A new biobank concept to optimize the quality of data-rich specimens

<p><strong>Poster has been presented at the 26th European Congress of Pathology</strong></p> <p> </p> <p><strong>Objective</strong><br>High quality of biological specimen collection and a repeatable process are imperative for biobanking. We present a new biobanking concept that ensures the integrity of annotation data and the biological process quality.</p> <p><strong>Method</strong><br>We use an automated cryopreservation system (Smartfreezer®), storing specimens in the gasiform nitrogen phase at -180 C°. Individual specimens can be stored and retrieved. This ensures that only selected specimens are removed from the nitrogen phase. To enhance data quality and allow easier integration of data from heterogeneous resources we will implement a data management, which will use an ontology coded in Web Ontology Language 2. For this purpose we will re-use and extend a pre-existing ontology developed by UAMS in cooperation with BBMRI Sweden.</p> <p><strong>Results</strong><br>Only selected tubes are subject to a change of environment, which minimize the risks for temperature deviation and ice crystal formation. Storage in a gasiform nitrogen phase ensures complete biological preservation. Semantic infrastructure will help integrating data easily with further information belonging to the donor. Ontology will also help managing access permissions for specimens.</p> <p><strong>Conclusion</strong><br>New technologies as automated cryopreservation and ontology based data management help to improve the process quality and assist in producing more reliable and accessible results.</p

Additional file 2: of Favorable outcome of patients with lung adenocarcinoma harboring POLE mutations and expressing high PD-L1

Figure S1. (A) Lollipop plot shows the distribution of POLE mutations in UCEC, LUAD and LUSC cancers. (B) TMB cannot stratify LUAD patients. Figure S2. PD-L1 expression cannot stratify (A) LUAD or (D) LUSC patients without POLE mutations. (B) POLE mutation is associated with higher mutation rates. (C) The combination of POLE mutations and PD-L1 expression is not predictive to LUSC patient outcomes. (E) POLE-mutant patients have slighter higher percentages of TIL. (F) Mut-High group of patients have lower TIL but better survivals. Figure S3. There were 96 genes that were identified to be significantly mutated in Mut-High group but not Mut-Low group with P < 0.05 (Fisher’s exact test). Figure S4. (A) Comparisons of immune-related gene expression in Mut-High and Mut-Low groups. (B) GSEA pathway enrichment and (C) GO function enrichment of the differentially expressed genes in Mut-High and Mut-Low groups. (DOCX 16386 kb

Additional file 1: of Favorable outcome of patients with lung adenocarcinoma harboring POLE mutations and expressing high PD-L1

Methods and Materials. (DOCX 30 kb

Additional file 2: Figure S1. of Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages

ctDNA mutational landscape for major cancer groups for the top 30 genes in total cohort. Figure S2. ctDNA mutational landscape of patients’ stage known for the top 30 genes in lung cancer cohort. Figure S3. Higher mutation numbers in the ctDNA are associated with decreased survival in lung cancers. Higher mutation numbers in ctDNA are associated with poor survival. “n” defines the number of mutations and survival plots are separated by mutation numbers: n = 1, 2, 3, 4, 5, and 6 mutations. Blue lines indicate more than “n” mutations and the pink lines indicate equal to or less than “n” mutations. P-values were derived using the log-rank test. Figure S4. The concordance of top mutated genes in the ctDNA and tDNA of 37 lung cancer patients. (DOC 1098 kb

Additional file 1: Table S1. of Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages

Clinical and treatment characteristics of the 18 cases with no ctDNA alterations detected. Table S2. Description of mutation load in total cohort (n = 177). Table S3. All mutations detected in patient ctDNA compared with other studies. (DOC 625 kb