Quality assessment of cryopreserved biospecimens reveals presence of intact biomolecules

Abstract

Recapitulation of tumor features in isolated biomolecules is preeminently dependent on obtaining reliable quality biospecimen. Moreover, quality assessment of biobanked specimens at regular intervals is an essential intervention for carrying out effective translational and clinical research. In the current study, genomic DNA was extracted from 140 fresh frozen tissues of oral, breast and colorectal specimens cryopreserved over a period of 3 to 8 months (short term) and 3 to 4 years (long term). Quantification of genomic DNA by absorption and fluorescence spectroscopy confirmed high concentration while qualitative analysis by gel electrophoresis showed intact bands for 94% and 87% of short‐ and long‐term cohorts, respectively. PC‐LDA based classification of Raman spectra showed overlapping groups of both cohorts suggesting the quality of DNA being preserved irrespective of storage period. To the best of our knowledge this is the first Indian biobank study reporting quality analysis of biospecimens cryopreserved at different time periods.

Raman Spectroscopy: An Exploratory Study to Identify Post-Radiation Cell Survival

“…The spectra were interpolated in 650–1750 cm −1 region, since this region lies in the fingerprint region. Spectra were smoothened (Savitzky–Golay method and window size three) and further vector normalized spectra 17,24,26,33,38–46 were subjected to multivariate unsupervised principal component analysis (PCA) and supervised principal component linear discriminant analysis (PC-LDA). PCA identifies the maximum variance between the data, while PC-LDA provides distinct classification between different groups.…”

“…Raman spectroscopy, a noninvasive and nondestructive optical vibrational spectroscopic method has been widely employed for cancer detection and diagnosis studies using cells and tissues. Discrimination between healthy and normal tissue, 15 living and dead cells, 16 assessing quality of DNA extracted from cryopreserved tumor and normal tissue, 17 detection of RBC and classification of different blood types, 18 detection of RBC variation in diabetes, 19 diagnosis of breast cancer, 20 esophageal cancer, 21 skin cancer, 22 and gastric cancer 23 are few of the applications studied using Raman spectroscopy. Modifications of functional groups determined by Raman shifts provides a unique molecular fingerprint, 24 which can thus be employed to evaluate the characteristic features representing the effect of radiation-induced cell death during the course of radiotherapy.…”

“…As outlined in this study, we carried out Raman spectroscopy analysis on cell pellets using 532 nm as the excitation source, which is widely used for ex vivo biomedical applications, such as assessing the quality of DNA extracted from cryopreserved tissues, detection of oral cancer, diagnosis of breast cancer, metastasis of breast cancer, and epigenetic modifications in breast cancer cell lines. 17,32–37 Cell pellets present stack of cells to the probing beam, the probed region could be from different areas of cells, such as different cell organelles and cellular compartments. This approach has been successfully verified in mixed cell populations, for the delineation of drug resistant and radioresistant phenotypes, in addition to an investigation of cervical and oral cancer specimens.…”