crossing96/oncoscreening huggingface dataset:
Matched biopsy and resection specimens of gastric and gastroesophageal adenocarcinoma show high concordance in HER2 status.	In advanced gastric and gastroesophageal junction (GEJ) adenocarcinomas that overexpress human epidermal growth factor receptor 2 (HER2), treatment with trastuzumab confers a survival benefit. To select patients for treatment, HER2 status is evaluated by immunohistochemistry (IHC) and in situ hybridization. Gastric and GEJ adenocarcinomas demonstrate heterogeneity in HER2 expression. Nonetheless, testing is often performed on biopsies alone, which raises the issue of nonrepresentative sampling. We investigated the correlation of HER2 status between matched biopsy and resection specimens and the role of tumor heterogeneity in contributing to discrepancy. A total of 128 patients with gastric or GEJ adenocarcinoma had tissue available from a biopsy and subsequent resection. HER2 IHC was performed and evaluated by the criteria used in the Trastuzumab for Gastric Cancer clinical trial. In situ hybridization was performed if IHC was equivocal (2+) in either the biopsy or resection and in discrepant cases. Tumor heterogeneity was defined as 3+ or 2+ staining in 10% to 60% of tumor cells. Overall, HER2 was overexpressed in 18 tumors (14%), with a biopsy-resection concordance of 96.1%. Five cases were discrepant; 2 were positive on biopsy only, and 3 were positive on resection only. Tumor heterogeneity was seen in 80% of discrepant biopsies and resections, compared with 24% of concordant cases (P = .016). Our study demonstrates strong concordance between biopsy and resection specimens for HER2 overexpression in gastric cancer. Discordance was correlated with tumor heterogeneity. Overall, both biopsy and resection specimens are appropriate for HER2 testing, but generous sampling for biopsy specimens is necessary to ensure accurate assessment.	esophagus
Cyclooxygenase inhibitors use is associated with reduced risk of esophageal adenocarcinoma in patients with Barrett's esophagus: a meta-analysis.	BACKGROUND: Esophageal adenocarcinoma (EAC) has high mortality and is increasing in incidence. Barrett's esophagus (BE) increases the risk for EAC. Studies have reported inconsistent findings on the association between use of cyclooxygenase (COX) inhibitors and the risk of neoplastic progression in BE patients. Therefore, we performed a meta-analysis to investigate this association. METHODS: A meta-analysis was undertaken among a total of 9 observational studies using fixed- and random-effects models, comprising 5446 participants; 605 had EAC or high-grade dysplasia (HGD). RESULTS: Overall, COX inhibitors use was associated with a reduced risk of EAC/HGD among BE patients (relative risk (RR)=0.64, 95% confidence interval (CI)=0.53-0.77). Aspirin use also reduced the risk of EAC/HGD (RR=0.63, 95% CI=0.43-0.94), as well as non-aspirin COX inhibitors (RR=0.50, 95% CI=0.32-0.78). The chemopreventive effect seemed to be independent of duration response. CONCLUSIONS: Cyclooxygenase inhibitors use is associated with a reduced risk of developing EAC in patients with BE. Both low-dose aspirin and non-aspirin COX inhibitors are associated with a reduced risk of neoplasia. More well-designed randomised controlled trials are needed to increase our understanding of the chemopreventive effect of COX inhibitors.	esophagus
Annual computed tomography scans do not improve outcomes following esophagectomy for cancer: a 10-year UK experience.	Evidence for the best approach to follow-up patients after esophagectomy for cancer is scant and conflicting, and has led to a wide variety in practice. The aim of this study was to evaluate whether our annual routine computed tomography (aCT) scan program changes outcomes. A retrospective review of 169 patients who underwent esophagectomy for cancer in our unit between 2001 and 2010 was performed. aCT scan was part of follow-up in all patients to 5 years. Minimum follow-up was 37 months. The primary outcome measure was survival. Recurrence was detected in 61 cases (36%). aCT scan diagnosed recurrence in only a minority of cases (17 cases, 28%). In the majority of patients, clinical evidence prompted an unplanned CT scan (uCT; 44 cases, 72%). There was no difference in unadjusted survival between the two groups (hazard ratio = 0.61, 95% confidence interval 0.34-1.08, P = 0.090), nor was one more likely to receive secondary oncological treatment (aCT 41% vs. uCT 44%, P = 1.000). When we adjusted survival patterns for confounding covariates, the uCT cohort showed a protective effect (hazard ratio = 0.54, 95% confidence interval 0.28-0.98, P = 0.042). These data suggest that aCT scans do not influence management or survival after esophagectomy. A consensus follow-up protocol for patients treated for esophageal cancer remains to be established.	esophagus
Current role of cardiac and extra-cardiac pathologies in clinically indicated cardiac computed tomography with emphasis on status before pulmonary vein isolation.	"PURPOSE: The aim of this study was to assess the incidence of cardiac and significant extra-cardiac findings in clinical computed tomography of the heart in patients with atrial fibrillation before pulmonary vein isolation (PVI). MATERIALS AND METHODS: 224 patients (64 ± 10 years; male 63 %) with atrial fibrillation were examined by cardiac 64-slice multidetector CT before PVI. Extra-cardiac findings were classified as ""significant"" if they were recommended to additional diagnostics or therapy, and otherwise as ""non-significant"". Additionally, cardiac findings were documented in detail. RESULTS: A total of 724 cardiac findings were identified in 203 patients (91 % of patients). Additionally, a total of 619 extra-cardiac findings were identified in 179 patients (80 % of patients). Among these extra-cardiac findings 196 (32 %) were ""significant"", and 423 (68 %) were ""non-significant"". In 2 patients (1 %) a previously unknown malignancy was detected (esophageal cancer and lung cancer, local stage, no metastasis). 203 additional imaging diagnostics followed to clarify the ""significant"" findings (124 additional CT, costs 38 314.69 US dollars). Overall, there were 3.2 cardiac and 2.8 extra-cardiac findings per patient. Extra-cardiac findings appear significantly more frequently in patients over 60 years old, in smokers and in patients with a history of cardiac findings (p <0.05). CONCLUSION: Cardiac CT scans before PVI should be screened for extracardiac incidental findings that could have important clinical implications for each patient."	esophagus
iRHOM2-dependent regulation of ADAM17 in cutaneous disease and epidermal barrier function.	iRHOM2 is a highly conserved, catalytically inactive member of the Rhomboid family, which has recently been shown to regulate the maturation of the multi-substrate ectodomain sheddase enzyme ADAM17 (TACE) in macrophages. Dominant iRHOM2 mutations are the cause of the inherited cutaneous and oesophageal cancer-susceptibility syndrome tylosis with oesophageal cancer (TOC), suggesting a role for this protein in epithelial cells. Here, using tissues derived from TOC patients, we demonstrate that TOC-associated mutations in iRHOM2 cause an increase in the maturation and activity of ADAM17 in epidermal keratinocytes, resulting in significantly upregulated shedding of ADAM17 substrates, including EGF-family growth factors and pro-inflammatory cytokines. This activity is accompanied by increased EGFR activity, increased desmosome processing and the presence of immature epidermal desmosomes, upregulated epidermal transglutaminase activity and heightened resistance to Staphylococcal infection in TOC keratinocytes. Many of these features are consistent with the presence of a constitutive wound-healing-like phenotype in TOC epidermis, which may shed light on a novel pathway in skin repair, regeneration and inflammation.	esophagus
Preoperative platelet lymphocyte ratio (PLR) is superior to neutrophil lymphocyte ratio (NLR) as a predictive factor in patients with esophageal squamous cell carcinoma.	BACKGROUND: Recent studies have shown that the presence of systemic inflammation correlates with poor survival in various cancers. The aim of this study was to determinate the prognostic value of the neutrophil lymphocyte ratio (NLR) and the platelet lymphocyte ratio (PLR) in patients with esophageal squamous cell carcinoma (ESCC). METHODS: Preoperative NLR and PLR were evaluated in 483 patients undergoing esophagectomy for ESCC from January 2005 to December 2008. The prognostic significance of both markers was then determined by both uni- and multivariate analytical methods. Receiver operating characteristic (ROC) curves were also plotted to verify the accuracy of NLR and PLR for survival prediction. RESULTS: High preoperative NLR (≥3.5 versus < 3.5, P = 0.039) and PLR (≥150 versus < 150, P < 0.001) were significantly associated with poor overall survival in multivariate analysis. However, our study demonstrated a better discrimination for the PLR in terms of hazard ratio(HR) than the NLR (HR = 1.840 versus HR = 1.339). Patients with NLR ≥3.5 had significantly poorer overall survival compared to NLR <3.5 (35.4% versus 57.7%, P < 0.001). Patients with PLR ≥150 also had significantly poorer overall survival compared to patients with PLR <150 (32.7% versus 63.5%, P < 0.001). The area under the curve (AUC) was 0.658 (95% confidence interval (CI): 0.610 to 0.706, P < 0.001) for NLR and 0.708 (95% CI: 0.662 to 0.754, P < 0.001) for PLR, indicating that PLR was superior to NLR as a predictive factor in ESCC. CONCLUSIONS: Preoperative NLR and PLR were significant predictors of overall survival in patients with ESCC. However, PLR is superior to NLR as a predictive factor in patients with ESCC.	esophagus
Endoscopic submucosal dissection versus endoscopic mucosal resection for the treatment of early esophageal carcinoma: a meta-analysis.	Endoscopic submucosal dissection (ESD) was originally developed for en bloc resection of large, flat gastrointestinal lesions. Compared with endoscopic mucosal resection (EMR), ESD is considered to be more time consuming and have more complications for treatment of early esophageal carcinoma, such as bleeding, stenosis and perforation. The objective of this study was to compare the efficacy and safety of ESD and EMR for such lesions. We searched databases, such as PubMed, EMBASE, Cochrane Library and Science Citation Index updated to 2013 for related trials. In the meta-analysis, the main outcome measurements were the en bloc resection rate, the histologically resection rate and the local recurrence rate. We also compared the operation time and the incidences of procedure-related complications. Five trials were identified, and a total of 710 patients and 795 lesions were included. The en bloc and histologically complete resection rates were higher in the ESD group compared with the EMR group (odds ratio (OR) 27.3; 95% CI, 11.5-64.8; OR 18.4; 95% CI, 8.82-38.59). The local recurrence rate was lower in the ESD group (OR 0.13, 95 % CI 0.04-0.43). The meta-analysis also showed ESD was more time consuming, but did not increase the complication rate (P=0.76). The results implied that compared with EMR, ESD showed better en bloc and histologically resection rates, and lower local recurrence, without increasing the incidence of procedure-related complications in the treatment of early esophageal carcinoma.	esophagus
Association of single nucleotide polymorphisms in the prostaglandin-endoperoxide synthase 2 (PTGS2) and phospholipase A₂ group IIA (PLA2G2A) genes with susceptibility to esophageal squamous cell carcinoma.	BACKGROUND: The prostaglandin-endoperoxide synthase 2 (PTGS2) and phospholipase A2 group IIA (PLA2G2A) genes encode enzymes that are involved in arachidonic acid and prostaglandin biosynthesis. Dysregulation of both genes is associated with inflammation and carcinogenesis, including esophageal squamous cell carcinoma (ESCC). We therefore hypothesized that there is an association between single nucleotide polymorphisms (SNPs) in these genes and susceptibility to ESCC. METHODS: We performed a gene-wide tag SNP-based association study to examine the association of SNPs in PTGS2 and PLA2G2A with ESCC in 269 patients and 269 healthy controls from Taihangshan Mountain, Henan and Hebei Provinces, the rural area of China which has the highest incidence of esophageal cancer in the world. Thirteen tag SNPs in PLA2G2A and 4 functional SNPs in PTGS2 were selected and genotyped using a high-throughput Mass Array genotyping platform. RESULTS: We found a modest increased risk of ESCC in subjects with the PTGS2 rs12042763 AA genotype (OR=1.23; 95% CI, 1.00- 3.04) compared with genotype GG. For PLA2G2A, a decreased risk of ESCC was observed in subjects with the rs11677 CT (OR=0.51, 95%CI, 0.29-0.85) or TT genotype (OR=0.51, 95%CI, 0.17-0.96) or the T carriers (CT+TT) (OR=0.52, 95%CI, 0.31-0.85) when compared with the CC genotype. Also for PLA2G2A, rs2236771 C allele carriers were more frequent in the control group (P=0.02). Subjects with the GC (OR=0.55, 95%CI, 0.33-0.93) or CC genotype (OR=0.38, 95% CI, 0.16-0.94) or the C carriers (GC+CC) (OR=0.52, 95%CI, 0.32- 0.85) showed a negative association with ESCC susceptibility. CONCLUSIONS: Our results suggest that PTGS2 and PLA2G2A gene polymorphisms may modify the risk of ESCC development.	esophagus
Adjuvant or neoadjuvant therapy for operable esophagogastric cancer?	Esophagogastric cancer encompasses proximal squamous cell carcinoma of the esophagus, distal esophageal/junctional adenocarcinoma of the esophagus and gastric adenocarcinoma. These diseases have different etiologies, geographic incidences and biologies. This review mainly focuses on the treatment of operable esophagogastric adenocarcinoma. In Asia, adjuvant chemotherapy is commonly used for patients with gastric cancer following the landmark ACTS-GC trial. In contrast, perioperative chemotherapy is a standard of care in many Western countries based on the results of the MAGIC trial. Neoadjuvant chemotherapy is better tolerated than adjuvant therapy, and therefore dose intensity is likely to be maintained in a greater proportion of patients. In addition, neoadjuvant treatment can lead to tumor downstaging, increasing the likelihood of achieving a complete surgical resection. This may be particularly important in Western populations, as these patients often present with more advanced tumors than Asian patients. Adjuvant chemoradiotherapy is a standard treatment option in the USA for adenocarcinoma of the stomach or gastroesophageal junction as a result of the INT-0116 trial, but the benefit of this approach after a D2 resection has not been confirmed. Neoadjuvant chemoradiotherapy may reduce the risk of local recurrence and may be particularly beneficial for patients with squamous cell carcinoma as these tumors are more radiosensitive. However, patients with esophagogastric adenocarcinoma are more likely to relapse with distant disease, and therefore a systemic disease approach with chemotherapy is likely to be more beneficial than a purely localized treatment strategy for these patients.	esophagus
A systematic review of the predictive value of (18)FDG-PET in esophageal and esophagogastric junction cancer after neoadjuvant chemoradiation on the survival outcome stratification.	PURPOSE: We studied the predictive value of [(18) F]fluorodeoxyglucose-positron emission tomography ((18)FDG-PET) for assessing disease-free (DFS) and overall survival (OS) in esophageal and esophagogastric junction cancer. MATERIALS AND METHODS: A literature search (PUBMED/MEDLINE, EMBASE, Cochrane) was performed to identify full papers with (18)FDG-PET and survival data, using indexing terms and free text words. Studies with >10 patients with locally advanced esophageal cancer, presenting sequential or at least one post-adjuvant treatment (18)FDG-PET data and Kaplan-Meier survival curves with >6 months median follow-up period were included. We performed a meta-analysis for DFS and OS using the hazard ratio (HRs) as outcome measure. Sources of heterogeneity study were also explored. RESULTS: We identified 26 eligible studies including a total of 1,544 patients (average age 62 years, 82% males). The TNM distribution was as follows: stage I 7%, II 24%, III 53% and IV 15%. The pooled HRs for complete metabolic response versus no response were 0.51 for OS (95% CI, 0.4-0.64; P < 0.00001) and 0.47 for DFS (95% CI, 0.38-0.57; P < 0.00001), respectively. No statistical heterogeneity was present. To explore sources of clinical heterogeneity, we also realised subgroup and regression analyses. Taken into account the moderate correlation between OS and DFS (ρ = 0.54), we used joint bivariate random regression model. These analyses did not show a statistically significant impact of study characteristics and PET modalities on the pooled outcome estimates. CONCLUSION: Despite methodological and clinical heterogeneity, metabolic response on (18)FDG-PET is a significant predictor of long-term survival data.	esophagus
Comparative outcomes for three-dimensional conformal versus intensity-modulated radiation therapy for esophageal cancer.	Emerging data suggests a benefit for using intensity modulated radiation therapy (IMRT) for the management of esophageal cancer. We retrospectively reviewed patients treated at our institution who received definitive or preoperative chemoradiation with either IMRT or 3D conformal radiation therapy (3DCRT) between October 2000 and January 2012. Kaplan Meier analysis and the Cox proportional hazard model were used to evaluate survival outcomes. We evaluated a total of 232 patients (138 IMRT, 94 3DCRT) who received a median dose of 50.4 Gy (range, 44-64.8) to gross disease. Median follow up for all patients, IMRT patients alone, and 3DCRT patients alone was 18.5 (range, 2.5-124.2), 16.5 (range, 3-59), and 25.9 months (range, 2.5-124.2), respectively. We observed no significant difference based on radiation technique (3DCRT vs. IMRT) with respect to median overall survival (OS) (median 29 vs. 32 months; P = 0.74) or median relapse free survival (median 20 vs. 25 months; P = 0.66). On multivariable analysis (MVA), surgical resection resulted in improved OS (HR 0.444; P < 0.0001). Superior OS was also associated on MVA with stage I/II disease (HR 0.523; P = 0.010) and tumor length ≤5 cm (HR 0.567; P = 0.006). IMRT was also associated on univariate analysis with a significant decrease in acute weight loss (mean 6% + 4.3% vs 9% + 7.4%, P = 0.012) and on MVA with a decrease in objective grade ≥3 toxicity, defined as any hospitalization, feeding tube, or >20% weight loss (OR 0.51; P = 0.050). Our data suggest that while IMRT-based chemoradiation for esophageal cancer does not impact survival there was significantly less toxicity. In the IMRT group there was significant decrease in weight loss and grade ≥3 toxicity compared to 3DCRT.	esophagus
Association of Helicobacter pylori infection with esophageal adenocarcinoma and squamous cell carcinoma: a meta-analysis.	To evaluate the relationship of Helicobacter pylori and cytotoxin-associated gene A (CagA) positive strains with esophageal neoplasm, including esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), the authors conducted a meta-analysis using a predefined protocol. PubMed, Web of Science, China biology medical literature database, Wanfang, and China National Knowledge Infrastructure were searched for relevant articles from the first available year to April 8, 2013. The fixed or random effect pooled measure was selected based on heterogeneity among studies, which was evaluated using Q test and the I(2) of Higgins and Thompson. Metaregression was used to explore the sources of between-study heterogeneity. Publication bias was analyzed by Begg's funnel plot and Egger's regression test. The association was assessed by odds ratio (OR) with 95% confidence interval (CI). A total of 28 eligible studies were included in the meta-analysis. There was a significant inverse association between H. pylori infection (pooled OR, 0.57; 95% CI, 0.44-0.73) and EAC; CagA-positive H. pylori strains were less likely to be associated with EAC compared with CagA-negative strains (pooled OR, 0.64; 95% CI, 0.52-0.79). However, there was no statistically significant association between H. pylori/CagA-positive H. pylori strains infection and ESCC, and the pooled ORs were 1.16 (95% CI, 0.83-1.60) and 0.97 (95% CI, 0.79-1.19). But significant associations between CagA-positive H. pylori strains infection and ESCC risk were found in the stratified analysis of the study location (Asian and non-Asian), and the summary ORs were 0.74 (95% CI, 0.57-0.97) and 1.41 (95% CI, 1.02-1.94). H. pylori infection and CagA-positive strains are associated with decreased risk of EAC in the overall population. No significant association was found between H. pylori infection/CagA-positive strains and ESCC. But CagA-positive strains might have a positive association with ESCC in non-Asian population and an inverse association in Asian population.	esophagus
Clinical stage T1-T2N0M0 oesophageal cancer: accuracy of clinical staging and predictive factors for lymph node metastasis.	OBJECTIVES: The aim of this study was to evaluate the accuracy of clinical staging in patients with clinical stage T1-2N0M0 (cT1-T2N0M0) oesophageal cancer and to assess predictive factors associated with lymph node (LN) metastases in those patients. METHODS: From 2005 through 2010, 240 patients were identified with cT1-T2N0M0 oesophageal cancer followed by oesophageal resection without induction therapy. Clinical staging was performed by both endoscopic ultrasound (EUS) and positron-emission tomography (PET) scans. RESULTS: The study included 174 patients with cT1N0M0 and 66 patients with cT2N0M0 stage oesophageal cancer. Clinical T stage correlated with pathological T stage in 182 of 240 (76%) patients: 167 of 174 patients (96%) for cT1N0 and 15 of 66 patients (23%) for cT2N0. Nodal metastases occurred in 53 patients (22%) and the prevalence of nodal disease was 16% in cT1N0 patients and 39% in cT2N0 patients. Clinical tumour, nodal, metastasis (TNM) staging accurately predicted pathological TNM staging in 62% of patients (148 of 240), with an accuracy of 79% for cT1N0 and 15% for cT2N0. Among the 62 clinically understaged patients, 53 were pathologically upstaged because of nodal metastases. Significant factors associated with LN metastases on multivariate logistic regression were cT2 stage (odd ratios (ORs): 2.87, 95% confidence intervals (CIs): 1.44-5.69, P = 0.003), poor differentiation (well/unknown vs poor, OR: 5.51, CI: 1.38-22.00, P = 0.01) and maximum standardized uptake value (SUVmax) >3.15 (OR: 1.99, 95% CI: 1.01-3.96, P = 0.047). CONCLUSIONS: Clinical staging using both EUS and PET demonstrated high accuracy for predicting cT1N0M0 oesophageal cancer pathological staging, but was inadequate for predicting staging for cT2N0M0 cancer. Clinical factors such as SUVmax and tumour differentiation could help select patients with cT1-T2N0M0 tumours that might be upstaged because of unexpected LN metastases.	esophagus