Establishing a correlation between RIN and A 260/280 along with the multivariate evaluation of factors affecting the qua
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Establishing a correlation between RIN and A260/280 along with the multivariate evaluation of factors affecting the quality of RNA in cryopreserved cancer bio-specimen Sanket G. Shah . Mudasir Rashid . Tripti Verma . Madan Ludbe . Bharat Khade . Poonam B. Gera . Sanjay Gupta
Received: 21 November 2018 / Accepted: 12 August 2019 Ó Springer Nature B.V. 2019
Abstract Biomarkers are biological characteristic to measure and evaluate normal and pathological states. To define expression-based molecular biomarkers, high-quality tissue samples are a prerequisite for the preparation of standard RNA. It is already known that RIN number defines the RNA quality, however its relation with A260/280 ratio and Ct value is not defined clearly; therefore, understanding an association will provide a reliable method for describing RNA quality. Multiple cryopreserved human tumor tissue types from ACTREC Biorepository and TMH-INTTR were
Mudasir Rashid and Tripti Verma have equally contributed to this work.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10561-019-09782-7) contains supplementary material, which is available to authorized users. S. G. Shah M. Rashid T. Verma B. Khade S. Gupta (&) Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210, India e-mail: [email protected]
analyzed for the effect of storage time on RNA quality. The RNA from tumor samples were isolated and analyzed by RIN, A260/280 ratio, and Ct value to establish inter-relationships. Around 50% samples had a RIN of C 6.9 and A260/280 B 2.04; 27% had a RIN C 5 and A260/280 B 2.08, and remaining 23% displayed RIN \ 5 and A260/280 [ 2.08. However, the RNA quality has no association with the storage period of tissue samples. Moreover, all samples which had A260/280 B 2.08 showed acceptable Ct values of 17–24. The data clearly suggests that the A260/280 ratio is able to predict RNA quality. To the best of our knowledge, this is the first Indian report analyzing the labile nucleic acid-RNA quality from different cancer tissue types cryopreserved for diverse time periods. In conclusion, RIN and A260/280 ratio can help in predicting the quality of RNA independently; however, both together provide better assurance for further downstream processing. S. G. Shah M. Rashid T. Verma S. Gupta Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
M. Ludbe P. B. Gera (&) Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210, India e-mail: [email protected]
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Keywords RIN A260/280 Ct value Biorepository Tumor tissues Abbreviations IDC Infiltrating ductal carcinoma ADC Adenocarcinoma GBM Glioblastoma SN Seminoma ACTRECAdvanced Centre for
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