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Urtiaga GO, Domingues WB, Komninou ER, Martins AWS, Blödorn EB, Dellagostin EN, Woloski RDS, Pinto LS, Brum CB, Tovo-Rodrigues L, Campos VF. DNA microarray for forensic intelligence purposes: High-density SNP profiles obtained directly from casework-like samples with and without a DNA purification step. Forensic Sci Int 2022; 332:111181. [PMID: 35042181 DOI: 10.1016/j.forsciint.2022.111181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/16/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
SNP analyses from a forensic intelligence perspective have proven to be an important tool to restrict the number of suspected offenders and find missing persons. DNA microarray assays have been demonstrated as a potential feature in forensic analysis, like such as forensic genetic genealogy. The objective of this study was to describe the results from DNA microarray assay from saliva samples deposited on a glass surface collected from by a double swab technique, commonly applied in crime scenes. Eighteen samples from the same person were subjected to Infinium® Global Screening Array-24 v1.0 (~642.824 SNP markers) in two different protocols - with or without the DNA purification procedure. The measured genotype was compared with a Consensus Genotype, obtained from standard control samples, and the parameters such as Call Rate and GenCall Scores were evaluated. Results showed that the Call Rate parameter is enough to estimate the probability of obtaining a correct genotype in the SNP assay. Reliable genotypes with a confidence level of more than 90% (at least 90.15%) were observed in Call Rates above 69.41%, regardless of the experimental condition. Our data demonstrate that DNA Microarray from samples collected under conditions such as those found at crime scenes can generate high-density SNP genetic profiles with a confidence level greater than 90%. Enzymatic adjustments and protocol changes may enable DNA microarray assays for crime analysis and investigation purposes eliminating the purification step in the future. Our data suggest that DNA microarray can support criminal investigation teams from a forensic intelligence perspective.
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Affiliation(s)
- Gabriel O Urtiaga
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Núcleo de Identificação, Superintendência da Polícia Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eliza R Komninou
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Amanda W S Martins
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo B Blödorn
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo N Dellagostin
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rafael Dos S Woloski
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano S Pinto
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Clarice B Brum
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciana Tovo-Rodrigues
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius F Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
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Walker RM, MacGillivray L, McCafferty S, Wrobel N, Murphy L, Kerr SM, Morris SW, Campbell A, McIntosh AM, Porteous DJ, Evans KL. Assessment of dried blood spots for DNA methylation profiling. Wellcome Open Res 2019; 4:44. [PMID: 30984878 PMCID: PMC6446498 DOI: 10.12688/wellcomeopenres.15136.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 11/26/2022] Open
Abstract
Background: DNA methylation reflects health-related environmental exposures and genetic risk, providing insights into aetiological mechanisms and potentially predicting disease onset, progression and treatment response. An increasingly recognised need for large-scale, longitudinally-profiled samples collected world-wide has made the development of efficient and straightforward sample collection and storage procedures a pressing issue. An alternative to the low-temperature storage of EDTA tubes of venous blood samples, which are frequently the source of the DNA used in such studies, is to collect and store at room temperature blood samples using purpose built filter paper, such as Whatman FTA® cards. Our goal was to determine whether DNA stored in this manner can be used to generate DNA methylation profiles comparable to those generated using blood samples frozen in EDTA tubes. Methods: DNA methylation profiles were obtained from matched EDTA tube and Whatman FTA® card whole-blood samples from 62 Generation Scotland: Scottish Family Health Study participants using the Infinium HumanMethylation450 BeadChip. Multiple quality control procedures were implemented, the relationship between the two sample types assessed, and epigenome-wide association studies (EWASs) performed for smoking status, age and the interaction between these variables and sample storage method. Results: Dried blood spot (DBS) DNA methylation profiles were of good quality and DNA methylation profiles from matched DBS and EDTA tube samples were highly correlated (mean
r = 0.991) and could distinguish between participants. EWASs replicated established associations for smoking and age, with no evidence for moderation by storage method. Conclusions: Our results support the use of Whatman FTA® cards for collecting and storing blood samples for DNA methylation profiling. This approach is likely to be particularly beneficial for large-scale studies and those carried out in areas where freezer access is limited. Furthermore, our results will inform consideration of the use of newborn heel prick DBSs for research use.
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Affiliation(s)
- Rosie M Walker
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Louise MacGillivray
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Sarah McCafferty
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Shona M Kerr
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Stewart W Morris
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Division of Psychiatry, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - David J Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
| | - Kathryn L Evans
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Midlothian, EH4 2XU, UK
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Bækvad-Hansen M, Bybjerg-Grauholm J, Poulsen JB, Hansen CS, Hougaard DM, Hollegaard MV. Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality. Mol Genet Metab Rep 2017; 11:36-45. [PMID: 28487825 PMCID: PMC5408502 DOI: 10.1016/j.ymgmr.2017.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/02/2017] [Accepted: 04/02/2017] [Indexed: 02/04/2023] Open
Abstract
Aim The overall aim of this study is to evaluate whole genome amplification of DNA extracted from dried blood spot samples. We wish to explore ways of optimizing the amplification process, while decreasing the amount of input material and inherently the cost. Our primary focus of optimization is on the amount of input material, the amplification reaction volume, the number of replicates and amplification time and temperature. Increasing the quality of the amplified DNA and the subsequent results of array genotyping is a secondary aim of this project. Methods This study is based on DNA extracted from dried blood spot samples. The extracted DNA was subsequently whole genome amplified using the REPLIg kit and genotyped on the PsychArray BeadChip (assessing > 570,000 SNPs genome wide). We used Genome Studio to evaluate the quality of the genotype data by call rates and log R ratios. Results The whole genome amplification process is robust and does not vary between replicates. Altering amplification time, temperature or number of replicates did not affect our results. We found that spot size i.e. amount of input material could be reduced without compromising the quality of the array genotyping data. We also showed that whole genome amplification reaction volumes can be reduced by a factor of 4, without compromising the DNA quality. Discussion Whole genome amplified DNA samples from dried blood spots is well suited for array genotyping and produces robust and reliable genotype data. However, the amplification process introduces additional noise to the data, making detection of structural variants such as copy number variants difficult. With this study, we explore ways of optimizing the amplification protocol in order to reduce noise and increase data quality. We found, that the amplification process was very robust, and that changes in amplification time or temperature did not alter the genotyping calls or quality of the array data. Adding additional replicates of each sample also lead to insignificant changes in the array data. Thus, the amount of noise introduced by the amplification process was consistent regardless of changes made to the amplification protocol. We also explored ways of decreasing material expenditure by reducing the spot size or the amplification reaction volume. The reduction did not affect the quality of the genotyping data.
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Affiliation(s)
- Marie Bækvad-Hansen
- Corresponding author at: Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark.Danish Center for Neonatal ScreeningDepartment of Congenital DiseasesStatens Serum InstitutArtillerivej 5Copenhagen SDK-2300Denmark
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DNA quality and quantity from up to 16 years old post-mortem blood stored on FTA cards. Forensic Sci Int 2016; 261:148-53. [DOI: 10.1016/j.forsciint.2016.02.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
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Giovaninni NP, Fuly JT, Moraes LI, Coutinho TN, Trarbach EB, Jorge AADL, Costalonga EF. Study of the association between 3111T/C polymorphism of the CLOCK gene and the presence of overweight in schoolchildren. J Pediatr (Rio J) 2014; 90:500-5. [PMID: 24818524 DOI: 10.1016/j.jped.2014.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/20/2013] [Accepted: 01/21/2014] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To evaluate the association between 3111T/C polymorphism of the CLOCK gene and the presence of obesity and sleep duration in children aged 6-13 years. In adults, this genetic variant has been associated with duration of sleep, ghrelin levels, weight, and eating habits. Although short sleep duration has been linked to obesity in children, no study has aimed to identify the possible molecular mechanisms of this association to date. METHODS Weight, height, and circumferences were transformed into Z-scores for age and gender. Genotyping was performed using TaqMan methodology. A questionnaire regarding hours of sleep was provided to parents. The appropriate statistical tests were performed. RESULTS This study evaluated 370 children (45% males, 55% females, mean age 8.5 ± 1.5 years). The prevalence of overweight was 18%. The duration of sleep was, on average, 9.7hours, and was inversely related to age (p<0.001). Genotype distribution was: 4% CC, 31% CT, and 65% TT. There was a trend toward higher prevalence of overweight in children who slept less than nine hours (23%) when compared to those who slept more than ten hours (16%, p=0.06). Genotype was not significantly correlated to any of the assessed outcomes. CONCLUSIONS The CLOCK 3111T/C polymorphism was not significantly associated with overweight or sleep duration in children in this city.
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Affiliation(s)
| | - Jeanne T Fuly
- Universidade Vila Velha (UVV), Vila Velha, ES, Brazil
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Study of the association between 3111T/C polymorphism of the CLOCK gene and the presence of overweight in schoolchildren. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2014. [DOI: 10.1016/j.jpedp.2014.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Fowler KE, Reitter CP, Walling GA, Griffin DK. Novel approach for deriving genome wide SNP analysis data from archived blood spots. BMC Res Notes 2012; 5:503. [PMID: 22974252 PMCID: PMC3497585 DOI: 10.1186/1756-0500-5-503] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 09/03/2012] [Indexed: 01/08/2023] Open
Abstract
Background The ability to transport and store DNA at room temperature in low volumes has the advantage of optimising cost, time and storage space. Blood spots on adapted filter papers are popular for this, with FTA (Flinders Technology Associates) Whatman™TM technology being one of the most recent. Plant material, plasmids, viral particles, bacteria and animal blood have been stored and transported successfully using this technology, however the method of porcine DNA extraction from FTA Whatman™TM cards is a relatively new approach, allowing nucleic acids to be ready for downstream applications such as PCR, whole genome amplification, sequencing and subsequent application to single nucleotide polymorphism microarrays has hitherto been under-explored. Findings DNA was extracted from FTA Whatman™TM cards (following adaptations of the manufacturer’s instructions), whole genome amplified and subsequently analysed to validate the integrity of the DNA for downstream SNP analysis. DNA was successfully extracted from 288/288 samples and amplified by WGA. Allele dropout post WGA, was observed in less than 2% of samples and there was no clear evidence of amplification bias nor contamination. Acceptable call rates on porcine SNP chips were also achieved using DNA extracted and amplified in this way. Conclusions DNA extracted from FTA Whatman cards is of a high enough quality and quantity following whole genomic amplification to perform meaningful SNP chip studies.
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Affiliation(s)
- Katie E Fowler
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NZ, UK.
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Caboux E, Lallemand C, Ferro G, Hémon B, Mendy M, Biessy C, Sims M, Wareham N, Britten A, Boland A, Hutchinson A, Siddiq A, Vineis P, Riboli E, Romieu I, Rinaldi S, Gunter MJ, Peeters PHM, van der Schouw YT, Travis R, Bueno-de-Mesquita HB, Canzian F, Sánchez MJ, Skeie G, Olsen KS, Lund E, Bilbao R, Sala N, Barricarte A, Palli D, Navarro C, Panico S, Redondo ML, Polidoro S, Dossus L, Boutron-Ruault MC, Clavel-Chapelon F, Trichopoulou A, Trichopoulos D, Lagiou P, Boeing H, Fisher E, Tumino R, Agnoli C, Hainaut P. Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC. PLoS One 2012; 7:e39821. [PMID: 22808065 PMCID: PMC3396633 DOI: 10.1371/journal.pone.0039821] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/27/2012] [Indexed: 01/12/2023] Open
Abstract
The European Prospective Investigation into Cancer and nutrition (EPIC) is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS) and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88%) performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.
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Affiliation(s)
- Elodie Caboux
- International Agency for Research on Cancer, Lyon, France
| | | | - Gilles Ferro
- International Agency for Research on Cancer, Lyon, France
| | - Bertrand Hémon
- International Agency for Research on Cancer, Lyon, France
| | - Maimuna Mendy
- International Agency for Research on Cancer, Lyon, France
| | - Carine Biessy
- International Agency for Research on Cancer, Lyon, France
| | - Matt Sims
- Medical Research Council (MRC) Epidemiology Unit, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Nick Wareham
- Medical Research Council (MRC) Epidemiology Unit, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Abigail Britten
- Medical Research Council (MRC) Epidemiology Unit, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Anne Boland
- Centre National de Génotypage, Institut Génomique, Commissariat à l’énergie Atomique, Evry, France
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, Maryland, United States of America
| | - Afshan Siddiq
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
| | | | - Sabina Rinaldi
- International Agency for Research on Cancer, Lyon, France
| | - Marc J. Gunter
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
| | - Petra H. M. Peeters
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, United Kingdom
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Yvonne T. van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruth Travis
- Cancer Epidemiology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - H. Bas Bueno-de-Mesquita
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria-José Sánchez
- Andalusian School of Public Health, Granada (Spain) and CIBER de Epidemiología y Salud Pública (CIBERESP), Granada, Spain
| | - Guri Skeie
- Institute of Community Medicine, University of Tromsø, Tromsø, Norway
| | | | - Eiliv Lund
- Institute of Community Medicine, University of Tromsø, Tromsø, Norway
| | - Roberto Bilbao
- Fundación Vasca de Innovación e Investigación Sanitarias, Sondika, Bizkaia, Spain
| | - Núria Sala
- Unit of Nutrition, Environment and Cancer, Catalan Institute of Oncology (ICO)-IDIBELL, Barcelona, Spain
| | - Aurelio Barricarte
- Navarre Public Health Institute, Pamplona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiología y Salud Pública-CIBERESP), Madrid, Spain
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute – ISPO, Florence, Italy
| | - Carmen Navarro
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiología y Salud Pública-CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Authority, Murcia, Spain
| | - Salvatore Panico
- Department of clinical and experimental medicine, Federico ii University, Naples, Italy
| | | | | | - Laure Dossus
- INSERM U1018, Gustave Roussy Institute, Paris South University, Villejuif, France
| | | | | | - Antonia Trichopoulou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, World Health Organization (WHO) Collaborating Center for Food and Nutrition Policies, University of Athens, Goudi, Athens, Greece
- Hellenic Health Foundation, Athens, Greece
| | - Dimitrios Trichopoulos
- Hellenic Health Foundation, Athens, Greece
- Department of Epidemiology, Harvard School of Public Health, Massachusetts, Boston, United States of America
- Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, World Health Organization (WHO) Collaborating Center for Food and Nutrition Policies, University of Athens, Goudi, Athens, Greece
- Department of Epidemiology, Harvard School of Public Health, Massachusetts, Boston, United States of America
- Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece
| | - Heiner Boeing
- Potsdam-Rehbrücke Department of Epidemiology, German Institute of Human Nutrition (DIfE), Nuthetal, Germany
| | - Eva Fisher
- Administrative Office of the Commission on Genetic Testing Robert Koch-Institute, Berlin, Germany
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, “Civile M. P. Arezzo” Hospital, Ragusa, Italy
| | - Claudia Agnoli
- Nutritional Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Pierre Hainaut
- International Prevention Research Institute, Lyon, France
- * E-mail:
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Halfon P, Ouzan D, Khiri H, Pénaranda G, Castellani P, Oulès V, Kahloun A, Amrani N, Fanteria L, Martineau A, Naldi L, Bourlière M. Detection of IL28B SNP DNA from buccal epithelial cells, small amounts of serum, and dried blood spots. PLoS One 2012; 7:e33000. [PMID: 22412970 PMCID: PMC3296767 DOI: 10.1371/journal.pone.0033000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 02/02/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND & AIMS Point mutations in the coding region of the interleukin 28 gene (rs12979860) have recently been identified for predicting the outcome of treatment of hepatitis C virus infection. This polymorphism detection was based on whole blood DNA extraction. Alternatively, DNA for genetic diagnosis has been derived from buccal epithelial cells (BEC), dried blood spots (DBS), and genomic DNA from serum. The aim of the study was to investigate the reliability and accuracy of alternative routes of testing for single nucleotide polymorphism allele rs12979860CC. METHODS Blood, plasma, and sera samples from 200 patients were extracted (400 µL). Buccal smears were tested using an FTA card. To simulate postal delay, we tested the influence of storage at ambient temperature on the different sources of DNA at five time points (baseline, 48 h, 6 days, 9 days, and 12 days). RESULTS There was 100% concordance between blood, plasma, sera, and BEC, validating the use of DNA extracted from BEC collected on cytology brushes for genetic testing. Genetic variations in HPTR1 gene were detected using smear technique in blood smear (3620 copies) as well as in buccal smears (5870 copies). These results are similar to those for whole blood diluted at 1/10. A minimum of 0.04 µL, 4 µL, and 40 µL was necessary to obtain exploitable results respectively for whole blood, sera, and plasma. No significant variation between each time point was observed for the different sources of DNA. IL28B SNPs analysis at these different time points showed the same results using the four sources of DNA. CONCLUSION We demonstrated that genomic DNA extraction from buccal cells, small amounts of serum, and dried blood spots is an alternative to DNA extracted from peripheral blood cells and is helpful in retrospective and prospective studies for multiple genetic markers, specifically in hard-to-reach individuals.
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Affiliation(s)
- Philippe Halfon
- Laboratoire Alphabio, Hôpital Ambroise Paré, Marseille, France.
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