Scientific Online Resource System

Scripta Scientifica Medica

Increasing detection sensitivity of low copy number transcripts through preamplification of cDNA molecules

Pantelis Dimaras, Oskan Tasinov, Desislava Ivanova, Yoana Kiselova-Kaneva, Diana Ivanova

Abstract

With the advances in the field of molecular biology and its applications in the clinical practice during the recent years, it has become crucial to perform molecular analyses on limited amount of tissue obtained through biopsies. Additionally, tissue is fixed in formalin and further embedded in paraffin (FFPE), a pro­cedure which causes extensive degradation of nucleic acids, mainly RNAs. Furthermore, when studying gene expression profiles of a set of genes, which present physiologically low expression, the number of transcripts is low and cannot be detected. In this study we focus on amplifying effectively cDNA molecules synthesized from small amounts of initial RNA before analyzing the expression levels through quantitative polymerase chain reaction (qPCR). By introducing the preamplification step in the procedure, we achieved highly effi­cacious detection and quantification of expression levels of low-expression genes.


Keywords

cDNA preamplification; qPCR; gene expression

Full Text


References

Lejnine S, Marton MJ, Wang IM, Howell BJ, Webber AL, Maxwell JW, et al. Gene expression analysis in serial Liver fine needle aspirates. J Viral Hepat. 2014;22(1):64–76. doi: 10.1111/jvh.12213

Austin MC, Smith C, Pritchard CC, Tait JF. DNA yield from tissue samples in surgical pathology and minimum tissue requirements for molecular testing. Arch Pathol Lab Med. 2016;140(2):130–3. doi: 10.5858/arpa.2015-0082-OA

von Ahlfen S, Missel A, Bendrat K, Schlumpberger M. Determinants of RNA quality from FFPE sam¬ples. PLoS One. 2007;2(12): e1261. doi: 10.1371/journal.pone.0001261

Andersson D, Akrap N, Svec D, Godfrey TE, Kubista M, Landberg G, et al. Properties of targeted preamplification in DNA and cDNA quantification. Expert Rev Mol Diagn [Internet]. 2015;15(8):1085– 100. Available from: http://www.pubmedcen¬tral. nih.gov/articlerender.fcgi?artid=4673511 &tool=pmcentrez&rendertype=abstract. doi: 10.1586/14737159.2015.1057124

Noutsias M, Rohde M, Block A, Klippert K, Lettau O, Blunert K, et al. Preamplification techniques for real-time RT-PCR analyses of endomyocardial biopsies. BMC Mol Biol. 2008;9(DCM):3. doi: 10.1186/1471-2199-9-3

Zeka F, Vanderheyden K, De Smet E, Cuvelier C a., Mestdagh P, Vandesompele J. Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples. Sci Rep [Internet]. 2016;6(February):21418. Available from: http://www.nature.com/articles/srep21418%5Cnhttp://www. ncbi.nlm.nih.gov/pubmed/26898768%5Cnhttp:// www.pubmedcentral.nih.gov/articlerender. fcgi?artid=PMC4761903. doi: 10.1038/srep21418

Baak-Pablo R, Dezentje V, Guchelaar H-J, van der Straaten T. Genotyping of DNA samples isolated from formalin-fixed paraffin-embedded tissues using preamplification. J Mol Diagn [Internet]. 2010;12(6):746–9. Available from: http://www. pubmedcentral.nih.gov/articlerender.fcgi?artid=29 63916&tool=pmcentrez&rendertype=abstract. doi: 10.2353/jmoldx.2010.100047

Kroneis T, Jonasson E, Andersson D, Dolatabadi S, Ståhlberg A. Global preamplification simplifies targeted mRNA quantification. Sci Rep [Internet]. 2017 Mar 23;7:45219. Available from: http://www. ncbi.nlm.nih.gov/pmc/articles/PMC5362892/. doi: 10.1038/srep45219

Mengual L, Burset M, Marín-Aguilera M, Ribal MJ, Alcaraz A. Multiplex preamplification of specific cDNA targets prior to gene expression analysis by TaqMan Arrays. BMC Res Notes. 2008;1:21. doi: 10.1186/1756-0500-1-21

Lekanne Deprez RH, Fijnvandraat AC, Ruijter JM, Moorman AF. Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis con¬ditions. Anal Biochem [Internet]. 2002;307(1):63– 9. Available from: http://www.sciencedirect.com/ science/article/pii/S0003269702000210




DOI: http://dx.doi.org/10.14748/ssm.v49i2.2180
Array
About The Authors

Pantelis Dimaras
Medical University of Varna
Bulgaria

Department of Biochemistry, Molecular Medicine and Nutrigenomics, Faculty of Pharmacy

Oskan Tasinov
Medical University of Varna
Bulgaria

Department of Biochemistry, Molecular Medicine and Nutrigenomics, Faculty of Pharmacy

Desislava Ivanova
Medical University of Varna
Bulgaria

Department of Biochemistry, Molecular Medicine and Nutrigenomics, Faculty of Pharmacy

Yoana Kiselova-Kaneva
Medical University of Varna
Bulgaria

Department of Biochemistry, Molecular Medicine and Nutrigenomics, Faculty of Pharmacy

Diana Ivanova
Medical University of Varna
Bulgaria

Department of Biochemistry, Molecular Medicine and Nutrigenomics, Faculty of Pharmacy

Font Size


|