Quality, quantity and recovery of DNA content from routine blood samples and genotyping success rate: comparison between phenol chloroform method (PCM) with a new kit-based DNA extraction method (KBM)


  • Gopisankar M. G. Department of Pharmacology, JIPMER, Puducherry, India
  • Surendiran A. Department of Pharmacology, JIPMER, Puducherry, India
  • Hemachandren M. Department of Pharmacology, JIPMER, Puducherry, India
  • Rajan S. Department of Pharmacology, JIPMER, Puducherry, India




Genotype detection, Kit based DNA method, Phenol chloroform method


Background: DNA extraction has become a baseline method for molecular biology studies. There are a variety of methods available for this purpose. Newer kit-based methods (KBM) are easy and less time consuming than traditional chemical methods of extraction like phenol chloroform method (PCM). Though estimates of quality from different methods are available in labels, this study compared the practical outcomes regarding quantity, quality, DNA recovery rate and assessed the outcomes at two different time points.

Methods: This study was done as a secondary analysis from an ongoing project. The quantity and quality of DNA isolated from the same group of 100 deidentified blood samples by PCM and KBM were analysed using Multi analyzer and repeated after a period of 3 months. Genotyping of the samples were done by RT-PCR. The quantity, quality and amplification proportion were compared between two groups to reach the inference.

Results: The median (range) concentration of DNA by PCM was 543.27 (960.59) µg/ml and that of KBM was 32.115 (36.73) µg/ml. The quality of DNA as measured by absorbance at 260/280 nm was 1.84 in PCM and 1.81 in KBM (p>0.05). Genotyping success rate was 78% in PCM and 98% in KBM (p = 0.002). The DNA recovery rate was 96% in PCM and 80% in KBM (p=0.014).

Conclusions: The median concentration of DNA obtained from PCM was more compared to KBM. The quality of DNA was comparable in both the groups. The genotyping success rate was more in KBM group. The DNA recovery rate at 3 months was more in PCM group.


Edinburgh Genomics ARK Genomics;2013. Available at: http://www.ark-genomics.org/news/ edinburgh-genomics. Accessed 12th June 2018.

LGC Group. DNA extraction kits. Available at: https://www.lgcgroup.com/our-science/genomics-solutions/nucleic-acid-extraction/dna-extraction-kits/#.Wx_e4YozbIU. Accessed 12th June 2018.

Brandt P, Gerdts G, Boersma M, Wiltshire KH, Wichels A. Comparison of different DNA-extraction techniques to investigate the bacterial community of marine copepods. Helgoland Marine Res. 2010 Dec;64(4):331-42.

Javadi A, Shamaei M, Ziazi LM, Pourabdollah M, Dorudinia A, Seyedmehdi SM, et al. Qualification study of two genomic DNA extraction methods in different clinical samples. Tanaffos. 2014;13(4):41.

Rohland N, Hofreiter M. Comparison and optimization of ancient DNA extraction. BioTechniques. 2007;42:343-52.

Gaikwad AB. DNA extraction: comparison of methodologies. Scribd. Available at: https://www.scribd.com/document/290953477/DNA-Extraction-Comparison-of-Methodologies.

QIAamp DNA Mini and Blood Mini Handbook-EN -QIAGEN. Available at: https://www.qiagen.com/us/ resources/resourcedetail?id=62a200d6-faf4-469b-b50f-2b59cf738962andlang=en. Accessed 12th June 2018.

Psifidi A, Dovas CI, Banos G. A comparison of six methods for genomic DNA extraction suitable for PCR-based genotyping applications using ovine milk samples. Mol Cell Probes. 2010;24:93-8.

Rodger A. Concentration Determination Using Beer-Lambert Law. InEncyclopedia of Biophysics 2013 (pp. 360-361). Springer, Berlin, Heidelberg.

Cady NC, Stelick S, Batt CA. Nucleic acid purification using microfabricated silicon structures. Biosensors and Bioelectronics. 2003 Oct 30;19(1):59-66.

Khare P, Raj V, Chandra S, Agarwal S. Quantitative and qualitative assessment of DNA extracted from saliva for its use in forensic identification. J Forensic Dental Sci. 2014 May;6(2):81.

Ghadia B, Singh AK, Khatnani T, Hirpara M, Patel S, Joshi P. An improved method of DNA purification from secondary metabolites rich medicinal plants using certain chaotropic agents. Acta physiologiae plantarum. 2016 Aug 1;38(8):207.

Philibert RA, Zadorozhnyaya O, Beach SR, Brody GH. A comparison of the genotyping results using DNA obtained from blood and saliva. Psychiatric genetics. 2008 Dec;18(6):275.

Gudiseva HV, Hansen M, Gutierrez L, Collins DW, He J, Verkuil LD, et al. Saliva DNA quality and genotyping efficiency in a predominantly elderly population. BMC medical genomics. 2016;9(1):17.




How to Cite

M. G., G., A., S., M., H., & S., R. (2018). Quality, quantity and recovery of DNA content from routine blood samples and genotyping success rate: comparison between phenol chloroform method (PCM) with a new kit-based DNA extraction method (KBM). International Journal of Basic & Clinical Pharmacology, 7(10), 1863–1868. https://doi.org/10.18203/2319-2003.ijbcp20183826



Original Research Articles