Assays for Qualification and Quality Stratification of Clinical Biospecimens Used in Research: A Technical Report from the ISBER Biospecimen Science Working Group

Betsou, Fay; Bulla, Alexandre; Cho, Sang Yun; Clements, Judith A.; Chuaqui, Rodrigo F.; Coppola, Domenico; Souza, Yvonne De; Wilde, Annemieke De; Grizzle, William E.; Guadagni, Fiorella; Gunter, Elaine W.; Heil, Stacey; Hodgkinson, Verity S.; Kessler, Joseph; Kiehntopf, Michael; Kim, Hee Sung; Koppandi, Iren; Shea, Katheryn; Singh, Rajeev Kumar; Sobel, Marc; Somiari, Stella; Spyropoulos, Demetri D.; Stone, Mars; Tybring, Gunnel; Valyi‐Nagy, Klara; Eynden, Gert Van den; Wadhwa, Lalita

doi:10.1089/bio.2016.0018

Cited by 42 publications

(28 citation statements)

References 49 publications

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“…Aiming to clarify this gap in knowledge, a new discipline called Biospecimen Science (BS) emerged in the field of biobanks focused on studying how pre-analytical factors may alter integrity of samples 5 . It also focuses on discovering new quality biomarkers that could help us to assess quality of human biospecimens using standard and validated analytical techniques 6,7 .…”

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confidence: 99%

Impact of different stabilization methods on RT-qPCR results using human lung tissue samples

Esteva-Socias

Gómez-Romano

Carrillo-Ávila

et al. 2020

Sci Rep

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Aiming to increase the reproducibility of biomedical research results, biobanks obtain human tissues of the highest quality and carry out different storage methods adapted to the needs of analytical technique to be performed by the biomedical researchers. However, there is much controversy and little data concerning the real impact of different stabilization methods on tissue quality, integrity and functionality of derived biomolecules. The influence of four stabilization methods [RNAlater (RNL), snap freezing (SF), snap freezing using Optimal Cutting Tissue compound (SF-OCT) and formalin-fixed paraffin-embedded (FFPE)] on RNA quality and integrity was evaluated in paired samples of lung tissue. RNA integrity was evaluated through PCR-endpoint assays amplifying six fragments of different length of the HPRT1 gene and RNA Integrity Number (RIN). To evaluate the difference of tissue functionality among the stabilization methods tested, RT-qPCRs were performed focusing on the differential expression of the HPRT1, SNRPD3 and Jun genes. RNA from the samples preserved with the RNL or SF-OCT method showed better integrity compared to SF and FFPE, measured by PCR-endpoint and RT-qPCR assays. However, only statistically significant differences were observed between the RNA from FFPE and other stabilization methods when gene expression of HPRT1, SNRPD3 and Jun housekeeping genes were determined by RT-qPCR. For the three mentioned genes, Cq and RIN values were highly correlated. The present work describes the fragility of SF samples, being critical the moment just before RNA extraction, although further experiments of tissue RNA are needed. Standardization pre-analytic workflow can lead to improved reproducibility between biomedical research studies. The present study demonstrated clear evidences about the impact of the stabilization method on RNA derived from lung human tissue samples.diluted cDNA and 0,6 µl of PCR-grade water. All PCRs were performed in triplicate from one sample taken from each preservation condition in all 20 patients included. PCR reactions were carried out in 96 well plates and using the CFX96 Real-Time PCR Detection System (Bio-Rad) following the steps: 95 °C for 2 minutes, 40 cycles of amplification (denaturation at 95 °C for 5 seconds, annealing for 10 seconds, and extension at 72 °C for 20 seconds) and final melt curve analysis from 65 °C to 95 °C to exclude unspecific PCR products.The reproducibility and dynamic ranges for qPCR assays were determined by constructing a standard curve, beginning with 100 ng of RNA template as initial concentration and then serial diluted 1/5 until five linear concentration points. For Cq values acquisition, RFU threshold value was adjusted to 50 RFUs for each run.Statistics. All data generated from integrity and functional studies of RNA samples were analysed using multiple comparison tests: ANOVA test with Bonferroni correction to detect significant differences between procedures with at least a signification of p value <0.01. The spearman r index between RNA integ...

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mentioning

confidence: 99%

Impact of different stabilization methods on RT-qPCR results using human lung tissue samples

Esteva-Socias

Gómez-Romano

Carrillo-Ávila

et al. 2020

Sci Rep

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“…In addition to prognostic and predictive biomarker development, a particularly important application of this standardized collection scheme is discovery and validation of blood biomarkers for the early detection of cancers. This should be facilitated by the availability of samples from eight different cancer diagnoses collected in the same logistic pipeline with careful preanalytic annotation, which is likely to simplify evaluation of tumor-type specificity for such biomarkers [18].…”

Section: Discussionmentioning

confidence: 99%

U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden

et al. 2017

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Background: Progress in cancer biomarker discovery is dependent on access to high-quality biological materials and high-resolution clinical data from the same cases. To overcome current limitations, a systematic prospective longitudinal sampling of multidisciplinary clinical data, blood and tissue from cancer patients was therefore initiated in 2010 by Uppsala and Umeå Universities and involving their corresponding University Hospitals, which are referral centers for one third of the Swedish population. Material and Methods: Patients with cancer of selected types who are treated at one of the participating hospitals are eligible for inclusion. The healthcare-integrated sampling scheme encompasses clinical data, questionnaires, blood, fresh frozen and formalin-fixed paraffin-embedded tissue specimens, diagnostic slides and radiology bioimaging data. Results: In this ongoing effort, 12,265 patients with brain tumors, breast cancers, colorectal cancers, gynecological cancers, hematological malignancies, lung cancers, neuroendocrine tumors or prostate cancers have been included until the end of 2016. From the 6914 patients included during the first five years, 98% were sampled for blood at diagnosis, 83% had paraffin-embedded and 58% had fresh frozen tissues collected. For Uppsala County, 55% of all cancer patients were included in the cohort. Conclusions: Close collaboration between participating hospitals and universities enabled prospective, longitudinal biobanking of blood and tissues and collection of multidisciplinary clinical data from cancer patients in the U-CAN cohort. Here, we summarize the first five years of operations, present U-CAN as a highly valuable cohort that will contribute to enhanced cancer research and describe the procedures to access samples and data.ARTICLE HISTORY

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“…2,54,55 Recent efforts by biobanking experts to address this problem after the fact include the development of batteries of assays for measurands in specimens that are affected by preanalytical factors. These ''pretests'' help to classify or disqualify specimens of unknown provenance for molecular analysis [56][57][58][59][60][61][62] but are rarely used in clinical settings.…”

Section: The Scope Of the Problem And The Pressing Need For A Solutionmentioning

confidence: 99%

Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine

Compton

Robb

Anderson

et al. 2019

Archives of Pathology &Amp; Laboratory Medicine

107

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Biospecimens acquired during routine medical practice are the primary sources of molecular information about patients and their diseases that underlies precision medicine and translational research. In cancer care, molecular analysis of biospecimens is especially common because it often determines treatment choices and may be used to monitor therapy in real time. However, patient specimens are collected, handled, and processed according to routine clinical procedures during which they are subjected to factors that may alter their molecular quality and composition. Such artefactual alteration may skew data from molecular analyses, render analysis data uninterpretable, or even preclude analysis altogether if the integrity of a specimen is severely compromised. As a result, patient care and safety may be affected, and medical research dependent on patient samples may be compromised. Despite these issues, there is currently no requirement to control or record preanalytical variables in clinical practice with the single exception of breast cancer tissue handled according to the guideline jointly developed by the American Society of Clinical Oncology and College of American Pathologists (CAP) and enforced through the CAP Laboratory Accreditation Program. Recognizing the importance of molecular data derived from patient specimens, the CAP Personalized Healthcare Committee established the Preanalytics for Precision Medicine Project Team to develop a basic set of evidence-based recommendations for key preanalytics for tissue and blood specimens. If used for biospecimens from patients, these preanalytical recommendations would ensure the fitness of those specimens for molecular analysis and help to assure the quality and reliability of the analysis data.

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Assays for Qualification and Quality Stratification of Clinical Biospecimens Used in Research: A Technical Report from the ISBER Biospecimen Science Working Group

Cited by 42 publications

References 49 publications

Impact of different stabilization methods on RT-qPCR results using human lung tissue samples

Impact of different stabilization methods on RT-qPCR results using human lung tissue samples

U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden

Preanalytics and Precision Pathology: Pathology Practices to Ensure Molecular Integrity of Cancer Patient Biospecimens for Precision Medicine

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