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Ferro P, Ortega-Pinazo J, Martínez B, Jiménez Á, Gómez-Zumaquero JM, Hortas ML, Díaz T. On the Use of Buffy or Whole Blood for Obtaining DNA of High Quality and Functionality: What Is the Best Option? Biopreserv Biobank 2019; 17:577-582. [PMID: 31429592 DOI: 10.1089/bio.2019.0024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human biobanks are collections of biological samples and health information that allow the organization of biomedical research for upgrading the knowledge of human disorders from different diseases (cancer, allergies, rare diseases, etc.), and reach real answers for diagnosis and treatment. A wide range of samples can be stored in these biorepositories such as hair, nails, urine, tissue, whole blood, red blood cells, buffy coat, plasma, serum, DNA, and RNA. Among these, buffy coat and whole blood are widely used by researchers because they can obtain DNA and RNA from these matrices. Some preliminary studies have been performed on animals to evaluate the quality and functionality of the nucleic acids obtained from some of these matrices, although more in-depth studies are needed in this area. In this study, blood samples extracted by venipuncture from 30 healthy volunteers were used to obtain DNA from buffy coat and whole blood. The purity and integrity of the nucleic acids obtained were assessed by spectrophotometry, fluorimetry, and agarose electrophoresis, and functionality was assessed by PCR and real-time PCR. Another aspect tested in this study was based on the comparison between short-term and long-term storage at -80°C and fresh samples from both matrices to evaluate the storage conditions at the biobank. Results showed differences in the yield obtained from both matrices as a function of the storage time, although the functionality of all the obtained DNA remained intact.
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Affiliation(s)
- Pedro Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Jesús Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - Beatriz Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Álvaro Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | | | | | - Tatiana Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
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Koshy L, Anju AL, Harikrishnan S, Kutty VR, Jissa VT, Kurikesu I, Jayachandran P, Jayakumaran Nair A, Gangaprasad A, Nair GM, Sudhakaran PR. Evaluating genomic DNA extraction methods from human whole blood using endpoint and real-time PCR assays. Mol Biol Rep 2016; 44:97-108. [PMID: 27686559 DOI: 10.1007/s11033-016-4085-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 09/22/2016] [Indexed: 11/29/2022]
Abstract
The extraction of genomic DNA is the crucial first step in large-scale epidemiological studies. Though there are many popular DNA isolation methods from human whole blood, only a few reports have compared their efficiencies using both end-point and real-time PCR assays. Genomic DNA was extracted from coronary artery disease patients using solution-based conventional protocols such as the phenol-chloroform/proteinase-K method and a non-phenolic non-enzymatic Rapid-Method, which were evaluated and compared vis-a-vis a commercially available silica column-based Blood DNA isolation kit. The appropriate method for efficiently extracting relatively pure DNA was assessed based on the total DNA yield, concentration, purity ratios (A260/A280 and A260/A230), spectral profile and agarose gel electrophoresis analysis. The quality of the isolated DNA was further analysed for PCR inhibition using a murine specific ATP1A3 qPCR assay and mtDNA/Y-chromosome ratio determination assay. The suitability of the extracted DNA for downstream applications such as end-point SNP genotyping, was tested using PCR-RFLP analysis of the AGTR1-1166A>C variant, a mirSNP having pharmacogenetic relevance in cardiovascular diseases. Compared to the traditional phenol-chloroform/proteinase-K method, our results indicated the Rapid-Method to be a more suitable protocol for genomic DNA extraction from human whole blood in terms of DNA quantity, quality, safety, processing time and cost. The Rapid-Method, which is based on a simple salting-out procedure, is not only safe and cost-effective, but also has the added advantage of being scaled up to process variable sample volumes, thus enabling it to be applied in large-scale epidemiological studies.
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Affiliation(s)
- Linda Koshy
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India.
| | - A L Anju
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - S Harikrishnan
- Department of Cardiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, 695 011, India
| | - V R Kutty
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, 695 011, India
| | - V T Jissa
- Achutha Menon Centre for Health Science Studies, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, 695 011, India
| | - Irin Kurikesu
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - Parvathy Jayachandran
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - A Jayakumaran Nair
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - A Gangaprasad
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India.,Deparment of Botany, University of Kerala, Trivandrum, 695 581, India
| | - G M Nair
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India
| | - P R Sudhakaran
- Department of Biotechnology, Inter-University Centre for Genomics and Gene Technology, University of Kerala, Trivandrum, 695 581, India.,Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, 695 581, India
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Permenter J, Ishwar A, Rounsavall A, Smith M, Faske J, Sailey CJ, Alfaro MP. Quantitative analysis of genomic DNA degradation in whole blood under various storage conditions for molecular diagnostic testing. Mol Cell Probes 2015; 29:449-453. [DOI: 10.1016/j.mcp.2015.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
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Bank S, Nexø BA, Andersen V, Vogel U, Andersen PS. High-Quality and -Quantity DNA Extraction from Frozen Archival Blood Clots for Genotyping of Single-Nucleotide Polymorphisms. Genet Test Mol Biomarkers 2013; 17:501-3. [DOI: 10.1089/gtmb.2012.0429] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Steffen Bank
- Medical Department, Viborg Regional Hospital, Viborg, Denmark
- Institute of Biomedicine, University of Aarhus, Aarhus, Denmark
| | | | - Vibeke Andersen
- Medical Department, Viborg Regional Hospital, Viborg, Denmark
- Medical Department, SHS Aabenraa, Aabenraa, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Ulla Vogel
- National Research Center for the Working Environment, Copenhagen, Denmark
- Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Paal Skytt Andersen
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
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Elliott P, Peakman TC. The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. Int J Epidemiol 2008; 37:234-44. [PMID: 18381398 DOI: 10.1093/ije/dym276] [Citation(s) in RCA: 496] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND UK Biobank is a large prospective study in the UK to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. Extensive data and biological samples are being collected from 500,000 participants aged between 40 and 69 years. The biological samples that are collected and how they are processed and stored will have a major impact on the future scientific usefulness of the UK Biobank resource. AIMS The aim of the UK Biobank sample handling and storage protocol is to specify methods for the collection and storage of participant samples that give maximum scientific return within the available budget. Processing or storage methods that, as far as can be predicted, will preclude current or future assays have been avoided. METHODS The protocol was developed through a review of the literature on sample handling and processing, wide consultation within the academic community and peer review. Protocol development addressed which samples should be collected, how and when they should be processed and how the processed samples should be stored to ensure their long-term integrity. The recommended protocol was extensively tested in a series of validation studies. UK Biobank collects about 45 ml blood and 9 ml of urine with minimal local processing from each participant using the vacutainer system. A variety of preservatives, anti-coagulants and clot accelerators is used appropriate to the expected end use of the samples. Collection of other material (hair, nails, saliva and faeces) was also considered but rejected for the full cohort. Blood and urine samples from participants are transported overnight by commercial courier to a central laboratory where they are processed and aliquots of urine, plasma, serum, white cells and red cells stored in ultra-low temperature archives. Aliquots of whole blood are also stored for potential future production of immortalized cell lines. A standard panel of haematology assays is completed on whole blood from all participants, since such assays need to be conducted on fresh samples (whereas other assays can be done on stored samples). By the end of the recruitment phase, 15 million sample aliquots will be stored in two geographically separate archives: 9.5 million in a -80 degrees C automated archive and 5.5 million in a manual liquid nitrogen archive at -180 degrees C. Because of the size of the study and the numbers of samples obtained from participants, the protocol stipulates a highly automated approach for the processing and storage of samples. Implementation of the processes, technology, systems and facilities has followed best practices used in manufacturing industry to reduce project risk and to build in quality and robustness. The data produced from sample collection, processing and storage are highly complex and are managed by a commercially available LIMS system fully integrated with the entire process. CONCLUSION The sample handling and storage protocol adopted by UK Biobank provides quality assured and validated methods that are feasible within the available funding and reflect the size and aims of the project. Experience from recruiting and processing the first 40,000 participants to the study demonstrates that the adopted methods and technologies are fit-for-purpose and robust.
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Affiliation(s)
- Paul Elliott
- Department of Epidemiology and Public Health, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK.
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Hoppin JA, Ulmer R, Calafat AM, Barr DB, Baker SV, Meltzer HM, Rønningen KS. Impact of urine preservation methods and duration of storage on measured levels of environmental contaminants. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2006; 16:39-48. [PMID: 16007114 DOI: 10.1038/sj.jea.7500435] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Collection of urine samples in human studies involves choices regarding shipping, sample preservation, and storage that may ultimately influence future analysis. As more studies collect and archive urine samples to evaluate environmental exposures in the future, we were interested in assessing the impact of urine preservative, storage temperature, and time since collection on nonpersistent contaminants in urine samples. In spiked urine samples stored in three types of urine vacutainers (no preservative, boric acid, and chlorhexidine), we measured five groups of contaminants to assess the levels of these analytes at five time points (0, 24, 48, and 72 h, and 1 week) and at two temperatures (room temperature and 4 degrees C). The target chemicals were bisphenol A (BPA), metabolites of organophosphate (OP), carbamate, and pyrethroid insecticides, chlorinated phenols, and phthalate monoesters, and were measured using five different mass spectrometry-based methods. Three samples were analyzed at each time point, with the exception of BPA. Repeated measures analysis of variance was used to evaluate effects of storage time, temperature, and preservative. Stability was summarized with percent change in mean concentration from time 0. In general, most analytes were stable under all conditions with changes in mean concentration over time, temperature, and preservative being generally less than 20%, with the exception of the OP metabolites in the presence of boric acid. The effect of storage temperature was less important than time since collection. The precision of the laboratory measurements was high allowing us to observe small differences, which may not be important when categorizing individuals into broader exposure groups.
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Affiliation(s)
- Jane A Hoppin
- Epidemiology Branch, NIEHS, NIH, DHHS, Research Triangle Park, NC, USA.
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Lin YW, Perkins JJ, Zhang Z, Aplan PD. Distinct mechanisms lead to HPRT gene mutations in leukemic cells. Genes Chromosomes Cancer 2004; 39:311-23. [PMID: 14978792 DOI: 10.1002/gcc.20005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Leukemias are considered malignant clonal disorders arising from the accumulation of mutations in hematopoietic cells; the majority of these mutations are thought to be acquired somatically. Measurement of mutation frequency (Mf) at the hypoxanthine phosphoribosyltransferase (HPRT) locus has been developed as a method for estimating genomic instability. We investigated the Mf in 16 leukemic cell lines to determine whether these cell lines showed evidence of genomic instability. Although some leukemic cell lines had markedly elevated Mfs, the Mfs at the HPRT locus in leukemic cell lines were not always higher than those of B-lymphoblastoid cell lines and T lymphocytes from normal individuals. We were able to identify the HPRT mutation for 159 of 160 individual HPRT mutants. The HPRT mutations were characterized at a molecular level and classified as either gross chromosomal rearrangements (GCRs) or point mutations, such as single-nucleotide substitutions, insertions, or deletions. With rare exceptions, individual leukemic cell lines showed either point mutations or GCR, but not both. Of note, all the cell lines that primarily showed point mutations are known to be defective in mismatch repair machinery.
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Affiliation(s)
- Ying-Wei Lin
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20889-510, USA.
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