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The incidence of esophageal adenocarcinoma (EAC) is rapidly rising and has a 5-year survival rate of20%. Beyond TNM (tumor-node-metastasis) staging, no reliable risk stratification tools exist and no large-scale studies have profiled circulating tumor DNA (ctDNA) at relapse in EAC. Here we analyze the prognostic potential of ctDNA dynamics in EAC, taking into account clonal hematopoiesis with indeterminate potential (CHIP).A total of 245 samples from 97 patients treated with neoadjuvant chemotherapy and surgery were identified from the prospective national UK Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium data set. A pan-cancer ctDNA panel comprising 77 genes was used. Plasma and peripheral blood cell samples were sequenced to a mean depth of 7082× (range 2196-28 524) and ctDNA results correlated with survival.Characteristics of the 97 patients identified were as follows: 83/97 (86%) male, median age 68 years (SD 9.5 years), 100% cT3/T4, 75% cN+. EAC-specific drivers had higher variant allele fractions than passenger mutations. Using stringent quality criteria 16/79 (20%) were ctDNA positive following resection; recurrence was observed in 12/16 (75%) of these. As much as 78/97 (80%) had CHIP analyses that enabled filtering for CHIP variants, which were found in 18/78 (23%) of cases. When CHIP was excluded, 10/63 (16%) patients were ctDNA positive and 9/10 of these (90%) recurred. With correction for CHIP, median cancer-specific survival for ctDNA-positive patients was 10.0 months versus 29.9 months for ctDNA-negative patients (hazard ratio 5.55, 95% confidence interval 2.42-12.71; P = 0.0003). Similar outcomes were observed for disease-free survival.We demonstrate in a large, national, prospectively collected data set that ctDNA in plasma following surgery for EAC is prognostic for relapse. Inclusion of peripheral blood cell samples can reduce or eliminate false positives from CHIP. In future, post-operative ctDNA could be used to risk stratify patients into high- and low-risk groups for intensification or de-escalation of adjuvant chemotherapy.

Funder: Biomedical Research Centre; Id: http://dx.doi.org/10.13039/100014461, AIMS: Barrett's oesophagus with indefinite for dysplasia (BE-IND) is a subjective diagnosis with a low interobserver agreement (IOA) among pathologists and uncertain clinical implications. This study aimed to assess the utility of p53 immunohistochemistry (p53-IHC) in assessing BE-IND specimens. METHODS AND RESULTS: Archive endoscopic biopsies with a BE-IND diagnosis from two academic centres were analysed. First, haematoxylin and eosin-stained slides (H&E) were reviewed by four expert gastrointestinal (GI) pathologists allocated into two groups (A and B). After a washout period of at least 8 weeks, H&E slides were reassessed side-to-side with p53-IHC available. We compared the rate of changed diagnosis and the IOA for all BE grades before and after p53-IHC. We included 216 BE-IND specimens from 185 patients, 44.0 and 32.9% of which were confirmed after H&E slide revision by groups A and B, respectively. More than half the cases were reclassified to a non-dysplastic BE (NDBE), while 5.6% of cases in group A and 7.4% in group B were reclassified to definite dysplasia. The IOA for NDBE, BE-IND, low-grade dysplasia (LGD) and high-grade dysplasia (HGD)/intramucosal cancer (IMC) was 0.31, 0.21, -0.03 and -0.02, respectively. Use of p53-IHC led to a >40% reduction in BE-IND diagnoses (P < 0.001) and increased IOA for all BE grades [κ = 0.46 (NDBE), 0.26 (BE-IND), 0.49 (LGD), 0.35 (HGD/IMC)]. An aberrant p53-IHC pattern significantly increased the likelihood of reclassifying BE-IND to definite dysplasia (odds ratio = 44.3, 95% confidence interval = 18.8-113.0). CONCLUSION: P53-IHC reduces the rate of BE-IND diagnoses and improves the IOA among pathologists when reporting BE with equivocal epithelial changes.

Recent studies show that aneuploidy and driver gene mutations precede cancer diagnosis by many years1–4. We assess whether these genomic signals can be used for early detection and pre-emptive cancer treatment using the neoplastic precursor lesion Barrett’s esophagus as an exemplar5. Shallow whole-genome sequencing of 777 biopsies, sampled from 88 patients in Barrett’s esophagus surveillance over a period of up to 15 years, shows that genomic signals can distinguish progressive from stable disease even 10 years before histopathological transformation. These findings are validated on two independent cohorts of 76 and 248 patients. These methods are low-cost and applicable to standard clinical biopsy samples. Compared with current management guidelines based on histopathology and clinical presentation, genomic classification enables earlier treatment for high-risk patients as well as reduction of unnecessary treatment and monitoring for patients who are unlikely to develop cancer. Longitudinal molecular profiling of copy number alterations in patients with Barrett’s esophagus can identify patients at higher risk of developing esophageal cancer.

SummaryCancer arises through a process of somatic evolution and recent studies have shown that aneuploidies and driver gene mutations precede cancer diagnosis by several years to decades1–4 Here, we address the question whether such genomic signals can be used for early detection and pre-emptive cancer treatment. To this end we study Barrett’s oesophagus, a genomic copy number driven neoplastic precursor lesion to oesophageal adenocarcinoma5. We use shallow whole genome sequencing of 777 biopsies sampled from 88 patients in surveillance for Barrett’s oesophagus over a period of up to 15 years. These data show that genomic signals exist that distinguish progressive from stable disease with an AUC of 0.87 and a sensitivity of 50% even ten years prior to histopathological disease transformation. These finding are validated on two independent cohorts of 75 and 248 patients. Compared against current patient management guidelines genomic risk classification enables earlier treatment for high risk patients as well as reduction of unnecessary treatment and monitoring for patients who are unlikely to develop cancer.

Background Oesophageal cancer is the eighth most frequently diagnosed form of cancer and has a dismal 5-year survival rate of 12%, with Oesophageal adenocarcinoma (OAC) being the most common sub-type in western countries (Ferlay et al., 2012). Previous studies in many cancer types have demonstrated potential clinical utility of circulating tumour DNA (ctDNA) for detecting minimal residual disease and tumour evolution through therapy, but there has been little investigation of this technology in large cohorts of OAC patients. Consequently, the aim of this study is to evaluate the clinical potential of longitudinal liquid biopsy sampling using 100 OAC cases. Methods Our approach uses the Roche-Avenio expanded panel and ultra-deep sequencing to detect genomic aberrations across 77 cancer genes in the ctDNA of OAC cases. All cases are late disease stage (T3 /T4) and have at least one plasma sample taken before surgery and on average two other samples taken at time points of clinical interest. One third of cases have associated whole genome sequencing of the primary tumour. Results Our results demonstrate that in spite of OAC being a low ctDNA shedding cancer type, ctDNA can be consistently detected in late disease cases. At least one mutation in OAC driver genes was identified in 69% of cases, some of which include TP53, SMAD4, and CDKN2A (Frankell et al., 2019). TP53 was the most frequently mutated gene, which is also observed in whole-genome sequencing (WGS) data. In addition, other OAC driver genes were mutated to a similar extent to the WGS data. Clinically relevant variants were identified in the plasma samples, such as SMAD4 which has been shown to be a prognostic biomarker in OAC. Therapeutically actionable targets not detected in the primary tumour were also captured, including ALK and PIK3CA. Moreover, minimal residual disease was detected after surgery in the majority of patients that went on to relapse. Conclusions These data suggest that ctDNA can be routinely detected in OAC and that clinically relevant alterations can also be identified at late stage of disease, which is when the majority of patients present. Overall our results indicate that there is potential for using targeted sequencing of ctDNA in the clinic. Legal entity responsible for the study The authors. Funding Educational grant from Roche for the library prep kits. Disclosure All authors have declared no conflicts of interest.