Smart Approach for Cost Effective Genotyping of Single Nucleotide Polymorphisms


  • Muhammad Usman Ghani University of the Punjab
  • Muhammad Farooq Sabar University of the Punjab
  • Muhammad Akram University of the Punjab



Assay, Genotyping, Single Nucleotide Polymorphism, Smart Approach, SNaPshot


Single Nucleotide Polymorphisms (SNPs) are in prime focus of genomic studies for their probable roles in diagnostics and prognosis of diseases and forensic science. SNaPshot/minisequencing reaction based genotyping of targeted SNPs is a method of choice due to its fast and reliable detection assay. Here we described smart modifications in minisequencing reaction to make it cost effective assay for the detection of 15 SNPs in a single assay. The target SNPs were amplified in a multiplex PCR from genomic DNA and these multiplex PCR amplicons were utilized as a template in modified SNaPshot reaction for SNPs identification.  Modified protocol was assessed for reproducibility on more than 50 human DNA samples and it was observed that this modified method is at least five times more productive than original protocol recommended by the manufacturer. The current smart modifications in SNaPshot reaction were successfully optimized for asthma susceptible SNPs. However, these can be applied for cost effective genotyping of any type of genomic Single Nucleotide Polymorphisms.


BABOL-POKORA, K. & BERENT, J. 2008. SNP-minisequencing as an excellent tool for analysing degraded DNA recovered from archival tissues. Acta Biochim Pol, 55, 815-9.

GHANI, M. U., SABAR, M. F., BANO, I., SHAHID, M., AKRAM, M., KHALID, I., MARYAM, A. & KHAN, M. U. 2019a. Evaluation of ADAM33 gene's single nucleotide polymorphism variants against asthma and the unique pattern of inheritance in Northern and Central Punjab, Pakistan. Saudi Med J, 40, 774-780.

GHANI, M. U., SABAR, M. F., BANO, I., SHAHID, M., AKRAM, M., KHALID, I., MARYAM, A. & KHAN, M. U. 2019b. Inheritance Pattern of Rs2280089, Rs2280090, Rs2280091 Snp Variants in Punjabi Population and Association with Asthma Disease. Chest, 155, 168A.

GILBERT, M. T., SANCHEZ, J. J., HASELKORN, T., JEWELL, L. D., LUCAS, S. B., VAN MARCK, E., BORSTING, C., MORLING, N. & WOROBEY, M. 2007. Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue. Electrophoresis, 28, 2361-7.

HURST, C. D., ZUIVERLOON, T. C., HAFNER, C., ZWARTHOFF, E. C. & KNOWLES, M. A. 2009. A SNaPshot assay for the rapid and simple detection of four common hotspot codon mutations in the PIK3CA gene. BMC Res Notes, 2, 66.

SABAR, M. F., GHANI, M. U., SHAHID, M., SUMRIN, A., ALI, A., AKRAM, M., TARIQ, M. A. & BANO, I. 2016. Genetic variants of ADAM33 are associated with asthma susceptibility in the Punjabi population of Pakistan. J Asthma, 53, 341-8.

SABAR, M. F., SHAHID, M., BANO, I., GHANI, M. U., AKRAM, M., IQBAL, F., KOUSAR, S., IQBAL, Z., ALTAF, S. & HUSNAIN, T. 2017. rs12603332 is associated with male asthma patients specifically in urban areas of Lahore, Pakistan. J Asthma, 54, 887-892.

SHAHID, M., SABAR, M. F., BANO, I., RAHMAN, Z., IQBAL, Z., FATIM ALI, S. S., GHANI, M. U., IQBAL, M. & HUSNAIN, T. 2015. Sequence variants on 17q21 are associated with the susceptibility of asthma in the population of Lahore, Pakistan. J Asthma, 52, 777-84.

SHAHID, M., TAYYAB, U., KOUSAR, S., GHANI, M. U., SABAR, M. F. & HUSNAIN, T. 2019. Rs153109 as Possible Indicator of Effectiveness of Vitamin D Supplements for Suppressing Copd Symptoms. Chest, 155, 219A.

TEBBUTT, S. J., JAMES, A. & PARÉ, P. D. 2007. Single-Nucleotide Polymorphisms and Lung Disease*. Chest, 131, 1216-1223.