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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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2
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Morgunova A, Ibrahim P, Chen GG, Coury SM, Turecki G, Meaney MJ, Gifuni A, Gotlib IH, Nagy C, Ho TC, Flores C. Preparation and processing of dried blood spots for microRNA sequencing. Biol Methods Protoc 2023; 8:bpad020. [PMID: 37901452 PMCID: PMC10603595 DOI: 10.1093/biomethods/bpad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023] Open
Abstract
Dried blood spots (DBS) are biological samples commonly collected from newborns and in geographic areas distanced from laboratory settings for the purposes of disease testing and identification. MicroRNAs (miRNAs)-small non-coding RNAs that regulate gene activity at the post-transcriptional level-are emerging as critical markers and mediators of disease, including cancer, infectious diseases, and mental disorders. This protocol describes optimized procedural steps for utilizing DBS as a reliable source of biological material for obtaining peripheral miRNA expression profiles. We outline key practices, such as the method of DBS rehydration that maximizes RNA extraction yield, and the use of degenerate oligonucleotide adapters to mitigate ligase-dependent biases that are associated with small RNA sequencing. The standardization of miRNA readout from DBS offers numerous benefits: cost-effectiveness in sample collection and processing, enhanced reliability and consistency of miRNA profiling, and minimal invasiveness that facilitates repeated testing and retention of participants. The use of DBS-based miRNA sequencing is a promising method to investigate disease mechanisms and to advance personalized medicine.
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Affiliation(s)
- Alice Morgunova
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Pascal Ibrahim
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Gary Gang Chen
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Saché M Coury
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Gustavo Turecki
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Brenner Centre for Molecular Medicine, Singapore City 138632, Singapore
| | - Anthony Gifuni
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
| | - Corina Nagy
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Tiffany C Ho
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Cecilia Flores
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
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Marcotte EL, Spector LG, Mendes-de-Almeida DP, Nelson HH. The Prenatal Origin of Childhood Leukemia: Potential Applications for Epidemiology and Newborn Screening. Front Pediatr 2021; 9:639479. [PMID: 33968846 PMCID: PMC8102903 DOI: 10.3389/fped.2021.639479] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/22/2021] [Indexed: 12/22/2022] Open
Abstract
Childhood leukemias are heterogeneous diseases with widely differing incident rates worldwide. As circulating tumors, childhood acute leukemias are uniquely accessible, and their natural history has been described in greater detail than for solid tumors. For several decades, it has been apparent that most cases of childhood acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) initiate in utero. Circumstantial evidence in support of this contention includes the young age of onset and high rate of concordance among identical twins. "Backtracking" of leukemic somatic mutations, particularly gene translocations, to cord blood and dried blood spots collected during the perinatal period has provided molecular proof of prenatal leukemogenesis. Detection of a patient's leukemia translocation in easily accessible birth samples, such as dried blood spots, is straightforward with the knowledge of their idiosyncratic breakpoints. However, to translate these findings into population-based screening and leukemia prevention requires novel methods able to detect translocations at all possible breakpoints when present in a low frequency of cells. Several studies have attempted to screen for leukemic translocations, mainly the common ETV6-RUNX1 translocation, in cord blood samples from healthy children. Most studies have reported finding translocations in healthy children, but estimates of prevalence have varied widely and greatly exceed the incidence of leukemia, leading to concerns that technical artifact or contamination produced an artificially inflated estimate of translocation prevalence at birth. New generation techniques that capture the presence of these translocations at birth have the potential to vastly increase our understanding of the epidemiology of acute leukemias. For instance, if leukemic translocations are present at birth in a far higher proportion of children than eventually develop acute leukemia, what are the exposures and somatic molecular events that lead to disease? And could children with translocations present at birth be targeted for prevention of disease? These questions must be answered before large-scale newborn screening for leukemia can occur as a public health initiative. Here, we review the literature regarding backtracking of acute leukemias and the prevalence of leukemic translocations at birth. We further suggest an agenda for epidemiologic research using new tools for population screening of leukemic translocations.
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Affiliation(s)
- Erin L. Marcotte
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Logan G. Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Daniela P. Mendes-de-Almeida
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Department of Hematology, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- Division of Molecular Carcinogenesis, Research Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Heather H. Nelson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, United States
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McClendon-Weary B, Putnick DL, Robinson S, Yeung E. Little to Give, Much to Gain-What Can You Do With a Dried Blood Spot? Curr Environ Health Rep 2021; 7:211-221. [PMID: 32851603 DOI: 10.1007/s40572-020-00289-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Technological advances have allowed dried blood spots (DBS) to be utilized for various measurements, helpful in population-based studies. The following is a review of the literature highlighting the advantages and disadvantages of DBS and describing their use in multiple areas of research. RECENT FINDINGS DBS can track pollutant exposure to understand their impact on health. DBS can also be used for (epi-)genetic studies, to measure clinical biomarkers, and to monitor drug adherence. Advantages of DBS include being minimally invasive, requiring low blood volume, and being cost-effective to collect, transport, and store. Disadvantages of DBS include the hematocrit effect, which is related to the viscosity of the blood affecting its spread on to the filter paper, causing a major source of error when assessing concentrations, and the possibility of low DNA volume. Numerous uses for DBS make them an important source of biomaterial but they require additional validation for accuracy and reproducibility.
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Affiliation(s)
- Bryttany McClendon-Weary
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Diane L Putnick
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Sonia Robinson
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, 20817, USA.
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Kumar A, Mhatre S, Godbole S, Jha P, Dikshit R. Optimization of extraction of genomic DNA from archived dried blood spot (DBS): potential application in epidemiological research & bio banking. Gates Open Res 2019; 2:57. [PMID: 31815249 DOI: 10.12688/gatesopenres.12855.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Limited infrastructure is available to collect, store and transport venous blood in field epidemiological studies. Dried blood spot (DBS) is a robust potential alternative sample source for epidemiological studies & bio banking. A stable source of genomic DNA (gDNA) is required for long term storage in bio bank for its downstream applications. Our objective is to optimize the methods of gDNA extraction from stored DBS and with the aim of revealing its utility in large scale epidemiological studies. Methods: The purpose of this study was to extract the maximum amount of gDNA from DBS on Whatman 903 protein saver card. gDNA was extracted through column (Qiagen) & magnetic bead based (Invitrogen) methods. Quantification of extracted gDNA was performed with a spectrophotometer, fluorometer, and integrity analyzed by agarose gel electrophoresis. Result: Large variation was observed in quantity & purity (260/280 ratio, 1.8-2.9) of the extracted gDNA. The intact gDNA bands on the electrophoresis gel reflect the robustness of DBS for gDNA even after prolonged storage time. The extracted gDNA amount 2.16 - 24 ng/µl is sufficient for its PCR based downstream application, but unfortunately it can't be used for whole genome sequencing or genotyping from extracted gDNA. Sequencing or genotyping can be achieved by after increasing template copy number through whole genome amplification of extracted gDNA. The obtained results create a base for future research to develop high-throughput research and extraction methods from blood samples. Conclusion: The above results reveal, DBS can be utilized as a potential and robust sample source for bio banking in field epidemiological studies.
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Affiliation(s)
- Abhinendra Kumar
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sharayu Mhatre
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sheela Godbole
- Department of Biostatistics and Epidemiology, National AIDS Research Institute, Pune, Maharashtra, 411026, India
| | - Prabhat Jha
- Li Ka Shing Knowledge Institiute, St Michael's Hospital, Center for Global Health Research, Toronto, ON, Canada
| | - Rajesh Dikshit
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
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Kumar A, Mhatre S, Godbole S, Jha P, Dikshit R. Optimization of extraction of genomic DNA from archived dried blood spot (DBS): potential application in epidemiological research & bio banking. Gates Open Res 2019; 2:57. [PMID: 31815249 PMCID: PMC6883222 DOI: 10.12688/gatesopenres.12855.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Limited infrastructure is available to collect, store and transport venous blood in field epidemiological studies. Dried blood spot (DBS) is a robust potential alternative sample source for epidemiological studies & bio banking. A stable source of genomic DNA (gDNA) is required for long term storage in bio bank for its downstream applications. Our objective is to optimize the methods of gDNA extraction from stored DBS and with the aim of revealing its utility in large scale epidemiological studies. Methods: The purpose of this study was to extract the maximum amount of gDNA from DBS on Whatman 903 protein saver card. gDNA was extracted through column (Qiagen) & magnetic bead based (Invitrogen) methods. Quantification of extracted gDNA was performed with a spectrophotometer, fluorometer, and integrity analyzed by agarose gel electrophoresis. Result: Large variation was observed in quantity & purity (260/280 ratio, 1.8-2.9) of the extracted gDNA. The intact gDNA bands on the electrophoresis gel reflect the robustness of DBS for gDNA even after prolonged storage time. The extracted gDNA amount 2.16 – 24 ng/µl is sufficient for its PCR based downstream application, but unfortunately it can’t be used for whole genome sequencing or genotyping from extracted gDNA. Sequencing or genotyping can be achieved by after increasing template copy number through whole genome amplification of extracted gDNA. The obtained results create a base for future research to develop high-throughput research and extraction methods from blood samples. Conclusion: The above results reveal, DBS can be utilized as a potential and robust sample source for bio banking in field epidemiological studies.
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Affiliation(s)
- Abhinendra Kumar
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sharayu Mhatre
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sheela Godbole
- Department of Biostatistics and Epidemiology, National AIDS Research Institute, Pune, Maharashtra, 411026, India
| | - Prabhat Jha
- Li Ka Shing Knowledge Institiute, St Michael's Hospital, Center for Global Health Research, Toronto, ON, Canada
| | - Rajesh Dikshit
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
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7
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Kumar A, Mhatre S, Godbole S, Jha P, Dikshit R. Optimization of extraction of genomic DNA from archived dried blood spot (DBS): potential application in epidemiological research & bio banking. Gates Open Res 2019; 2:57. [DOI: 10.12688/gatesopenres.12855.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
Background:Limited infrastructure is available to collect, store and transport venous blood in field epidemiological studies. Dried blood spot (DBS) is a robust potential alternative sample source for epidemiological studies & bio banking. A stable source of genomic DNA (gDNA) is required for long term storage in bio bank for its downstream applications. Our objective is to optimize the methods of gDNA extraction from stored DBS and with the aim of revealing its utility in large scale epidemiological studies. Methods:The purpose of this study was to extract the maximum amount of gDNA from DBS on Whatman 903 protein saver card. gDNA was extracted through column (Qiagen) & magnetic bead based (Invitrogen) methods. Quantification of extracted gDNA was performed with a spectrophotometer, fluorometer, and integrity analyzed by agarose gel electrophoresis. Result:Large variation was observed in quantity & purity (260/280 ratio, 1.8-2.9) of the extracted gDNA. The intact gDNA bands on the electrophoresis gel reflect the robustness of DBS for gDNA even after prolonged storage time. The extracted gDNA amount 2.16 – 24 ng/µl is sufficient for its PCR based downstream application, but unfortunately it can’t be used for whole genome sequencing or genotyping from extracted gDNA. Sequencing or genotyping can be achieved by after increasing template copy number through whole genome amplification of extracted gDNA. The obtained results create a base for future research to develop high-throughput research and extraction methods from blood samples.Conclusion:The above results reveal, DBS can be utilized as a potential and robust sample source for bio banking in field epidemiological studies.
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Rovito R, Warnatz HJ, Kiełbasa SM, Mei H, Amstislavskiy V, Arens R, Yaspo ML, Lehrach H, Kroes ACM, Goeman JJ, Vossen ACTM. Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome. PLoS One 2018; 13:e0200652. [PMID: 30024899 PMCID: PMC6053152 DOI: 10.1371/journal.pone.0200652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/30/2018] [Indexed: 01/16/2023] Open
Abstract
Congenital Cytomegalovirus infection (cCMV) is the leading infection in determining permanent long-term impairments (LTI), and its pathogenesis is largely unknown due to the complex interplay between viral, maternal, placental, and child factors. The cellular activity, considered to be the result of the response to exogenous and endogenous factors, is captured by the determination of gene expression profiles. In this study, we determined whole blood transcriptomes in relation to cCMV, CMV viral load and LTI development at 6 years of age by using RNA isolated from neonatal dried blood spots (DBS) stored at room temperature for 8 years. As DBS were assumed to mainly reflect the neonatal immune system, particular attention was given to the immune pathways using the global test. Additionally, differential expression of individual genes was performed using the voom/limma function packages. We demonstrated feasibility of RNA sequencing from archived neonatal DBS of children with cCMV, and non-infected controls, in relation to LTI and CMV viral load. Despite the lack of statistical power to detect individual genes differences, pathway analysis suggested the involvement of innate immune response with higher CMV viral loads, and of anti-inflammatory markers in infected children that did not develop LTI. Finally, the T cell exhaustion observed in infected neonates, in particular with higher viral load, did not correlate with LTI, therefore other mechanisms are likely to be involved in the long-term immune dysfunction. Despite these data demonstrate limitation in determining prognostic markers for LTI by means of transcriptome analysis, this exploratory study represents a first step in unraveling the pathogenesis of cCMV, and the aforementioned pathways certainly merit further evaluation.
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Affiliation(s)
- Roberta Rovito
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
| | - Hans-Jörg Warnatz
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Szymon M. Kiełbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Vyacheslav Amstislavskiy
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Aloys C. M. Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J. Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Ann C. T. M. Vossen
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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Reust MJ, Lee MH, Xiang J, Zhang W, Xu D, Batson T, Zhang T, Downs JA, Dupnik KM. Dried Blood Spot RNA Transcriptomes Correlate with Transcriptomes Derived from Whole Blood RNA. Am J Trop Med Hyg 2018; 98:1541-1546. [PMID: 29512483 PMCID: PMC5953367 DOI: 10.4269/ajtmh.17-0653] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/14/2018] [Indexed: 01/14/2023] Open
Abstract
Obtaining RNA from clinical samples collected in resource-limited settings can be costly and challenging. The goals of this study were to 1) optimize messenger RNA extraction from dried blood spots (DBS) and 2) determine how transcriptomes generated from DBS RNA compared with RNA isolated from blood collected in Tempus tubes. We studied paired samples collected from eight adults in rural Tanzania. Venous blood was collected on Whatman 903 Protein Saver cards and in tubes with RNA preservation solution. Our optimal DBS RNA extraction used 8 × 3-mm DBS punches as the starting material, bead beater disruption at maximum speed for 60 seconds, extraction with Illustra RNAspin Mini RNA Isolation kit, and purification with Zymo RNA Concentrator kit. Spearman correlations of normalized gene counts in DBS versus whole blood ranged from 0.887 to 0.941. Bland-Altman plots did not show a trend toward over- or under-counting at any gene size. We report a method to obtain sufficient RNA from DBS to generate a transcriptome. The DBS transcriptome gene counts correlated well with whole blood transcriptome gene counts. Dried blood spots for transcriptome studies could be an option when field conditions preclude appropriate collection, storage, or transport of whole blood for RNA studies.
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Affiliation(s)
- Mary J. Reust
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Myung Hee Lee
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, New York
| | - Wei Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, New York
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, New York
| | - Tatiana Batson
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, New York
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, New York
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Ho NT, Busik JV, Resau JH, Paneth N, Khoo SK. Effect of storage time on gene expression data acquired from unfrozen archived newborn blood spots. Mol Genet Metab 2016; 119:207-213. [PMID: 27553879 PMCID: PMC5083152 DOI: 10.1016/j.ymgme.2016.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/13/2016] [Indexed: 01/11/2023]
Abstract
Unfrozen archived newborn blood spots (NBS) have been shown to retain sufficient messenger RNA (mRNA) for gene expression profiling. However, the effect of storage time at ambient temperature for NBS samples in relation to the quality of gene expression data is relatively unknown. Here, we evaluated mRNA expression from quantitative real-time PCR (qRT-PCR) and microarray data obtained from NBS samples stored at ambient temperature to determine the effect of storage time on the quality of gene expression. These data were generated in a previous case-control study examining NBS in 53 children with cerebral palsy (CP) and 53 matched controls. NBS sample storage period ranged from 3 to 16years at ambient temperature. We found persistently low RNA integrity numbers (RIN=2.3±0.71) and 28S/18S rRNA ratios (~0) across NBS samples for all storage periods. In both qRT-PCR and microarray data, the expression of three common housekeeping genes-beta cytoskeletal actin (ACTB), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and peptidylprolyl isomerase A (PPIA)-decreased with increased storage time. Median values of each microarray probe intensity at log2 scale also decreased over time. After eight years of storage, probe intensity values were largely reduced to background intensity levels. Of 21,500 genes tested, 89% significantly decreased in signal intensity, with 13,551, 10,730, and 9925 genes detected within 5years, > 5 to <10years, and >10years of storage, respectively. We also examined the expression of two gender-specific genes (X inactivation-specific transcript, XIST and lysine-specific demethylase 5D, KDM5D) and seven gene sets representing the inflammatory, hypoxic, coagulative, and thyroidal pathways hypothesized to be related to CP risk to determine the effect of storage time on the detection of these biologically relevant genes. We found the gender-specific genes and CP-related gene sets detectable in all storage periods, but exhibited differential expression (between male vs. female or CP vs. control) only within the first six years of storage. We concluded that gene expression data quality deteriorates in unfrozen archived NBS over time and that differential gene expression profiling and analysis is recommended for those NBS samples collected and stored within six years at ambient temperature.
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Affiliation(s)
- Nhan T Ho
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Julia V Busik
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - James H Resau
- Graduate School, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Nigel Paneth
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI, USA; Department of Pediatrics & Human Development, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
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Kohrt BA, Worthman CM, Adhikari RP, Luitel NP, Arevalo JMG, Ma J, McCreath H, Seeman TE, Crimmins EM, Cole SW. Psychological resilience and the gene regulatory impact of posttraumatic stress in Nepali child soldiers. Proc Natl Acad Sci U S A 2016; 113:8156-61. [PMID: 27402736 PMCID: PMC4961140 DOI: 10.1073/pnas.1601301113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adverse social conditions in early life have been linked to increased expression of proinflammatory genes and reduced expression of antiviral genes in circulating immune cells-the conserved transcriptional response to adversity (CTRA). However, it remains unclear whether such effects are specific to the Western, educated, industrialized, rich, and democratic (WEIRD) cultural environments in which previous research has been conducted. To assess the roles of early adversity and individual psychological resilience in immune system gene regulation within a non-WEIRD population, we evaluated CTRA gene-expression profiles in 254 former child soldiers and matched noncombatant civilians 5 y after the People's War in Nepal. CTRA gene expression was up-regulated in former child soldiers. These effects were linked to the degree of experienced trauma and associated distress-that is, posttraumatic stress disorder (PTSD) severity-more than to child soldier status per se. Self-perceived psychological resilience was associated with marked buffering of CTRA activation such that PTSD-affected former child soldiers with high levels of personal resilience showed molecular profiles comparable to those of PTSD-free civilians. These results suggest that CTRA responses to early life adversity are not restricted to WEIRD cultural contexts and they underscore the key role of resilience in determining the molecular impact of adverse environments.
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Affiliation(s)
- Brandon A Kohrt
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27708; Duke Global Health Institute, Duke University, Durham, NC 27710; Transcultural Psychosocial Organization Nepal, Kathmandu 44616, Nepal;
| | | | - Ramesh P Adhikari
- Transcultural Psychosocial Organization Nepal, Kathmandu 44616, Nepal
| | - Nagendra P Luitel
- Transcultural Psychosocial Organization Nepal, Kathmandu 44616, Nepal
| | - Jesusa M G Arevalo
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095; Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095
| | - Jeffrey Ma
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095; Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095
| | - Heather McCreath
- Division of Geriatrics, Department of Medicine, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095
| | - Teresa E Seeman
- Division of Geriatrics, Department of Medicine, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095; Department of Epidemiology, University of California, Los Angeles School of Public Health, Los Angeles, CA 90095
| | - Eileen M Crimmins
- Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - Steven W Cole
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095; Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095
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Cunningham S, O’Doherty KC, Sénécal K, Secko D, Avard D. Public concerns regarding the storage and secondary uses of residual newborn bloodspots: an analysis of print media, legal cases, and public engagement activities. J Community Genet 2015; 6:117-28. [PMID: 25533753 PMCID: PMC4356669 DOI: 10.1007/s12687-014-0206-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 12/03/2014] [Indexed: 11/29/2022] Open
Abstract
Recently, public concerns have been expressed regarding the non-consented storage and secondary research uses of residual newborn bloodspot (RBS) samples. The purpose of this paper is to examine public responses to the storage and secondary uses of RBS that can be identified through analysis of media, legal cases, and documented public engagement activities. Coverage in the examined print media confirmed the importance of RBS to journalists and those people who expressed their concerns to these journalists. Several lawsuits, brought by parents concerned about the storage of newborn bloodspots, placed the practice of storing NBS into the spotlight. This resulted in controversial debates and the mandatory destruction of millions of samples. Analysis of public engagement activities across several jurisdictions indicated that across (inter)national boundaries there are common elements to what is perceived as inappropriate governance of RBS. Public concerns were grouped into five main themes: trust, transparency, confidentiality, ownership, and stigmatization/discrimination. The results of our analysis help to make a compelling case for placing citizens at the center of the debate and developing policy about the storage and secondary uses of newborn bloodspots.
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Affiliation(s)
| | - Kieran C. O’Doherty
- />Department of Psychology, University of Guelph, Guelph, ON Canada NIG 2 W1
| | | | - David Secko
- />McGill University, Montréal, Quebec Canada
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Wei C, Lu Q, Khoo SK, Lenski M, Fichorova R, Leviton A, Paneth N. Comparison of frozen and unfrozen blood spots for gene expression studies. J Pediatr 2014; 164:189-191.e1. [PMID: 24209717 PMCID: PMC4326080 DOI: 10.1016/j.jpeds.2013.09.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 07/16/2013] [Accepted: 09/12/2013] [Indexed: 01/15/2023]
Abstract
We studied gene expression in 9 sets of paired newborn blood spots stored for 8-10 years in either the frozen state or the unfrozen state. Fewer genes were expressed in unfrozen spots, but the average correlation coefficient for overall gene expression comparing the frozen and unfrozen state was 0.771 (95% CI, 0.700-0.828).
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Affiliation(s)
- Changshuai Wei
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Qing Lu
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Sok Kean Khoo
- Laboratory of Microarray Technology, Van Andel Research Institute, Grand Rapids, MI
| | - Madeleine Lenski
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Raina Fichorova
- Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA
| | - Alan Leviton
- Neuroepidemiology Unit, Department of Neurology, Boston Children's Hospital, Harvard University, Boston, MA
| | - Nigel Paneth
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI; Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing, MI.
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Song Y, Fahs A, Feldman C, Shah S, Gu Y, Wang Y, Machado RF, Wunderink RG, Chen J. A reliable and effective method of DNA isolation from old human blood paper cards. SPRINGERPLUS 2013; 2:616. [PMID: 24307984 PMCID: PMC3847035 DOI: 10.1186/2193-1801-2-616] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/07/2013] [Indexed: 11/10/2022]
Abstract
Blood paper cards provide an effective DNA storage method. In this study, we used three DNA dissolving reagents (Tris-EDTA [TE] buffer, Tris–HCl buffer, and water) and one common commercially available kit (DN131 from MRC Inc) to elute DNA from 105 human blood paper cards collected up to 10 years ago. These DNA samples were used as templates for amplification of a single nucleotide polymorphism (SNP, C125T) region of human caspase-12 by PCR and a specific Taqman genotyping assay using the same amount of DNA. We show that DNA isolated by Tris–HCl buffer has higher yield and quality in comparison to DN131 solution. PCR success rate to amplify caspase-12 C125T SNP using Tris–HCl is comparable to the method using DN131 (89.5% vs 87.6%). The Taqman genotyping success rate using Tris–HCl is higher than using DN131 (81.9% vs 70.5%). Using TE or water, PCR success rates are lower than using DN131 (73.3% [TE]; 72.4% [H2O]), but Taqman genotyping success rates are comparable to the method using DN131 (70.5% [TE]; 79.1% [H2O]). We concluded that using Tris–HCl is a reliable and effective method to elute DNA from old human blood paper cards. The crude DNA isolated by Tris–HCl can be used to study genetic polymorphisms in human populations.
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Affiliation(s)
- Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
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15
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Slaughter J, Wei C, Korzeniewski SJ, Lu Q, Beck JS, Khoo SK, Brovont A, Maurer J, Martin D, Lenski M, Paneth N. High correlations in gene expression between paired umbilical cord blood and neonatal blood of healthy newborns on Guthrie cards. J Matern Fetal Neonatal Med 2013; 26:1765-7. [PMID: 23668672 DOI: 10.3109/14767058.2013.804050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To examine the correlation in genes expressed in paired umbilical cord blood (UCB) and newborn blood (NB). METHOD Total mRNA and mRNA of three gene sets (inflammatory, hypoxia, and thyroidal response) was assessed using microarray in UCB and NB spotted on Guthrie cards from 7 mother/infant pairs. RESULTS The average gene expression correlation between paired UCB and NB samples was 0.941 when all expressed genes were considered, and 0.949 for three selected gene sets. CONCLUSION The high correlation of UCB and NB gene expression suggest that either source may be useful for examining gene expression in the perinatal period.
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Affiliation(s)
- Jaime Slaughter
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University , East Lansing, MI , USA
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Ho NT, Furge K, Fu W, Busik J, Khoo SK, Lu Q, Lenski M, Wirth J, Hurvitz E, Dodge N, Resau J, Paneth N. Gene expression in archived newborn blood spots distinguishes infants who will later develop cerebral palsy from matched controls. Pediatr Res 2013; 73:450-6. [PMID: 23269123 PMCID: PMC4350763 DOI: 10.1038/pr.2012.200] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Gene expression in archived newborn blood spots remaining from newborn screening may reflect pathophysiological disturbances useful in understanding the etiology of cerebral palsy (CP). METHODS We quantified the expression of gene sets representing four physiological pathways hypothesized to contribute to CP in archived unfrozen residual newborn blood spot specimens from 53 children with CP and 53 age-, gender-, and gestational age-matched controls. We selected four empirical and three canonical gene sets representing the inflammatory, hypoxic, coagulative, and thyroidal pathways and examined mRNA expression using an 8 × 60,000 oligonucleotide microarray. The log2 fold change of gene expression between matched cases and controls was analyzed using the generally applicable gene set enrichment method. RESULTS The empirical inflammatory and empirical hypoxic gene sets were significantly downregulated in term-born CP cases (n = 33) as compared with matched controls (P = 0.0007 and 0.0009, respectively), whereas both gene sets were significantly upregulated (P =0.0055 and 0.0223, respectively) in preterm-born CP cases (n = 20). The empirical thyroidal gene set was significantly upregulated in preterm-born CP cases (P = 0.0023). CONCLUSION The newborn blood spot transcriptome can serve as a platform for investigating distinctive gene expression patterns in children who later develop CP.
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Affiliation(s)
- Nhan Thi Ho
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Kyle Furge
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI
| | - Wenjiang Fu
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Julia Busik
- Department of Physiology, Michigan State University, East Lansing, MI
| | - Sok Kean Khoo
- Laboratory of Microarray Technology, Program in Biospecimen Science; Van Andel Research Institute, Grand Rapids, MI
| | - Qing Lu
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Madeleine Lenski
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Julia Wirth
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI
| | - Edward Hurvitz
- Department of Physical Medicine and Rehabilitation, University of Michigan, Ann Arbor, MI
| | | | - James Resau
- Laboratory of Microarray Technology, Program in Biospecimen Science; Van Andel Research Institute, Grand Rapids, MI
| | - Nigel Paneth
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State, University, East Lansing, MI
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Resau JH, Ho NT, Dykema K, Faber MS, Busik JV, Nickolov RZ, Furge KA, Paneth N, Jewell S, Khoo SK. Evaluation of sex-specific gene expression in archived dried blood spots (DBS). Int J Mol Sci 2012; 13:9599-9608. [PMID: 22949818 PMCID: PMC3431816 DOI: 10.3390/ijms13089599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/25/2012] [Accepted: 07/30/2012] [Indexed: 11/16/2022] Open
Abstract
Screening newborns for treatable serious conditions is mandated in all US states and many other countries. After screening, Guthrie cards with residual blood (whole spots or portions of spots) are typically stored at ambient temperature in many facilities. The potential of archived dried blood spots (DBS) for at-birth molecular studies in epidemiological and clinical research is substantial. However, it is also challenging as analytes from DBS may be degraded due to preparation and storage conditions. We previously reported an improved assay for obtaining global RNA gene expression from blood spots. Here, we evaluated sex-specific gene expression and its preservation in DBS using oligonucleotide microarray technology. We found X inactivation-specific transcript (XIST), lysine-specific demethylase 5D (KDM5D) (also known as selected cDNA on Y, homolog of mouse (SMCY)), uncharacterized LOC729444 (LOC729444), and testis-specific transcript, Y-linked 21 (TTTY21) to be differentially-expressed by sex of the newborn. Our finding that trait-specific RNA gene expression is preserved in unfrozen DBS, demonstrates the technical feasibility of performing molecular genetic profiling using such samples. With millions of DBS potentially available for research, we see new opportunities in using newborn molecular gene expression to better understand molecular pathogenesis of perinatal diseases.
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Affiliation(s)
- James H. Resau
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Nhan T. Ho
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
| | - Karl Dykema
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Matthew S. Faber
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Julia V. Busik
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; E-Mails: (M.S.F.); (J.V.B.)
| | - Radoslav Z. Nickolov
- Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA; E-Mail:
| | - Kyle A. Furge
- Laboratory of Computational Biology, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (K.D.); (K.A.F.)
| | - Nigel Paneth
- Department of Epidemiology & Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA; E-Mails: (N.T.H.); (N.P.)
- Department of Pediatrics & Human Development, College of Human Medicine, Michigan State University, East Lansing, MI 48823, USA
| | - Scott Jewell
- Program of Biospecimen Science, Van Andel Research Institute, Grand Rapids, MI 49503, USA; E-Mails: (J.H.R.); (S.J.)
| | - Sok Kean Khoo
- Laboratory of Microarray Technology, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-616-234-5536; Fax: +1-616-234-5537
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Dietz JA, Johnson KL, Wick HC, Bianchi DW, Maron JL. Optimal techniques for mRNA extraction from neonatal salivary supernatant. Neonatology 2012; 101:55-60. [PMID: 21791940 PMCID: PMC3151004 DOI: 10.1159/000328026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 03/31/2011] [Indexed: 11/19/2022]
Abstract
BACKGROUND Gene expression profiling of the salivary supernatant is emerging as a new and important source of real-time, systemic, biological information. However, existing technologies prevent RNA extraction of small quantities found in neonatal salivary supernatant. OBJECTIVE The aim of this study was to develop techniques to enhance extraction of cell-free RNA from neonatal salivary supernatant. METHODS Two saliva samples (10-100 μl) were serially collected from newborns (36-41 weeks' gestation) (n = 13) and stabilized. Total RNA was extracted from salivary supernatant with the use of two modified extraction techniques: Qiagen RNAprotect® Saliva Mini Kit (method 1) and the QIAamp Viral RNA Mini Kit (method 2). Quantitative RT-PCR amplification for GAPDH was performed on extracted salivary samples. Statistical analyses were performed on mean threshold cycle (Ct) levels to compare RNA yield from each protocol. Paired microarray analyses were made between neonatal whole saliva and supernatant (n = 3) to discern gene expression differences between these biolayers. RESULTS mRNA was successfully extracted and amplified from all salivary supernatant samples. Extraction with method 2 yielded more RNA than with method 1 (p = 0.008). There was a 7.5% discordance between paired gene expression analyses for whole saliva and supernatant. Genes that were statistically significantly upregulated in supernatant highlighted 16 distinct biological functions not seen in whole saliva. Conversely, only two biological functions were unique to whole saliva. CONCLUSION Neonatal cell-free salivary supernatant mRNA may be readily extracted and utilized on downstream applications. These technical enhancements allow for further exploration of the diagnostic potential of the neonatal salivary transcriptome.
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Affiliation(s)
- Jessica A Dietz
- Division of Newborn Medicine, Department of Pediatrics, The Floating Hospital for Children at Tufts Medical Center, Medford, MA, USA
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Storage and use of residual newborn screening blood spots: a public policy emergency. Genet Med 2011; 13:619-20. [PMID: 21673578 DOI: 10.1097/gim.0b013e31822176df] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Hollegaard MV, Grove J, Grauholm J, Kreiner-Møller E, Bønnelykke K, Nørgaard M, Benfield TL, Nørgaard-Pedersen B, Mortensen PB, Mors O, Sørensen HT, Harboe ZB, Børglum AD, Demontis D, Ørntoft TF, Bisgaard H, Hougaard DM. Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source. BMC Genet 2011; 12:58. [PMID: 21726430 PMCID: PMC3142526 DOI: 10.1186/1471-2156-12-58] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 07/04/2011] [Indexed: 12/17/2022] Open
Abstract
Background The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS) samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined with clinical information from medical registries, DBS samples could provide a rich source for productive research. However, the amounts of DNA which can be extracted from these precious samples are minute and may be prohibitive for numerous genotypings. Previously, we demonstrated that DBS DNA can be whole-genome amplified and used for reliable genetic analysis on different platforms, including genome-wide scanning arrays. However, it remains unclear whether this approach is workable on a large sample scale. We examined the robustness of using DBS samples for whole-genome amplification following genome-wide scanning, using arrays from Illumina and Affymetrix. Results This study is based on 4,641 DBS samples from the Danish Newborn Screening Biobank, extracted for three separate genome-wide association studies. The amount of amplified DNA was significantly (P < 0.05) affected by the year of storage and storage conditions. Nine (0.2%) DBS samples failed whole-genome amplification. A total of 4,586 (98.8%) samples met our criterion of success of a genetic call-rate above 97%. The three studies used different arrays, with mean genotyping call-rates of 99.385% (Illumina Infinium Human610-Quad), 99.722% (Illumina Infinium HD HumanOmni1-Quad), and 99.206% (Affymetrix Axiom Genome-Wide CEU). We observed a concordance rate of 99.997% in the 38 methodological replications, and 99.999% in the 27 technical replications. Handling variables such as time of storage, storage conditions and type of filter paper were shown too significantly (P < 0.05) affect the genotype call-rates in some of the arrays, although the effect was minimal. Conclusion Our study indicates that archived DBS samples from the Danish Newborn Screening Biobank represent a reliable resource of DNA for whole-genome amplification and subsequent genome-wide association studies. With call-rates equivalent to high quality DNA samples, our results point to new opportunities for using the neonatal biobanks available worldwide in the hunt for genetic components of disease.
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Affiliation(s)
- Mads V Hollegaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Ørestads Boulevard, Copenhagen, DK-2300, Denmark.
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Genetic information from archived blood spots. Bioanalysis 2011; 3:1173-5. [PMID: 21649492 DOI: 10.4155/bio.11.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Khoo SK, Dykema K, Vadlapatla NM, LaHaie D, Valle S, Satterthwaite D, Ramirez SA, Carruthers JA, Haak PT, Resau JH. Acquiring genome-wide gene expression profiles in Guthrie card blood spots using microarrays. Pathol Int 2010; 61:1-6. [DOI: 10.1111/j.1440-1827.2010.02611.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Maron JL, Johnson KL, Parkin C, Iyer L, Davis JM, Bianchi DW. Cord blood genomic analysis highlights the role of redox balance. Free Radic Biol Med 2010; 49:992-6. [PMID: 20566327 PMCID: PMC2921475 DOI: 10.1016/j.freeradbiomed.2010.05.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 05/17/2010] [Accepted: 05/28/2010] [Indexed: 12/12/2022]
Abstract
Neonates are exposed to elevated levels of reactive oxygen species as they transition from a hypoxic intrauterine to a normoxic extrauterine environment at birth. This increased oxidative stress is associated with neonatal morbidity. Current antioxidant supplementation treatment strategies have yet to translate into improved neonatal outcomes. Our understanding of a newborn's intricate redox balance, particularly at the genomic level, remains limited. Here, we performed genomic microarray analyses (approximately 14,500 genes) on extracted mRNA from umbilical cord whole blood at term gestation (n=10). Bioinformatic analyses identified 282 genes (2.0%) that were consistently present within the highest quintile of expressed genes. These genes were highly associated with oxidant stress and included superoxide dismutase 1, catalase, peroxiredoxins, and uncoupling proteins. Pathway analyses identified statistically significantly overrepresented functional pathways including "oxidative stress," "oxidative stress response mediated by nuclear factor-erythroid 2-related factor," "hypoxia-inducible factor signaling," and "mitochondrial dysfunction" (p<0.05). These results suggest that neonates require high levels of antioxidants and an intricate cellular redox balance to ensure a successful transition to the extrauterine environment. Understanding the genes necessary to maintain this delicate redox balance may lead to the development of alternative treatment strategies.
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Affiliation(s)
- Jill L Maron
- Division of Newborn Medicine, Department of Pediatrics, Floating Hospital for Children at Tufts Medical Center, Boston, MA 02111, USA.
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Abstract
BACKGROUND One source of deoxyribonucleic acid (DNA) for genetic studies is the utilization of dried blood spots stored on paper cards (Guthrie cards) collected shortly after birth. These cards represent an important source of material for epidemiologic and population-based genetic studies. Extraction of DNA from these cards can lead to variable amounts of recovered DNA. We report here results of our efforts to maximize yield from this valuable, but nonrenewable, resource. METHOD Commercial methods of DNA extraction from blood cards were used, and protocol modifications were introduced that enhanced DNA yield. RESULTS Use of a commercial solvent prior to DNA extraction steps gave greater yields than extraction without the solvent. Modification of the elution step by use of prewarmed extraction buffer and a soaking step at an elevated temperature increased yield by 6- to 10-fold. CONCLUSIONS The modified DNA extraction method yielded as much as 660 ng of DNA from a single 5-mm-diameter punch of a blood spot card. The DNA performed well in downstream, polymerase chain reaction-based applications.
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Affiliation(s)
- Julie A Lane
- Children's Hospital Oakland Research Institute, Oakland, California 94609 , USA
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25
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Gauffin F, Nordgren A, Barbany G, Gustafsson B, Karlsson H. Quantitation of RNA decay in dried blood spots during 20 years of storage. Clin Chem Lab Med 2010; 47:1467-9. [PMID: 19863301 DOI: 10.1515/cclm.2009.351] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Diseases with an onset during childhood or adult life can have their origin during fetal life or at birth. Neonatal blood dried on filter paper (Guthrie cards) collected for screening purposes is routinely stored for decades. In addition to clinical use, these filters in combination with patient registers constitute an invaluable resource for epidemiological and pathophysiological research. Although RNA has been successfully recovered from such filters even after decades of storage, the potential decay of RNA over time has not previously been investigated using quantitative methods. METHODS Filter papers (n=5) with dried blood spots from the Swedish National PKU register, stored for 1, 5, 10, 15 or 20 years were randomly selected. RNA was isolated from each sample, quantitated by spectrophotometry and reverse transcribed following DNase I treatment. Amplifiable cDNA was subsequently detected by real-time PCR using primers specific for transcripts encoding beta-actin. RESULTS Transcripts encoding beta-actin were detected in all 25 samples analyzed at a mean threshold cycle (Ct) of 25 (SD 1.9). A one-way ANOVA indicated no significant effect of storage time on Ct values. CONCLUSIONS The lack of significant decay of RNA in dried blood filters stored for up to 20 years suggests that such filters are useful for studies of RNA determinants of diseases with an onset in childhood as well as adult life.
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Affiliation(s)
- Fredrika Gauffin
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
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26
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Paneth N. Potential of neonatal blood spot data to clarify the etiology of cerebral palsy. FUTURE NEUROLOGY 2010. [DOI: 10.2217/fnl.09.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Nigel Paneth
- Departments of Epidemiology and Pediatrics & Human Development, College of Human Medicine, Michigan State University, 218 West Fee Hall, MI, USA
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Hardin J, Finnell RH, Wong D, Hogan ME, Horovitz J, Shu J, Shaw GM. Whole genome microarray analysis, from neonatal blood cards. BMC Genet 2009; 10:38. [PMID: 19624846 PMCID: PMC2722673 DOI: 10.1186/1471-2156-10-38] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Accepted: 07/22/2009] [Indexed: 11/24/2022] Open
Abstract
Background Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology. Results A new technology is employed for efficient DNA release from a standard neonatal blood card. Using standard Guthrie cards, stored an average of ten years post-collection, about 1/40th of the air-dried neonatal blood specimen (two 3 mm punches) was processed to obtain DNA that was sufficient in mass and quality for direct use in microarray-based whole genome scanning. Using that same DNA release technology, it is also shown that approximately 1/250th of the original purified DNA (about 1 ng) could be subjected to whole genome amplification, thus yielding an additional microgram of amplified DNA product. That amplified DNA product was then used in microarray analysis and yielded statistical concordance of 99% or greater to the primary, unamplified DNA sample. Conclusion Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.
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Affiliation(s)
- Jill Hardin
- University of California Berkeley, School of Public Health, Berkeley, CA 94720, USA.
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Hollegaard MV, Grauholm J, Børglum A, Nyegaard M, Nørgaard-Pedersen B, Ørntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM. Genome-wide scans using archived neonatal dried blood spot samples. BMC Genomics 2009; 10:297. [PMID: 19575812 PMCID: PMC2713266 DOI: 10.1186/1471-2164-10-297] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 07/04/2009] [Indexed: 12/01/2022] Open
Abstract
Background Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference. Results Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% – 99.73% (mean 99.56%, N = 16), and conflicts with reference DNA in only three per 10,000 genotype calls. Conclusion Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.
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Affiliation(s)
- Mads V Hollegaard
- Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, Denmark.
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