Bibliographic record
Abstract
Background: It is generally recognized that the integrity of tissue specimens preserved at temperatures below the gas state is stable long-term. Studies in literature have not typically extended beyond a few years. As many biobanks today may store specimens for over a decade, this assumption should be tested to provide the data to support extended long-term storage and verify that stored samples continue to be fit-for-purpose. Since its inception in 2004, the Ontario Tumour Bank (OTB) has had an ongoing commitment to quality and, in accordance with biobanking best practices, has embedded stringent quality control (QC) and quality assurance (QA) measures into its routine procedures. One such measure, triggered twice annually, includes the random selection of cryopreserved tissues to undergo quality assessment (EXTQA) to measure the integrity of the tissueu2019s DNA and RNA. As an extension of OTBu2019s routine EXTQA, we analyzed second aliquots of previously evaluated tissues collected between 2005 and 2014 to determine if RNA (presented at the ISBER annual conference in 2017) or DNA integrity (presented here) is affected by extended long-term storage in liquid nitrogen vapour phase. Methods: As previously presented, RNA was extracted from duplicate aliquots of 70 cryopreserved tissue samples across 11 disease sites and quality was determined by the RNA Integrity Number (RIN) assigned by the Agilent Bioanalyzer. As an extended fit-for-purpose assessment, DNA was extracted from 20 samples to determine if DNA Integrity is associated with time in storage. The DNA integrity of the sample, as defined by its DIN value, was determined using the Agilent 2200 Tapestation and Genomic DNA Screen Tape.Results: As presented previously, there was no significant correlation between the quality of RNA versus storage time. New to this study, there was also no significant correlation between the quality of DNA versus storage time (r=0.250, p= 0.287). As a secondary observation, DNA quality is not correlated to RNA quality (r=0.2362, p=0.3147). Conclusions: This data suggests that, as for RNA, the extended long-term storage of tumour tissue samples in vapour phase in liquid nitrogen tanks does not negatively affect the quality of DNA derivatives. As a secondary observation, RNA integrity (RIN) is not a good predictor of DNA integrity, which supports previous recommendations to consider appropriate fit-for-purpose tests for different downstream applications rather than relying solely on RIN.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.045 | 0.076 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.001 | 0.004 |
| Scholarly communication | 0.007 | 0.014 |
| Open science | 0.004 | 0.006 |
| Research integrity | 0.004 | 0.004 |
| Insufficient payload (model declined to judge) | 0.014 | 0.008 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".