Improvement of HER2I655V TARMS-PCR Performance by DNA Quality Analysis

Bugi Ratno Budiarto, Azamris Azamris, Desriani Desriani

Abstract


Reliable TARMS-PCR is a prerequisite in constructing a solid conclusion in genetic diagnostics. The validity of data generated by this molecular technique is hampered by a false positive result. In attempt to develop a  TARMS-PCR for HER2I655V genotyping with no interfering of bias we used DNase I to eliminate DNA contaminant resided in PCR reagent. TARMS-PCR without enzyme treatment using recombinant plasmids that contained HER2I655V gene with represented its alleles was used to evaluate the presence of false positive  result while DNase I treated-PCR reagent was used in TARMS-PCR to evaluate the effective dose of the enzyme and further to adjust the TARMS-PCR conditions.  PCR master mix kit used in this study produced a false positive result on HER2I655V TARMS-PCR as proven by the presence of multiple PCR products in Non-Template Control (NTC) and 0.1 U of the enzyme could eliminate this DNA contaminant effectively, although this pretreatment altered the specificity of HER2I655V TARMS-PCR genotyping on certain genotype. Combination of touchdown TARMS-PCR with another allele-specific primer recovered specificity of detection on this model system. Interestingly, this optimized HER2I655V TARMS-PCR can only be used for genotyping the clinical samples if only further optimization was done using genomic DNA as template


Keywords


TARMS-PCR, HER2I655V, DNase I, Polymorphism

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Aloui, C., Sut, C., Cognasse, F., Granados, V., Hassine, M., Chakroun, T., & Laradi, S. (2015). Development of a highly resolutive method, using a double quadruplex tetra-primer-ARMS-PCR coupled with capillary electrophoresis to study CD40LG polymorphisms. Molecular and cellular probes, 29(6), 335-342.

Ayyadevara, S., Thaden, J. J., & Reis, R. J. S. (2000). Discrimination of primer 3′-nucleotide mismatch by Taq DNA polymerase during polymerase chain reaction. Analytical biochemistry, 284(1), 11-18.

Baris, I., Etlik, O., Koksal, V., & Arican-Baris, S. T. (2010). Rapid diagnosis of spinal muscular atrophy using tetra-primer ARMS PCR assay: simultaneous detection of SMN1 & SMN2 deletion. Molecular and cellular probes, 24(3), 138-141.

Borst, A., Box, A. T. A., & Fluit, A. C. (2004). False-positive results and contamination in nucleic acid amplification assays: suggestions for a prevent and destroy strategy. European journal of clinical microbiology and infectious diseases, 23(4), 289-299.

Budiarto, B. R., & Desriani. (2016). Dataset reporting detection of breast cancer-related HER2 I655V polymorphism using allele-specific polymerase chain reaction. Data in brief, 9, 689-695.

Bui, M., & Liu, Z. (2009). Simple allele-discriminating PCR for cost-effective and rapid genotyping and mapping. Plant Methods, 5(1), 1.

Carroll, N. M., Adamson, P., & Okhravi, N. (1999). Elimination of bacterial DNA from TaqDNA polymerases by restriction endonuclease digestion. Journal of clinical microbiology, 37(10), 3402-3404.

Champlot, S., Berthelot, C., Pruvost, M., Bennett, E. A., Grange, T., & Geigl, E. M. (2010). An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS One, 5(9), e13042.

Czurda, S., Smelik, S., Preuner-Stix, S., Nogueira, F., & Lion, T. (2016). Occurrence of fungal DNA contamination in PCR reagents: approaches to control and decontamination. Journal of clinical microbiology, 54(1), 148-152.

Dubey, P. K., Goyal, S., Aggarwal, J., Gahlawat, S. K., Kathiravan, P., Mishra, B. P., & Kataria, R. S. (2012). Development of tetra-primers ARMS-PCR assay for the detection of A1551G polymorphism in TLR8 gene of riverine buffalo. Journal of applied animal research, 40(1), 17-19.

Etlik, O., Koksal, V., Arican-Baris, S. T., & Baris, I. (2011). Development and validation of a cost-effective in-house method, tetra-primer ARMS PCR assay, in genotyping of seven clinically important point mutations. Molecular and cellular probes, 25(4), 177-181.

Furtado, L. F., & Rabelo, É. M. (2015). Development of a new amplification-refractory mutation system for detection of a single nucleotide polymorphism linked to drug resistance in Ancylostoma caninum. Genetics and Molecular Research, 14(2), 5103-5111.

Glassing, A., Dowd, S. E., Galandiuk, S., Davis, B., & Chiodini, R. J. (2016). Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut pathogens, 8(1), 24.

Guan, F., Shi, G., Wan, P., Dai, R., Tang, H., Wang, H., & Luo, Y. (2014). Development of cost-effective tetra-ARMS PCR for detection of FecB genotype in sheep. Animal Science Papers and Reports, 32(3), 229-237.

Han, B., Zong, L., Li, Q., Zhang, Z., Wang, D., Lan, L., & Wang, Q. (2013). Newborn genetic screening for high risk deafness-associated mutations with a new Tetra-primer ARMS PCR kit. International journal of pediatric otorhinolaryngology, 77(9), 1440-1445.

Hanaki, K., Nakatake, H., Yamamoto, K., Odawara, T., & Yoshikura, H. (2000). DNase I activity retained after heat inactivation in standard buffer. BioTechniques, 29(1), 38.

Heininger, A., Binder, M., Ellinger, A., Botzenhart, K., Unertl, K., & Döring, G. (2003). DNase pretreatment of master mix reagents improves the validity of universal 16S rRNA gene PCR results. Journal of clinical microbiology, 41(4), 1763-1765.

Hosking, L., Lumsden, S., Lewis, K., Yeo, A., McCarthy, L., Bansal, A., & Chun-Fang, X. (2004). Detection of genotyping errors by Hardy-Weinberg equilibrium testing. European journal of human genetics: EJHG, 12(5), 395.

Islam, M., Awan, F. R., & Baig, S. M. (2014). Development of ARMS-PCR assay for genotyping of Pro12Ala SNP of PPARG gene: a cost effective way for case–control studies of type 2 diabetes in developing countries. Molecular biology reports, 41(9), 5585-5591.

Lievano, F. A., Reynolds, M. A., Waring, A. L., Ackelsberg, J., Bisgard, K. M., Sanden, G. N., & Smith, P. F. (2002). Issues associated with and recommendations for using PCR to detect outbreaks of pertussis. Journal of clinical microbiology, 40(8), 2801-2805.

Liu, J., Huang, S., Sun, M., Liu, S., Liu, Y., Wang, W., ... & Hua, W. (2012). An improved allele-specific PCR primer design method for SNP marker analysis and its application. Plant Methods, 8(1), 34.

Mesrian Tanha, H., Mojtabavi Naeini, M., Rahgozar, S., Rasa, S. M. M., & Vallian, S. (2015). Modified tetra-primer ARMS PCR as a single-nucleotide polymorphism genotyping tool. Genetic testing and molecular biomarkers, 19(3), 156-161.

Miranzadeh-Mahabadi, H., Nikpour, P., Emadi-Baygi, M., & Kelishadi, R. (2015). Comparison of TaqMan Real-Time and Tetra-Primer ARMS PCR Techniques for Genotyping of Rs 8066560 Variant in Children and Adolescents with Metabolic Syndrome. Advances in clinical and experimental medicine: official organ Wroclaw Medical University, 24(6), 951-955.

Mühl, H., Kochem, A. J., Disqué, C., & Sakka, S. G. (2010). Activity and DNA contamination of commercial polymerase chain reaction reagents for the universal 16S rDNA real-time polymerase chain reaction detection of bacterial pathogens in blood. Diagnostic microbiology and infectious disease, 66(1), 41-49.

Newton, C. R., Graham, A., Heptinstall, L. E., Powell, S. J., Summers, C., Kalsheker, N., & Markham, A. F. (1989). Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic acids research, 17(7), 2503-2516.

Ou, C. Y., Moore, J. L., & Schochetman, G. (1991). Use of UV irradiation to reduce false positivity in polymerase chain reaction. Biotechniques, 10(4), 442-444.

Pao, C. C., Hor, J. J., Tsai, P. L., & Horng, M. Y. (1993). Inhibition of in vitro enzymatic DNA amplification reaction by ultra-violet light irradiation. Molecular and cellular probes, 7(3), 217-219.

Randhawa, R., Duseja, A., & Changotra, H. (2017). A novel Tetra-primer ARMS-PCR based assay for genotyping SNP rs12303764 (G/T) of human Unc-51 like kinase 1 gene. Molecular biology reports, 44(1), 1-4.

Rand, K. H., & Houck, H. (1990). Taq polymerase contains bacterial DNA of unknown origin. Molecular and cellular probes, 4(6), 445-450.

Ray, P. F, & Handyside, A.H. (1996). Increasing the denaturation temperature during the first cycles of amplification reduced allele dropout from single cells for preimplantation genetic diagnosis. MHR: Basic science of reproductive medicine, 2(3), 213-218.

Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., & Walker, A. W. (2014). Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC biology, 12(1), 87.

Schrader, C., Schielke, A., Ellerbroek, L., & Johne, R. (2012). PCR inhibitors–occurrence, properties and removal. Journal of applied microbiology, 113(5), 1014-1026.

Simsek, M., & Adnan, H. (2000). Effect of single mismatches at 3′–end of primers on polymerase chain reaction. Journal for scientific research. Medical sciences/Sultan Qaboos University, 2(1), 11.

Suhda, S., Paramita, D. K., & Fachiroh, J. (2016). Tetra-primer ARMS PCR optimization to detect single nucleotide polymorphisms of the CYP2E1 gene. Asian Pac J Cancer Prev, 17(7), 3065-3069.

Silkie, S. S., Tolcher, M. P., & Nelson, K. L. (2008). Reagent decontamination to eliminate false-positives in Escherichia coli qPCR. Journal of microbiological methods, 72(3), 275-282.

Soler, S., Rittore, C., Touitou, I., & Philibert, L. (2011). A comparison of restriction fragment length polymorphism, tetra primer amplification refractory mutation system PCR and unlabeled probe melting analysis for LTA+ 252 C> T SNP genotyping. Clinica Chimica Acta, 412(5), 430-434.

Spangler, R., Goddard, N. L., & Thaler, D. S. (2009). Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria. PloS one, 4(9), e7010.

Wang, Z. N., Cai, H. F., Li, M. X., Cao, X. K., Lan, X. Y., Lei, C. Z., & Chen, H. (2016). Tetra-primer ARMS-PCR identified four pivotal genetic variations in bovine PNPLA3 gene and its expression patterns. Gene, 575(2), 191-198.

Ye, S., Dhillon, S., Ke, X., Collins, A. R., & Day, I. N. (2001). An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic acids research, 29(17), e88-e88.

You, F. M., Huo, N., Gu, Y. Q., Luo, M. C., Ma, Y., Hane, D., & Anderson, O. D. (2008). BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC bioinformatics, 9(1), 253.

Zhang, S., Dang, Y., Zhang, Q., Qin, Q., Lei, C., Chen, H., & Lan, X. (2015). Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) rapidly identified a critical missense mutation (P236T) of bovine ACADVL gene affecting growth traits. Gene, 559(2), 184-188.




DOI: http://dx.doi.org/10.14203/ann.bogor.2017.v21.n2.52-62

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