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Additional file 5: Figure S2. Overview of TapeStation results. Results from TapeStation of all cfDNA samples purified with one of the six (co-)purification kits. There are 13/46 samples that have concentrations below LOD (20 pg/µl), and 2/46 samples without any peaks (flat profiles). For 1/46 samples there was not enough material left for TapeStation.

Additional file 6: Figure S3. Detailed description of laboratory workflow. Workflow used to determine co-purification performance of each kit and subsequent calculations to determine the concentrations in each eluate: (A) MIRA and CCF, (B) MIR, (C) CAT, (D) MAX, and (E) MAP.

Additional file 7: Figure S4. Experimental overview of a combined cfDNA/cfRNA quantification and a parallel quantification of cfDNA and cfRNA.

In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy and disease esophageal tissue sample were included. In total, this comprehensive dataset consists of 102 sequenced libraries from 51 samples. Based on this data, 119 expression profiles are available for three biotypes, including miRNA (51), mRNA (51) and circRNA (17). This unique resource allows for discovery of novel biomarkers and disease mechanisms, comparison of tissue and liquid biopsy profiles, integration of coding and non-coding RNA patterns, and can serve as a validation dataset in other RNA landscaping studies. Moreover, structural RNA differences can be identified in this dataset, including protein coding mutations, fusion genes, and circular RNAs.

Aim In this study we will explore several RNA types in blood, including microRNA, messenger RNA, long non-coding RNA and circular RNA as a potential liquid biomarker to facilitate early diagnosis, prognosis and monitoring of esophageal adenocarcinoma Background & Methods In the past decades the incidence of esophageal adenocarcinoma (EAC) has increased dramatically in most Western populations. Due to the lack of symptoms EAC is often detected in a late stage, contributing to a poor 5-year survival rate. The potential of RNA (coding and miRNA) as circulating biomarker in blood has already been shown for many cancer entities but requires further investigation for EAC. Blood and tissue samples from patients with non-dysplastic Barrett’s esophagus (NDBE), high-grade dysplasia (HGD) and EAC have been collected. Currently, our biobank includes >5000 samples from 120 patients. A proof-of-concept study was conducted including 17 patients from three groups (EAC, HGD and NDBE). For each patient, biopsies from diseased tissue and healthy tissue as well as blood were collected and analyzed using small RNA and total RNA sequencing. Results Gene expression analysis was performed to identify differentially expressed genes across the three groups. The highest number of significantly differentially expressed m(i)RNAs were present in the tissues of EAC versus NDBE patients, while these differences were much lower or even absent in the plasma samples. Moreover, we have identified between 1500 and 7500 unique circular RNAs in individual EAC cancer patients’ plasma, indicating promising opportunities for a blood-based liquid biomarker for BE and EAC. Conclusion An exploration of several RNA types in blood and tissue biopsies has been done in patients with Barrett’s Esophagus and esophageal adenocarcinoma. Additional samples are needed to significantly increase the power of the differential expression study as well as to verify the results of our proof-of-concept study.

In the past decades the incidence of esophageal adenocarcinoma (EAC) has increased dramatically in most Western populations. Due to the lack of symptoms EAC is often detected in a late stage, contributing to a poor 5-year survival rate. The potential of RNA (coding and miRNA) as circulating biomarker in blood has already been shown for many cancer entities but requires further investigation for EAC. In this study we will explore several RNA types in blood, including microRNA, messenger RNA, long non-coding RNA and circular RNA as a potential liquid biomarker to facilitate early diagnosis, prognosis and monitoring of esophageal adenocarcinoma We have been collecting blood and tissue samples from patients with non-dysplastic Barrett’s esophagus (NDBE), high-grade dysplasia (HGD) and EAC. Currently, our biobank includes >5000 samples from 120 patients. A proof-of-concept study was conducted including 17 patients from three groups (EAC, HGD and NDBE). For each patient, biopsies from diseased tissue and healthy tissue as well as blood were collected and analyzed using small RNA and total RNA sequencing. Gene expression analysis was performed to identify differentially expressed genes across the three groups. The highest number of significantly differentially expressed m(i)RNAs were present in the tissues of EAC versus NDBE patients, while these differences were much lower or even absent in the plasma samples. Moreover, we have identified between 1500 and 7500 unique circular RNAs in individual EAC cancer patients’ plasma, indicating promising opportunities for a blood-based liquid biomarker for BE and EAC. Currently, we are collecting additional samples to significantly increase the power of the differential expression study as well as to verify the results of our proof-of-concept study.