The Nationwide Cancer Genome Screening Projects for Gastrointestinal Cancer in Japan, Efficient Identification of Actionable Cancer Genome Alterations in Advanced Non-Colorectal Gastrointestinal Cancer (SCRUM-Japan GI Screen 2015-01-Non-CRC)
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ABSTRACT:
DISEASE(S): Gastrointestinal Cancer
PROVIDER: 2631666 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
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Project description:The treatment strategies and prognoses of patients with metastatic colorectal cancer (CRC) differ according to the sidedness of the primary tumor. TP53 gain-of-function (GOF) and non-GOF variants have been reported to be differentially associated with prognosis by sidedness. We aimed to evaluate the sidedness-dependent prognostic impact of gene alterations in metastatic CRC. Patients enrolled between April 2017 and March 2019 were included in this study. Those excluded were individuals whose tumor tissues were obtained after chemotherapy and those who were enrolled in the study more than six months after starting first-line chemotherapy. Finally, we assessed 531 patients who underwent complete gene sequencing. The study revealed a significant difference in overall survival between individuals with left-sided CRC (n = 355) and right-sided colon cancer (CC) (n = 176) when considering the TP53 non-GOF variant, KRAS wild-type, NOTCH1 wild-type, NOTCH1 covariant, NOTCH3 sole variant, and MYC amplification. Multivariate analysis on each side revealed that the TP53 GOF and KRAS variants were independent poor prognostic factors for left-sided CRC (p = 0.03 and p < 0.01, respectively), and the TP53 non-GOF variant, BRAF V600E, and MYC amplification for right-sided CC (p < 0.05, p < 0.01, and p = 0.02, respectively). The NOTCH3 sole variant was an independent and favorable prognostic factor for left-sided CRC (p < 0.01). The prognostic significance of gene alterations differed between left-sided CRC and right-sided CC.
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Project description:BackgroundEmergency gastrointestinal surgery, although rare, is known for its high mortality and morbidity. However, the risks of emergency surgery for gastrointestinal cancer have not been investigated in depth. This study aimed to investigate the impact of emergency surgery on mortality and morbidity in patients with gastrointestinal cancers and to identify associated risk factors.MethodsWe extracted data from the National Clinical Database, a nationwide surgery registration system in Japan, for patients with gastrointestinal cancer who underwent esophageal resection, total gastrectomy, distal gastrectomy, right hemicolectomy, or low anterior resection between 2012 and 2017. The impacts of emergency surgery on 30-day mortality and incidence of overall postoperative complications were compared with those of non-emergency surgery. Risk factors for mortality and overall postoperative complications were then sought in patients who underwent emergency surgery.ResultsThirty-day mortality and incidence of overall postoperative complications were significantly higher in emergency surgeries for gastric, colon, and rectal cancers than in non-emergency surgeries (odds ratios 4.86-6.98 and 1.68-2.18, respectively; all P < .001). Various risk factors were identified in the group that underwent emergency surgery, including preoperative sepsis and lower body mass index. Some of the risk factors were common to all types of surgery and others were specific to a certain type of surgery.ConclusionThe actual risk of emergency surgery and the risk factors for overall postoperative complications in emergency cases are shown to serve as a reference for postoperative management. Emergency surgery had an additional burden on patients depending on the type of surgery.
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Project description:We report here the complete genome sequence of Lactobacillus johnsonii strain Byun-jo-01, which was isolated from the murine gastrointestinal tract. The genome was determined using both PacBio and Illumina sequencing. L. johnsonii strain Byun-jo-01 contains a single circular chromosome of 1,959,519 bp, and its GC content is 34.7%.
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Project description:In the nationwide cancer genome screening project SCRUM-Japan GI-SCREEN, 2590 archival formalin-fixed paraffin-embedded (FFPE) tumor tissues from 19 institutions were analyzed with two tissue-based next-generation sequencing (NGS) panels at the Clinical Laboratory Improvement Amendments (CLIA)-certified College of American Pathologists (CAP)-accredited central laboratory. The Oncomine Cancer Research Panel (OCP; 143 genes) succeeded in producing validated results for only 68.3% of the samples (%OCP-success). CE-IVD (25 genes) succeeded in 45.9% of the OCP-failed samples, leading to an overall NGS success (%combined-success) rate as high as 82.9%. Among 2573 samples, the DNA-integrity (ΔCt )-high (ΔCt < 4.4, n = 1253) samples showed significantly higher %OCP- and %combined-success rates (90.2% and 97.4%, respectively) than the DNA-integrity-intermediate (4.4 < ΔCt < 6.3, n = 911; 68.9% and 88.7%) and DNA-integrity-low ones (ΔCt > 6.3 or polymerase chain reaction-failed, n = 409; 5.6% and 24.7%). Other factors associated with NGS success included the FFPE-sample storage period (<4 years), the specimen type (surgical) and the primary tumor site (colorectal). Multivariable analysis revealed DNA integrity as the factor with the strongest independent association with NGS success, although it was suggested that other institution-specific factors contribute to the discordance of inter-institutional NGS success rates. Our results emphasize the importance of DNA quality in FFPE samples for NGS tests and the impact of DNA integrity on quality monitoring of pathology specimens for achieving successful NGS.
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Project description:BackgroundWe previously reported that the incidence of hepatocellular carcinoma (HCC) with non-viral etiologies increased rapidly between 1991 and 2010 in Japan.MethodsTo update this investigation, we enrolled patients who were initially diagnosed as having non-B, non-C HCC at participating hospitals between 2011 and 2015. In addition to the patient characteristics investigated in the previous report, we also investigated the duration of alcohol consumption. The overall survival rate was analyzed using the Kaplan-Meier method, and the hazard function against the body mass index (BMI) was plotted using cubic splines.ResultsA total of 2087 patients were enrolled. The proportion of patients with non-viral etiologies has continued to increase from 10.0% in 1991 to 32.5% in 2015. Patients were also older (median ages, 70-73 years) and more obese (median BMIs, 23.9-24.2 kg/m2), and the proportions of patients with diabetes mellitus (46.1% to 51.6%), hypertension (42.7% to 58.6%), dyslipidemia (14.6% to 22.9%), and fatty liver (24.0% to 28.8%) had all increased significantly. There was a significant inverse relationship between the duration and the amount of daily alcohol consumption. The improvement in the overall survival was relatively small, with a decreased proportion of patients under surveillance (41.3% to 31.6%). A hazard function plot showed a curve similar to that in our previous report, with a lowest hazard of ~ 26 kg/m2.ConclusionsThe proportion of HCC patients with non-viral etiologies continues to increase in Japan. Lifetime total amount of alcohol consumption may be a risk factor.
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Project description:BackgroundNon-alcoholic fatty liver disease (NAFLD) is the leading cause of liver disease globally with an estimated prevalence of 25%, with the clinical and economic burden expected to continue to increase. In the United States, non-variceal upper gastrointestinal bleeding (NVUGIB) has an estimated incidence of 61-78 cases per 100000 people with a mortality rate of 2%-15% based on co-morbidity burden.AimTo identify the outcomes of NVUGIB in NAFLD hospitalizations in the United States.MethodsWe utilized the National Inpatient Sample from 2016-2019 to identify all NVUGIB hospitalizations in the United States. This population was divided based on the presence and absence of NAFLD. Hospitalization characteristics, outcomes and complications were compared.ResultsThe total number of hospitalizations for NVUGIB was 799785, of which 6% were found to have NAFLD. NAFLD and GIB was, on average, more common in younger patients, females, and Hispanics than GIB without NAFLD. Interestingly, GIB was less common amongst blacks with NAFLD. Multivariate logistic regression analysis was conducted, controlling for the multiple covariates. The primary outcome of interest, mortality, was found to be significantly higher in patients with NAFLD and GIB [adjusted odds ratio (aOR) = 1.018 (1.013-1.022)]. Secondary outcomes of interest, shock [aOR = 1.015 (1.008-1.022)], acute respiratory failure [aOR = 1.01 (1.005-1.015)] and acute liver failure [aOR = 1.016 (1.013-1.019)] were all more likely to occur in this cohort. Patients with NAFLD were also more likely to incur higher total hospital charges (THC) [$2148 ($1677-$2618)]; however, were less likely to have a longer length of stay [0.27 d (0.17-0.38)]. Interestingly, in our study, the patients with NAFLD were less likely to suffer from acute myocardial infarction [aOR = 0.992 (0.989-0.995)]. Patients with NAFLD were not more likely to suffer acute kidney injury, sepsis, blood transfusion, intubation, or dialysis.ConclusionNVUGIB in NAFLD hospitalizations had higher inpatient mortality, THC, and complications such as shock, acute respiratory failure, and acute liver failure compared to those without NAFLD.
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Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
| 2643590 | ecrin-mdr-crc