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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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McFarlin BK, Bridgeman EA, Vingren JL, Hill DW. Dry blood spot samples to monitor immune-associated mRNA expression in intervention studies: Impact of Baker's yeast beta glucan. Methods 2023; 219:39-47. [PMID: 37741562 DOI: 10.1016/j.ymeth.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023] Open
Abstract
Monitoring immunological response to physical stressors in a field setting is challenging because existing methods require a laboratory visit and traditional blood collection via venipuncture. The purpose of this study was to determine if our optimized dry blood spot (DBS) methodology yields sufficient total RNA to quantify the effect of Baker's Yeast Beta Glucan supplementation (BYBG; Wellmune; 250 mg/d) on post-exercise mRNA expression. Participants had venous DBS samples collected prior to (PRE), and immediately (POST), 2 (2H), and 4 (4H) hrs after completion of a 90 min run/walk trial in a hot, humid environment. Total RNA extracted from DBS was analyzed using a 574-plex Human Immunology mRNA panel (Nanostring). BYBG supplementation was associated with the increased expression of 12 mRNAs (LTB4R, PML, PRFM1, TNFRSF14, LCK, MYD88, STAT3, CCR1, TNFSF10, LILRB3, MME, and STAT6) and decreased expression of 4 mRNAs (MAP4K1, IKBKG, CD5, and IL4R) across all post-exercise time points. In addition to individually changed mRNA targets, we found eleven immune-response pathways that were significantly enriched by BYBG following exercise (TNF Family signaling, immunometabolism, oxidative stress, toll-like receptor (TLR) signaling, Treg differentiation, autophagy, chemokine signaling, complement system, Th2 differentiation, cytokine signaling, and innate immune). The present approach showed that DBS samples can be used to yield useful information about mRNA biomarkers in an intervention study. We have found that BYBG supplementation induces changes at the mRNA level that support the immune system and reduce susceptibility to opportunistic infection (i.e., upper respiratory tract infection) and facilitate improved physical recovery from exercise. Future studies may look to use DBS sampling for testing other nutritional, health, or medical interventions.
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Affiliation(s)
- Brian K McFarlin
- University of North Texas, Applied Physiology Laboratory, Dept. of KHPR (Kinesiology, Health Promotion, and Recreation), United States; University of North Texas, Dept. of Biological Sciences, United States.
| | - Elizabeth A Bridgeman
- University of North Texas, Applied Physiology Laboratory, Dept. of KHPR (Kinesiology, Health Promotion, and Recreation), United States; University of North Texas, Dept. of Biological Sciences, United States
| | - Jakob L Vingren
- University of North Texas, Applied Physiology Laboratory, Dept. of KHPR (Kinesiology, Health Promotion, and Recreation), United States; University of North Texas, Dept. of Biological Sciences, United States
| | - David W Hill
- University of North Texas, Applied Physiology Laboratory, Dept. of KHPR (Kinesiology, Health Promotion, and Recreation), United States
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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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Pan X, Muk T, Ren S, Nguyen DN, Shen RL, Gao F, Sangild PT. Blood transcriptomic markers of necrotizing enterocolitis in preterm pigs. Pediatr Res 2022; 91:1113-1120. [PMID: 34112973 DOI: 10.1038/s41390-021-01605-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/29/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC), a severe gut disorder in preterm infants, is difficult to predict due to poor specificity and sensitivity of clinical signs and biomarkers. Using preterm piglets as a model, we hypothesized that early development of NEC affects blood gene expression, potentially related to early systemic immune responses. METHODS A retrospective analysis of clinical, tissue, and blood data was performed on 129 formula-fed piglets with NEC diagnosis at necropsy on day 5. Subgroups of NEC (n = 20) and control piglets (CON, n = 19) were analyzed for whole-blood transcriptome. RESULTS Preterm piglets had variable NEC lesions, especially in the colon region, without severe clinical signs (e.g. normal growth, activity, hematology, digestion, few piglets with bloody stools). Transcriptome analysis showed 344 differentially expressed genes (DEGs) between NEC and CON piglets. Validation experiment showed that AOAH, ARG2, FKBP5, PAK2, and STAT3 were among the genes affected by severe lesions on day 5, when analyzed in whole blood and in dried blood spots (DBS). CONCLUSION Whole-blood gene expressions may be affected in preterm pigs before clinical signs of NEC get severe. Blood gene expression analysis, potentially using DBS samples, is a novel tool to help identify new early biomarkers of NEC. IMPACT Preterm pig model was used to investigate if blood transcriptomics could be used to identify new early blood biomarkers of NEC progression. Whole-blood transcriptome revealed upregulation of target genes in NEC cases when clinical symptoms are subtle, and mainly colon regions were affected. Differential NEC-associated gene expressions could be detected also in dried blood spots, potentially allowing easy collection of small blood volumes in infants.
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Affiliation(s)
- Xiaoyu Pan
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tik Muk
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shuqiang Ren
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Duc Ninh Nguyen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rene L Shen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fei Gao
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Per Torp Sangild
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,H.C. Andersen Childrens Hospital, Odense University Hospital, University of Southern Denmark, Odense, Denmark. .,Department of Neonatology, Rigshospitalet, Copenhagen, Denmark.
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5
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Carpentieri D, Colvard A, Petersen J, Marsh W, David-Dirgo V, Huentelman M, Pirrotte P, Sivakumaran TA. Mind the Quality Gap When Banking on Dry Blood Spots. Biopreserv Biobank 2021; 19:136-142. [PMID: 33567235 DOI: 10.1089/bio.2020.0131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Dry blood spots (DBS) offer many advantages over other blood banking protocols due to the reduction of time and equipment needed for collection and the ease of processing, storage, and shipment. In addition, the sample size makes it a very attractive method when considering the banking of small pediatric samples. On that note, the Centers for Disease Control and Prevention (CDC) preanalytical standards for DBS are commonly used in the worldwide mass spectrometry-based inborn errors of metabolism screening programs. However, these guidelines may not apply for analytes and protocols not included in these programs. In fact, the availability of leftover samples and the ongoing interest in protocols outside this scenario are providing us with new DBS biobanking insights. Herein, we review the literature for indicators that should be considered in the design of prospective fit for purpose DBS biobanks, especially for those focused mostly on pediatric and OMIC platforms.
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Affiliation(s)
- David Carpentieri
- Department of Pathology and Laboratory Medicine, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Amber Colvard
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Jackie Petersen
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - William Marsh
- Department of Biorepository, Mayo Clinic, Phoenix, Arizona, USA
| | - Victoria David-Dirgo
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matt Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - T A Sivakumaran
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
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6
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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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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. [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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Mbunkah HA, Marzel A, Schmutz S, Kok YL, Zagordi O, Shilaih M, Nsanwe NN, Mbu ET, Besong LM, Sama BA, Orock E, Kouyos RD, Günthard HF, Metzner KJ. Low prevalence of transmitted HIV-1 drug resistance detected by a dried blood spot (DBS)-based next-generation sequencing (NGS) method in newly diagnosed individuals in Cameroon in the years 2015-16. J Antimicrob Chemother 2019; 73:1917-1929. [PMID: 29635462 DOI: 10.1093/jac/dky103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/02/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives To determine the most recent prevalence, transmission patterns and risk factors of transmitted drug-resistance mutations (TDRMs) in Cameroon, we initiated a multicentre study monitoring HIV-1 drug resistance in newly HIV-1-diagnosed individuals using a novel next-generation sequencing (NGS) assay applicable to fingerprick dried blood spot (DBS) samples. Methods Fingerprick DBS samples and questionnaires were collected from 360 newly HIV-1-diagnosed individuals in four hospitals in urban areas in Cameroon in the years 2015-16. We developed an HIV-1 protease and reverse transcriptase drug resistance genotyping assay applicable to DBS samples and HIV-1 genomes of groups M, N and O. The WHO 2009 list of mutations for surveillance of transmitted drug-resistant HIV strains was used to analyse TDRMs. Results Applying our 'DBS-NGS-genotypic resistance test', baseline HIV-1 drug resistance data were successfully obtained from 82.8% (298/360) of newly diagnosed individuals. At nucleotide frequencies >15%, TDRMs to NRTIs were observed in 3.0% (9/298), to NNRTIs in 4.0% (12/298) and to PIs in 1.3% (3/240). The NNRTI mutation K103N was most commonly detected (2.7%). Expanding the analysis to low-abundance TDRMs, i.e. 3%-15%, 12 additional individuals (4.0%) harbouring TDRMs were identified. Having unprotected sex with a known HIV-1-positive person was significantly associated with the transmission of DRMs (adjusted OR 9.6; 95% CI 1.79-51.3). Conclusions The prevalence of transmitted HIV-1 drug resistance is currently low in the study sites in Cameroon. Evidence of some risky sexual behaviours depicts a public health problem with possible implications for the prevention of new HIV-1 infections.
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Affiliation(s)
- Herbert A Mbunkah
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Life Science Zurich Graduate School, Microbiology and Immunology PhD Programme, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Alex Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Yik Lim Kok
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Mohaned Shilaih
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland
| | - Ndi N Nsanwe
- Regional Hospital Bamenda, PO Box 863, Mankon-Bamenda, Cameroon
| | - Eyongetah T Mbu
- Regional Hospital Bamenda, PO Box 863, Mankon-Bamenda, Cameroon
| | - Lydia M Besong
- District Hospital Kumba, Meme Division, South-West Region, Cameroon
| | - Bella A Sama
- District Hospital Ndop, Ngoketunjia Division, North-West Region, Cameroon
| | - Emmanuel Orock
- Regional Hospital Ngaoundere, Avenue Rue Ahidjo Ngaoundéré, Adamawa, Cameroon
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, CH-8091 Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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9
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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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10
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Ortega-Pinazo J, Díaz T, Martínez B, Jiménez A, Pinto-Medel MJ, Ferro P. Quality assessment on the long-term cryopreservation and nucleic acids extraction processes implemented in the andalusian public biobank. Cell Tissue Bank 2019; 20:255-265. [PMID: 30903409 DOI: 10.1007/s10561-019-09764-9] [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] [Received: 11/28/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
Human samples are commonly collected and long-term stored in biobanks for current and future analyses. Even though techniques for freezing human blood are well established, the storage time can compromise the cell viability as well as the yield and quality of nucleic acids (RNA and DNA) extracted from them. In this study, a protocol to obtain peripheral blood mononuclear cells (PBMCs) from 70 subjects, which were stored at - 196 °C from EDTA tubes for a long-term, was assessed. In parallel; a protocol to obtain DNA from the same subjects, which were stored at - 80 °C from citrate tubes, was also studied. Samples stored from 2008 to 2012 were studied and the results obtained showed that there were no statistically significant differences in the RNA or DNA extracted in terms of purity, integrity and functionality The freezing protocol used by the Málaga Biobank shows that viable PBMCs and DNA could be kept for a period of, at least, 10 years, with a high quality and performance. Furthermore, RNA extracted from these PBMCs presents also a good quality and performance. Therefore, the samples frozen according to the conditions of the protocols assessed in this study could be optimal for biomedical research.
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Affiliation(s)
- J Ortega-Pinazo
- Neuroscience UGC, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - T Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - B Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - A Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - M J Pinto-Medel
- Neuroscience UGC, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - P Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain.
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11
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Murphy MSQ, Hawken S, Cheng W, Wilson LA, Lamoureux M, Henderson M, Potter B, Little J, Chakraborty P, Wilson K. Metabolic profiles derived from residual blood spot samples: A longitudinal analysis. Gates Open Res 2018; 2:28. [PMID: 30234195 PMCID: PMC6139383 DOI: 10.12688/gatesopenres.12822.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Secondary use of newborn screening dried blood spot samples include use for biomedical or epidemiological research. However, the effects of storage conditions on archival samples requires further examination. The objective of this study was to determine the utility of residual newborn samples for deriving reliable metabolic gestational age estimates. Methods: Residual newborn dried blood spot samples that had been stored for 2-, 4-, 6-, or 12-months in temperature controlled (21°C) conditions were re-analyzed for the full panel of newborn screening analytes offered by a provincial newborn screening lab in Ottawa, Canada. Data from re-analyzed samples were compared to corresponding baseline newborn screening values for absolute agreement, and Pearson and intraclass correlation. Performance of a gestational age estimation algorithm originally developed from baseline newborn screening values was then validated on data derived from stored samples. Results: A total of 307 samples were used for this study. 17-hydroxyprogesterone and newborn hemoglobin profiles measured by immunoassay and high-performance liquid chromatography, respectively, were among the most stable markers across all time points of analysis. Acylcarnitines exhibited the greatest degree of variation in stability upon repeat measurement. The largest shifts in newborn analyte profiles and the poorest performance of metabolic gestational age algorithms were observed when samples were analyzed 12-months after sample collection. Conclusions: Duration of sample storage, independent of temperature and humidity, affects newborn screening profiles and gestational age estimates derived from metabolic gestational dating algorithms. When considering use of dried blood spot samples either for clinical or research purposes, care should be taken when interpreting data stemming from secondary use.
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Affiliation(s)
- Malia S Q Murphy
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Steven Hawken
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Wei Cheng
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Lindsay A Wilson
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Monica Lamoureux
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, K1H 5B2, Canada
| | - Matthew Henderson
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, K1H 5B2, Canada
| | - Beth Potter
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, K1G 5Z3, Canada
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, K1G 5Z3, Canada
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, K1H 5B2, Canada
| | - Kumanan Wilson
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
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12
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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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13
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Björkesten J, Enroth S, Shen Q, Wik L, Hougaard DM, Cohen AS, Sörensen L, Giedraitis V, Ingelsson M, Larsson A, Kamali-Moghaddam M, Landegren U. Stability of Proteins in Dried Blood Spot Biobanks. Mol Cell Proteomics 2017; 16:1286-1296. [PMID: 28501802 PMCID: PMC5500761 DOI: 10.1074/mcp.ra117.000015] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/18/2017] [Indexed: 01/15/2023] Open
Abstract
An important motivation for the construction of biobanks is to discover biomarkers that identify diseases at early, potentially curable stages. This will require biobanks from large numbers of individuals, preferably sampled repeatedly, where the samples are collected and stored under conditions that preserve potential biomarkers. Dried blood samples are attractive for biobanking because of the ease and low cost of collection and storage. Here we have investigated their suitability for protein measurements. Ninety-two proteins with relevance for oncology were analyzed using multiplex proximity extension assays (PEA) in dried blood spots collected on paper and stored for up to 30 years at either +4 °C or -24 °C.Our main findings were that (1) the act of drying only slightly influenced detection of blood proteins (average correlation of 0.970), and in a reproducible manner (correlation of 0.999), (2) detection of some proteins was not significantly affected by storage over the full range of three decades (34 and 76% of the analyzed proteins at +4 °C and -24 °C, respectively), whereas levels of others decreased slowly during storage with half-lives in the range of 10 to 50 years, and (3) detectability of proteins was less affected in dried samples stored at -24 °C compared with at +4 °C, as the median protein abundance had decreased to 80 and 93% of starting levels after 10 years of storage at +4 °C or -24 °C, respectively. The results of our study are encouraging as they suggest an inexpensive means to collect large numbers of blood samples, even by the donors themselves, and to transport, and store biobanked samples as spots of whole blood dried on paper. Combined with emerging means to measure hundreds or thousands of protein, such biobanks could prove of great medical value by greatly enhancing discovery as well as routine analysis of blood biomarkers.
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Affiliation(s)
- Johan Björkesten
- From the ‡Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefan Enroth
- From the ‡Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Qiujin Shen
- From the ‡Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lotta Wik
- From the ‡Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - David M Hougaard
- §Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Arieh S Cohen
- §Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Lene Sörensen
- ¶Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Vilmantas Giedraitis
- ‖Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- ‖Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Anders Larsson
- **Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Masood Kamali-Moghaddam
- From the ‡Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Landegren
- From the ‡Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
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14
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Bybjerg-Grauholm J, Hagen CM, Khoo SK, Johannesen ML, Hansen CS, Bækvad-Hansen M, Christiansen M, Hougaard DM, Hollegaard MV. RNA sequencing of archived neonatal dried blood spots. Mol Genet Metab Rep 2016; 10:33-37. [PMID: 28053876 PMCID: PMC5198792 DOI: 10.1016/j.ymgmr.2016.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 01/25/2023] Open
Abstract
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of metabolism, hypothyroidism and other diseases. In Denmark, the Guthrie cards are stored at − 20 °C in the Danish Neonatal Screening Biobank and each sample is linked to elaborate social and medical registries. This provides a unique biospecimen repository to enable large population research at a perinatal level. Here, we demonstrate the feasibility to obtain gene expression data from DBS using next-generation RNA sequencing (RNA-seq). RNA-seq was performed on five males and five females. Sequencing results have an average of > 30 million reads per sample. 26,799 annotated features can be identified with 64% features detectable without fragments per kilobase of transcript per million mapped reads (FPKM) cutoff; number of detectable features dropped to 18% when FPKM ≥ 1. Sex can be discriminated using blood-based sex-specific gene set identified by the Genotype-Tissue Expression consortium. Here, we demonstrate the feasibility to acquire biologically-relevant gene expression from DBS using RNA-seq which provide a new avenue to investigate perinatal diseases in a high throughput manner.
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Affiliation(s)
- Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA
| | - Maria Louise Johannesen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christine Søholm Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Mads V Hollegaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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15
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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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16
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Robustness of comprehensive DNA- and RNA-based assays at diagnosis of acute myeloid leukemia using blood and bone marrow stored on filter cards. Leukemia 2016; 30:2123-2125. [DOI: 10.1038/leu.2016.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Grauholm J, Khoo SK, Nickolov RZ, Poulsen JB, Bækvad-Hansen M, Hansen CS, Hougaard DM, Hollegaard MV. Gene expression profiling of archived dried blood spot samples from the Danish Neonatal Screening Biobank. Mol Genet Metab 2015. [PMID: 26212339 DOI: 10.1016/j.ymgme.2015.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A large part of the human genome is transcribed into various forms of RNA, and the global gene expression profile (GEP) has been studied for several years using technology such as RNA-microarrays. In this study, we evaluate whether neonatal dried blood spot (DBS) samples stored in the Danish Neonatal Screening Biobank (DNSB) can be used for GEP. This paper is divided into sub-studies examining the effects of: 1) different whole transcriptome amplification kits (WTA); 2) years of storage and storage in room temperature (RT) versus freezers (-20°C) on DNSB DBS samples; 3) effects of RT storage vs freezer storage on DBS samples from the USA and DNSB, and 4) using smaller disc sizes, thereby decreasing DBS use. We present evidence that reliable and reproducible GEPs can be obtained using neonatal DBS samples. The main source of variation is the storage condition. When samples are stored at -20°C, the dynamic range is increased, and Pearson correlations are higher. Differential analysis reveals no statistically significant differences between samples collected a decade apart and stored at -20°C. However, samples stored at RT show differential expression for a third of the gene-specific probes. Our data also suggests that using alternate WTA kits significantly changes the GEP. Finally, the amount of input material, i.e., the size and number of DBS discs used, can be reduced to preserve this valuable and limited material. We conclude that DNSB DBS samples provide a reproducible resource for GEP. Results are improved if the cards are stored at -20°C. Furthermore, it is important to use a single type of kit for analysis because using alternate kits introduces differential expression.
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Affiliation(s)
- Jonas Grauholm
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA.
| | - Radoslav Z Nickolov
- Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA.
| | - Jesper B Poulsen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Marie Bækvad-Hansen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Christine S Hansen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - David M Hougaard
- Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Mads V Hollegaard
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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18
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Therrell BL, Padilla CD, Loeber JG, Kneisser I, Saadallah A, Borrajo GJC, Adams J. Current status of newborn screening worldwide: 2015. Semin Perinatol 2015; 39:171-87. [PMID: 25979780 DOI: 10.1053/j.semperi.2015.03.002] [Citation(s) in RCA: 347] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Newborn screening describes various tests that can occur during the first few hours or days of a newborn's life and have the potential for preventing severe health problems, including death. Newborn screening has evolved from a simple blood or urine screening test to a more comprehensive and complex screening system capable of detecting over 50 different conditions. While a number of papers have described various newborn screening activities around the world, including a series of papers in 2007, a comprehensive review of ongoing activities since that time has not been published. In this report, we divide the world into 5 regions (North America, Europe, Middle East and North Africa, Latin America, and Asia Pacific), assessing the current NBS situation in each region and reviewing activities that have taken place in recent years. We have also provided an extensive reference listing and summary of NBS and health data in tabular form.
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Affiliation(s)
- Bradford L Therrell
- National Newborn Screening and Genetics Resource Center (NNSGRC), Austin, TX; Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX.
| | - Carmencita David Padilla
- College of Medicine, University of the Philippines Manila, Manila, Philippines; Newborn Screening Reference Center, National Institutes of Health (Philippines), Manila, Ermita, Philippines
| | - J Gerard Loeber
- International Society for Neonatal Screening, Bilthoven, Netherlands
| | - Issam Kneisser
- Newborn Screening Unit, Medical Genetic Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Amal Saadallah
- Newborn Screening and Biochemical Genetics Laboratory, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Gustavo J C Borrajo
- Programa de Detección de Errores Congénitos, Fundación Bioquímica Argentina, La Plata, Argentina
| | - John Adams
- Canadian Organization for Rare Disorders, Toronto, Ontario, Canada
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19
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Development of a one-step probe based molecular assay for rapid immunodiagnosis of infection with M. tuberculosis using dried blood spots. PLoS One 2014; 9:e105628. [PMID: 25184553 PMCID: PMC4153573 DOI: 10.1371/journal.pone.0105628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/22/2014] [Indexed: 12/31/2022] Open
Abstract
Background Antigen specific release of IP-10 is the most promising alternative marker to IFN-γ for infection with M. tuberculosis. Compared to Interferon-γ release assays (IGRA), IP-10 is released in high levels enabling novel approaches such as field friendly dried blood spots (DBS) and molecular detection. Aim To develop a robust IP-10 based molecular assay for the diagnosis of infection with M. tubercuolsis from whole blood and DBS. Method We developed a one-step probe based multiplex RT-qPCR assay for detecting IP-10 and IFN-γ mRNA expression from whole blood and DBS samples. The assay was validated and applied for the diagnosis of M. tuberculosis infection in DBS samples from 43 patients with confirmed TB, 13 patients with latent TB and 96 presumed uninfected controls. In parallel, IP-10 and INF-γ levels were measured in Quantiferon (QFT-TB) plasma supernatants. Results IP-10 mRNA upregulation was detectable at 4 hours after stimulation (6 fold upregulation) peaking at 8 hours (108 fold upregulation). IFN-γ expression occurred in concert but levels were lower (peak 6.7 fold upregulation). IP-10 gene expression level was significantly higher in patients with tuberculosis (median 31.2, IQR 10.7–67.0) and persons with latent tuberculosis infection (LTBI) (41.2, IQR 9.8–64.9) compared to healthy controls (1.6, IQR 1.1–2.4; p<0.0001). The IP-10 mRNA and protein based tests had comparable diagnostic accuracy to QFT-TB, sensitivity (85% and 88% vs 85%) and specificity (96% and 96% vs 97%, p = ns.). Conclusion We developed a rapid, robust and accurate molecular immunodiagnostic test for M. tuberculosis infection. By combining DBS based sample acquisition, mail or currier based sample transport with centralized molecular detection, this immunodiagnostic test concept can reduce the local technological requirements everywhere and make it possible to offer highly accurate immunodiagnostic tests in low resource settings.
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20
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Andriamandimby SF, Heraud JM, Randrianasolo L, Rafisandratantsoa JT, Andriamamonjy S, Richard V. Dried-blood spots: a cost-effective field method for the detection of Chikungunya virus circulation in remote areas. PLoS Negl Trop Dis 2013; 7:e2339. [PMID: 23936570 PMCID: PMC3723542 DOI: 10.1371/journal.pntd.0002339] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 06/16/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In 2005, there were outbreaks of febrile polyarthritis due to Chikungunya virus (CHIKV) in the Comoros Islands. CHIKV then spread to other islands in the Indian Ocean: La Réunion, Mauritius, Seychelles and Madagascar. These outbreaks revealed the lack of surveillance and preparedness of Madagascar and other countries. Thus, it was decided in 2007 to establish a syndrome-based surveillance network to monitor dengue-like illness. OBJECTIVE This study aims to evaluate the use of capillary blood samples blotted on filter papers for molecular diagnosis of CHIKV infection. Venous blood samples can be difficult to obtain and the shipment of serum in appropriate temperature conditions is too costly for most developing countries. METHODOLOGY AND PRINCIPAL FINDINGS Venous blood and dried-blood blotted on filter paper (DBFP) were collected during the last CHIKV outbreak in Madagascar (2010) and as part of our routine surveillance of dengue-like illness. All samples were tested by real-time RT-PCR and results with serum and DBFP samples were compared for each patient. The sensitivity and specificity of tests performed with DBFP, relative to those with venous samples (defined as 100%) were 93.1% (95% CI:[84.7-97.7]) and 94.4% (95% CI:[88.3-97.7]), respectively. The Kappa coefficient 0.87 (95% CI:[0.80-0.94]) was excellent. CONCLUSION This study shows that DBFP specimens can be used as a cost-effective alternative sampling method for the surveillance and monitoring of CHIKV circulation and emergence in developing countries, and probably also for other arboviruses. The loss of sensitivity is insignificant and involved a very small number of patients, all with low viral loads. Whether viruses can be isolated from dried blood spots remains to be determined.
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Barbany G, Gauffin F, Öfverholm I, Karlsson H, Thörn I, Arvidson J, Heyman M, Gustafsson B, Nordgren A. TheETV6/RUNX1fusion transcript is not detected in RNA isolated from neonatal dried blood spots from children later diagnosed with the corresponding leukemia. Leuk Lymphoma 2013; 54:2742-4. [DOI: 10.3109/10428194.2013.786068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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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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Cruickshank MN, Pitt J, Craig JM. Going back to the future with Guthrie-powered epigenome-wide association studies. Genome Med 2012; 4:83. [PMID: 23131117 PMCID: PMC3580452 DOI: 10.1186/gm384] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2012] [Indexed: 12/01/2022] Open
Abstract
Epigenome-wide association studies (EWAS) can be used to investigate links between early life environment, epigenetics and disease. However, such studies raise the question of which came first: the mark or the malady? A recent study has demonstrated that EWAS can be performed on neonatal 'Guthrie' heel-prick blood spots. As Guthrie cards are collected from all newborn infants and stored indefinitely in many countries, they represent an important timepoint to compare with later disease-associated epigenetic marks.
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Affiliation(s)
- Mark N Cruickshank
- Division of Leukaemia and Cancer Research, Telethon Institute for Child Health Research, Centre for Child Health, University of Western Australia, WA, Australia
| | - James Pitt
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, VIC, Australia
| | - Jeffrey M Craig
- Early Life Epigenetics Group, Murdoch Childrens Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
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Murphy SC, Prentice JL, Williamson K, Wallis CK, Fang FC, Fried M, Pinzon C, Wang R, Talley AK, Kappe SHI, Duffy PE, Cookson BT. Real-time quantitative reverse transcription PCR for monitoring of blood-stage Plasmodium falciparum infections in malaria human challenge trials. Am J Trop Med Hyg 2012; 86:383-94. [PMID: 22403305 PMCID: PMC3284350 DOI: 10.4269/ajtmh.2012.10-0658] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 11/12/2011] [Indexed: 11/07/2022] Open
Abstract
To detect pre-patent parasitemia, we developed a real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for the asexual 18S ribosomal RNA (rRNAs) of Plasmodium falciparum. Total nucleic acids extracted from whole blood were combined with control RNA and tested by qRT-PCR. The assay quantified > 98.7% of parasite-containing samples to ±0.5 log(10) parasites/mL of the nominal value without false positives. The analytical sensitivity was ≥ 20 parasites/mL. The coefficient of variation was 0.6% and 1.8% within runs and 1.6% and 4.0% between runs for high and low parasitemia specimens, respectively. Using this assay, we determined that A-type 18S rRNAs are stably expressed at 1 × 10(4) copies per ring-stage parasite. When used to monitor experimental P. falciparum infection of human volunteers, the assay detected blood-stage infections 3.7 days earlier on average than thick blood smears. This validated, internally controlled qRT-PCR method also uses a small (50 μL) sample volume requiring minimal pre-analytical handling, making it useful for clinical trials.
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Affiliation(s)
- Sean C Murphy
- Department of Laboratory Medicine, Division of Allergy and Infectious Diseases, University of Washington Medical Center, Seattle, 98195-7110, 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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