Scientific Publication

© 2012 INFOVALLEY. www.infovalley.net.my

Evaluation of quality of DNA extracted from buccal swabs

for microarray based genotyping

Livy Alex et al. (2011) Ind J Clin Biochem 27: 28-33

Full article published in:

Suitability of INFOHaem using blood DNA instead of buccal cell DNA

Indian Journal of Clinical Biochemistry

Buccal cell collection as a source of DNA was initially put forward as an efficient means of cost-effective DNA collection. However INFOHaem Molecular Screening Services prefer blood DNA to be collected for genetic predisposition and diagnostic tests. Although non-invasive DNA collection methods are preferred over phlebotomy, there have been conflicting reports about the methodology and results obtained from using buccal DNA. It is not very clear if phlebotomy can be confidently replaced by buccal cell DNA. To address this issue, this study compared the performance of buccal and blood DNA from same subjects in a genotyping experiment and this paper reports the results.

Cotton swab derived buccal cells were scraped from the inner side of cheeks from 16 subjects, and blood was also drawn from the same 16 subjects participating in a genotypic association study of a lipid disease. The DNA quality was assessed by resolving on agarose gels, checking purity (A260/A280) and finally by microarray hybridization. This study, by INFOVALLEY® , recommends increasing the total amount of DNA used as starting material in case of buccal DNA, at least greater than 250 ng. However, blood has the advantage that the yield of DNA is better and enough of reserve samples is available to repeat the experiment which is not possible with buccal samples. Genotyping results can be seriously compromised if care is not taken to check the quality and yields of such specimens. Therefore, blood is a better alternative than buccal DNA.

Subject ID Buccal Blood

Concentration

(ng/μl)

Purity

(A260/280)

Concentration

(ng/μl)

Purity

(A260/280)

1 257.96 1.28 51.26 2.0

2 296.86 1.22 30.36 2.1

3 172.6 1.3 100.76 1.9

4 26.03 0.9 98.03 1.6

5 166.8 1.3 91.12 2.0

6 106.23 1.3 61.3 1.5

7 433.2 1.9 78 1.7

8 166.8 1.8 51.4 2.0

9 185.03 1.4 100.86 1.5

10 129.16 2.0 100.66 1.7

11 63.33 1.2 100.96 1.6

12 98.36 1.2 87.6 1.5

13 33.6 1.1 67.8 1.6

14 18.95 0.8 93.05 1.7

15 58.6 1.2 76.16 1.6

16 29.8 1.3 65.9 1.6

Comparison of buccal and blood DNA yields and quality.

The purity of the buccal DNA is less that 1.7, with an average reading of 1.3, which indicates that there is protein contamination. However, blood DNA purity seems to be good averaging at 1.7