-associated methylation changes, in general, were greater at or near putative metastable epiallelic regions. Gene Set Enrichment Analysis of CL/P-associated DMRs showed an over-representation of genes involved in palate development such as WNT9B, MIR140 and LHX8. CL/P-associated DNA methylation changes may partly explain the mechanism by which orofacial clefts are responsive to maternal folate levels.
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Affiliation(s)
- Semira Gonseth
- a School of Public Health , University of California , Berkeley , CA , USA.,b Institute of Social and Preventive Medicine , Lausanne University Hospital , Lausanne , Switzerland
| | - Gary M Shaw
- c Department of Pediatrics , Stanford University School of Medicine , Stanford , CA , USA
| | - Ritu Roy
- d Cancer Research Institute , University of California , San Francisco , CA , USA
| | - Mark R Segal
- e Department of Epidemiology and Biostatistics , University of California , San Francisco , CA , USA
| | - Kripa Asrani
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Jasper Rine
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Joseph Wiemels
- g Center for Genetic Epidemiology , University of Southern California School of Medicine , Los Angeles , CA , USA
| | - Nicholas J Marini
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
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Walker RM, MacGillivray L, McCafferty S, Wrobel N, Murphy L, Kerr SM, Morris SW, Campbell A, McIntosh AM, Porteous DJ, Evans KL. Assessment of dried blood spots for DNA methylation profiling. Wellcome Open Res 2019; 4:44. [PMID: 30984878 PMCID: PMC6446498 DOI: 10.12688/wellcomeopenres.15136.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 11/26/2022] Open
Abstract
Background: DNA methylation reflects health-related environmental exposures and genetic risk, providing insights into aetiological mechanisms and potentially predicting disease onset, progression and treatment response. An increasingly recognised need for large-scale, longitudinally-profiled samples collected world-wide has made the development of efficient and straightforward sample collection and storage procedures a pressing issue. An alternative to the low-temperature storage of EDTA tubes of venous blood samples, which are frequently the source of the DNA used in such studies, is to collect and store at room temperature blood samples using purpose built filter paper, such as Whatman FTA® cards. Our goal was to determine whether DNA stored in this manner can be used to generate DNA methylation profiles comparable to those generated using blood samples frozen in EDTA tubes. Methods: DNA methylation profiles were obtained from matched EDTA tube and Whatman FTA® card whole-blood samples from 62 Generation Scotland: Scottish Family Health Study participants using the Infinium HumanMethylation450 BeadChip. Multiple quality control procedures were implemented, the relationship between the two sample types assessed, and epigenome-wide association studies (EWASs) performed for smoking status, age and the interaction between these variables and sample storage method. Results: Dried blood spot (DBS) DNA methylation profiles were of good quality and DNA methylation profiles from matched DBS and EDTA tube samples were highly correlated (mean
r = 0.991) and could distinguish between participants. EWASs replicated established associations for smoking and age, with no evidence for moderation by storage method. Conclusions: Our results support the use of Whatman FTA® cards for collecting and storing blood samples for DNA methylation profiling. This approach is likely to be particularly beneficial for large-scale studies and those carried out in areas where freezer access is limited. Furthermore, our results will inform consideration of the use of newborn heel prick DBSs for research use.
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Affiliation(s)
- Rosie M Walker
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Louise MacGillivray
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Sarah McCafferty
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Shona M Kerr
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Stewart W Morris
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Division of Psychiatry, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - David J Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Kathryn L Evans
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
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