Fit for purpose frozen tissue collections by RNA integrity number-based quality control assurance at the Erasmus MC tissue bank.

Author(s): Kap M, Oomen M, Arshad S, de Jong B, Riegman P

Publication: Biopreserv Biobank, 2014, Vol. 12, Page 81-90

PubMed ID: 24749874 PubMed Review Paper? No

Purpose of Paper

The purpose of this paper was to assess the RNA quality of biobanked tissue specimens collected and stored at different institutions. RNA integrity numbers (RIN) were compared for specimens that differed in tissue type, procurement method, cryopreservation method, storage temperature and storage duration.

Conclusion of Paper

When specimens were grouped by RIN, they observed large differences in distribution patterns between biobanks. The percentage of specimens with a RIN less than 5 ranged between 0 and 20.8%, those with a RIN between 5 and 6 ranged between 0 and 8.33%, those with a RIN between 6 and 8 ranged between 25 and 59%, and those with a RIN greater than or equal to 8 ranged between 39 and 45% depending on the biobank. Biopsies from the Clinical Pathology Frozen Biopsy Archive Collection had the broadest distribution. Statistical analysis failed to reveal any significant differences in RIN between specimens that differed in collection method, storage temperature, and storage duration. The potential impact of other variables, such as cold ischemia time, transport conditions, tissue type, and diagnosis were not assessed.

Studies

Study Purpose

The purpose of this study was to assess and compare the quality of RNA isolated from biobanked tissue specimens collected and stored by four different biobanking institutions (the number of specimens is indicated within parentheses): Erasmus Medical Center Tissue Bank (103), Cancer Institute Archive Collection (48), Liver Sample Archive Collection (123), and the Clinical Pathology Biopsy Archive Collection (24). RIN data was grouped and represented as the percentage of specimens that met fit-for-purpose thresholds identified using literature evidence. The fit-for-purpose criteria applied were as follows: RIN< 5, not reliable for downstream analysis; 5≤RIN<6, suitable for RT-qPCR; 6≤RIN<8, suitable for RT-qPCR and gene expression array; RIN≥8, suitable for all downstream analyses. RINs from specimens that differed in tissue type, diagnosis, procurement method, cold ischemia time, cryopreservation method, storage temperature and duration were compared. Tissue specimens with low RNA yields or that showed evidence of morphological degradation were excluded from analysis, although the threshold of RNA yield used by the authors was not specified.

Summary of Findings:

The number of specimens that were excluded from analysis due to low RNA yield or evidence of morphological degradation was as follows: 9.68% (9) out of the 103 specimens from the Eramus Medical Center Tissue Bank; 18.75% (9) out of the 48 specimens from the Cancer Institute Archive Collection; 9.8% (12) out of the 123 specimens from the Liver Sample Archive Collection; 20.83% (5) out of the 24 specimens from the Clinical Pathology Frozen Biopsy Archive Collection. When specimens were grouped by RIN, they observed large differences in distribution patterns between biobanks. The percentage of specimens with a RIN less than 5 ranged between 0 and 20.8%, those with a RIN between 5 and 6 ranged between 0 and 8.33%, those with a RIN between 6 and 8 ranged between 25 and 59%, and those with a RIN greater than or equal to 8 ranged between 39 and 45% depending on the biobank. Biopsies from the Clinical Pathology Frozen Biopsy Archive Collection had the broadest distribution, as the largest percentage of specimens having both the lowest and highest RIN were from this biobank. Statistical analysis failed to reveal any significant differences in RIN between specimens that differed in collection method, storage temperature, and storage duration. However, the authors note that while specimens from the Clinical Pathology Frozen Biopsy Archive Collection had a cold ischemia time of 30 min or less there is no information available on the condition of the specimens during transportation to the pathology laboratory. The potential impact of other variables on RIN distribution, such as cold ischemia time, transport conditions, tissue type, and diagnosis were not assessed.

Biospecimens

Preservative Types

Frozen

Diagnoses:

Normal
Hepatitis
Cirrhosis
Neoplastic - Carcinoma
Neoplastic - Benign

Platform:

Analyte	Technology Platform
RNA	Automated electrophoresis/Bioanalyzer

Pre-analytical Factors:

Classification	Pre-analytical Factor	Value(s)
Storage	Storage duration	1 y > 20 y 15 y 13 y
Biospecimen Acquisition	Cold ischemia time	5-30 min <30 min 30 min to 2 h 30 min- several hours
Storage	Storage temperature	-80°C Liquid nitrogen
Biospecimen Preservation	Cooling or freezing method/ rate	Pre-cooled isopentane Liquid nitrogen
Biospecimen Acquisition	Method of tissue acquisition	Biopsy Surgical resection

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