Applied Molecular-Based Quality Control of Biobanked Samples for Multi-Omics Approach

Abstract

Biobanks are vital for high-throughput translational research, but the rapid development of novel molecular techniques, especially in omics assays, poses challenges to traditional practices and recommendations. In our study, we used biospecimens from oncological patients in Polish clinics and collaborated with the Indivumed Group. For serum/plasma samples, we monitored hemolysis, controlled RNA extraction, assessed cDNA library quality and quantity, and verified NGS raw data. Tissue samples underwent pathologic evaluation to confirm histology and determine tumor content. Molecular quality control measures included evaluating the RNA integrity number, assessing cDNA library quality and quantity, and analyzing NGS raw data. Our study yielded the creation of distinct workflows for conducting preanalytical quality control of serum/plasma and fresh-frozen tissue samples. These workflows offer customization options to suit the capabilities of different biobanking entities. In order to ensure the appropriateness of biospecimens for advanced research applications, we introduced molecular-based quality control methods that align with the demands of high-throughput assays. The novelty of proposed workflows, rooted in innovative molecular techniques, lies in the integration of these QC methods into a comprehensive schema specifically designed for high-throughput research applications.

First insight about the ability of specific glycerophospholipids to discriminate non-small cell lung cancer subtypes

“…The exact time of resection start, vessel ligation, resection end, and tissue sample preservation were recorded and documented. The details of tissue samples collection in the clinical setting–macroscopic evaluation resected specimens were described previously ( Ciereszko et al, 2022 ), together with the biobanking conditions and Standard Operating Procedures ( Niklinski et al, 2017 ; Michalska-Falkowska et al, 2023 ). Cancer stages were determined following pathological tumour-node-metastasis (pTNM) staging.…”

Circulating serum miR-362-3p and miR-6721-5p as potential biomarkers for classification patients with adult-type diffuse glioma

“…In the presented study, serum samples were collected in the Clinical Hospital in Bialystok by Biobank at the Medical University of Bialystok, with high standards of strict biobanking procedures for multi-omics studies ( Niklinski et al, 2017 ; Michalska-Falkowska et al, 2023 ). The study group consisted of patients qualified for surgical treatment of adult-type diffuse gliomas at different stages of development ( WHO, 2021 grade 2–4).…”

Six-Gene Signature for Differential Diagnosis and Therapeutic Decisions in Non-Small-Cell Lung Cancer—A Validation Study

“…Inclusion criteria comprised an original diagnosis of lung adenocarcinoma (ADC) or squamous cell carcinoma (SCC) based on histologic evidence, complete resection of the tumor with free margins, stage IA to IIIA, a minimum of 3-year follow-up with monitoring for cancer recurrence events, availability of representative fresh-frozen tumor specimens (with at least 50% tumor cells for RNA extraction), and no history of neoadjuvant chemotherapy or radiotherapy. All procedures related to patient selection for the study and the study design adhered strictly to standard operating procedures, which were meticulously maintained throughout the experiment's duration [53,54].…”