Evaluation of efficacy of collection techniques for human genomic DNA: MAOA-uVNTR polymorphism

M.S. Siva Prasad¹ , Y Shibu Vardhanan²

1. Toxicology and Biochemistry Laboratory, Department of Zoology, University of Calicut, Malappuram, India.
2. Toxicology and Biochemistry Laboratory, Department of Zoology, University of Calicut, Malappuram, India.

Section:Research Paper, Product Type: Isroset-Journal
Vol.5 , Issue.3 , pp.6-11, Jun-2018

CrossRef-DOI:   https://doi.org/10.26438/ijsrbs/v5i3.611

Online published on Jun 30, 2018

Copyright © M.S. Siva Prasad , Y Shibu Vardhanan . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
 

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Abstract :
For large scale DNA related studies it is necessary for non-invasive and cost-effective method for obtaining sufficient quantity and quality of DNA. In this study we collected buccal cells, dried blood and saliva from 10 participants by commercially available two types of foam swabs (Puritan and HiMedia), blood collection card (NucleoSave) and saliva collection kit (Oragene OG-500) respectively. Genomic DNA was extracted from the seven days old buccal cells and dried blood using QIAamp DNA Mini Kit (Qiagen) with a modification in the final elution step which resulted in high yield of DNA. Oragene DNA extraction protocol was followed to extract DNA from saliva. Integrity, yield and purity of extracted DNA were compared by agarose gel electrophoresis, spectrophotometry and PCR amplification success for specific gene. Though, the DNA yield was significantly greater from samples of saliva than buccal cells and dried blood, contamination was more in DNA from saliva. Purity of DNA obtained from buccal cells collected by Puritan foam swabs was better for the PCR reaction as evidenced by the successful amplification of 30-bp repeat polymorphism in the promoter of the MAOA gene. Hence, we conclude that Puritan foam swab is an ample and cost-effective method for collecting buccal cells for extracting genomic DNA for epidemiological and forensic studies.

Key-Words / Index Term :
Saliva, buccal cell, dried blood, genomic DNA, PCR

References :
[1] S.A. Tishkoff, B.C. Verrelli, “Patterns of human genetic diversity: implications for human evolutionary history and disease”, Annual review of genomics and human genetics, Vol.4, Issue.1, pp.293-340, 2003.
[2] D. Quinque, R. Kittler, M. Kayser, M. Stoneking, I. Nasidze, “Evaluation of saliva as a source of human DNA for population and association studies”, Analytical biochemistry, Vol.353, Issue.2, pp.272-7, 2006.
[3] E.M. Rubin, K.A. Andrews, Y.W. Kan, “Newborn screening by DNA analysis of dried blood spots”, Human genetics, Vol.82, Issue.2, pp.134-6, 1989.
[4] L. Vigilant, R. Pennington, H. Harpending, T.D. Kocher, A.C. Wilson, “Mitochondrial DNA sequences in single hairs from a southern African population”, Proceedings of the National Academy of Sciences, Vol.86, Issue.23, pp.9350-4, 1989.
[5] B. Richards, J. Skoletsky, A.P. Shuber, R. Balfour, R.C. Stern, H.L. Dorkin, R.B. Parad, D. Witt, K.W. Klinger, “Multiplex PCR amplification from the CFTR gene using DNA prepared from buccal brushes/swabs”, Human molecular genetics, Vol.2, Issue.2, pp.159-63, 1993.
[6] C. Dawes, “Estimates, from salivary analyses, of the turnover time of the oral mucosal epithelium in humans and the number of bacteria in an edentulous mouth”, Archives of oral biology. Vol.48, Issue.5, pp.329-36, 2003.
[7] J.V. Dacie, “Dacie and Lewis practical haematology”, Elsevier Health Sciences, Churchill Livingstone, UK, 2006.
[8] N.L. Rogers, S.A. Cole, H.C. Lan, A. Crossa, E.W. Demerath, “New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies”, American Journal of Human Biology, Vol.19, Issue.3, pp.319-26, 2007.
[9] A. Brenton, C. Lee, K. Lewis, M. Sharma, S. Kantorovich, G.A. Smith, B. Meshkin, “A prospective, longitudinal study to evaluate the clinical utility of a predictive algorithm that detects risk of opioid use disorder”, Journal of pain research, Vol.11, p.119, 2018.
[10] J. Buscaino, A. Barican, L. Farrales, B. Goldman, J. Klevenberg, M. Kuhn, F. Lin, P. Nguyen, S. Salceda, R. Schueren, C. Smith, “Evaluation of a rapid DNA process with the RapidHIT® ID system using a specialized cartridge for extracted and quantified human DNA”, Forensic Science International: Genetics, Vol.34, pp.116-27, 2018.
[11] I.B. King, J.S. Abouta, M.D. Thornquist, J. Bigler, R.E. Patterson, A.R. Kristal, A.L. Shattuck, J.D. Potter, E. White, “Buccal cell DNA yield, quality, and collection costs: comparison of methods for large-scale studies”, Cancer Epidemiology and Prevention Biomarkers, Vol.11, Issue.10, pp.1130-3, 2002.
[12] H. Buerger, H. Schmidt, A. Beckmann, K.S. Zänker, W. Boecker, B. Brandt, “Genetic characterisation of invasive breast cancer: a comparison of CGH and PCR based multiplex microsatellite analysis”, Journal of clinical pathology, Vol.54, Issue.11, pp.836-40, 2001.
[13] M.O. Hoque, C.C Lee, P. Cairns, M. Schoenberg, D. Sidransky, “Genome-wide genetic characterization of bladder cancer: a comparison of high-density single-nucleotide polymorphism arrays and PCR-based microsatellite analysis”, Cancer research, Vol.63, Issue.9, pp.2216-22, 2003.
[14] K. Mackey, P. Chomczynski, “Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity”, Biotechniques, Vol.22, Issue.3, pp.474-481, 1997.
[15] S.Z. Sabol, S. Hu, D. Hamer, “A functional polymorphism in the monoamine oxidase A gene promoter”, Human genetics, Vol.103, Issue.3, pp.273-9, 1998.
[16] M. Das, A. Das Bhowmik, S. Sinha, A. Chattopadhyay, K. Chaudhuri, M. Singh, K. Mukhopadhyay, “MAOA promoter polymorphism and attention deficit hyperactivity disorder (ADHD) in Indian children”, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, Vol.141, Issue.6, pp.637-42, 2006.
[17] E.M. Heath, N.W. Morken, K.A. Campbell, D. Tkach, E.A. Boyd, D.A. Strom. “Use of buccal cells collected in mouthwash as a source of DNA for clinical testing”, Archives of pathology & laboratory medicine, Vol.125, Issue.1, pp.127-33, 2001.
[18] H.S. Feigelson, C. Rodriguez, A.S. Robertson, E.J. Jacobs, E.E. Calle, Y.A. Reid, M.J. Thun, “Determinants of DNA yield and quality from buccal cell samples collected with mouthwash”, Cancer Epidemiology and Prevention Biomarkers, Vol.10, Issue.9, pp.1005-8, 2001.
[19] E.A. Ehli, T. Lengyel-Nelson, J.J. Hudziak, G.E. Davies. “Using a commercially available DNA extraction kit to obtain high quality human genomic DNA suitable for PCR and genotyping from 11-year-old saliva saturated cotton spit wads”, BMC research notes, Vol.1, Issue.1, p.133, 2008.
[20] B. Freeman, J. Powell, D. Ball, L. Hill, I. Craig, R. Plomin, “DNA by mail: an inexpensive and noninvasive method for collecting DNA samples from widely dispersed populations”, Behavior genetics, Vol.27, Issue.3, pp.251-7, 1997.
[21] I. Meulenbelt, S. Droog, G.J. Trommelen, D.I. Boomsma, P.E. Slagboom, “High-yield noninvasive human genomic DNA isolation method for genetic studies in geographically dispersed families and populations”, American journal of human genetics, Vol.57, Issue.5, p.1252, 1995.
[22] M. Garcia-Closas, K.M. Egan, J. Abruzzo, P.A. Newcomb, L. Titus-Ernstoff, T. Franklin, P.K. Bender, J.C. Beck, L. Le Marchand, A. Lum, M. Alavanja, “Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash”, Cancer Epidemiology and Prevention Biomarkers, Vol.10, Issue.6, pp.687-96, 2001.
[23] A.F. Saftlas, M. Waldschmidt, N. Logsden-Sackett, E. Triche, E. Field, “Optimizing buccal cell DNA yields in mothers and infants for human leukocyte antigen genotyping”, American journal of epidemiology, Vol.160, Issue.1, pp.77-84, 2004.