Chilean Gastric Cancer Task Force (FORCE 1)
Chilean Gastric Cancer Task Force (FORCE 1)
Background. Gastric cancer (GC) is the world's second leading cause of neoplastic mortality.
 Genetic alterations, response to treatments and mortality rates are highly heterogeneous
 across different regions. In Chile, GC is the leading cause of cancer death, affecting 20 per
 100,000 people and >3,000 deaths/year. Clinical outcomes and response to "one size fits all"
 therapies are highly heterogeneous and thus a better stratification of patients may aid
 cancer treatment and response.

 Study design/methods. The Gastric Cancer Task Force (GCTF) is a Chilean collaborative,
 non-interventional retrospective study that seeks to stratify gastric adenocarcinomas (GACs)
 using retrospect clinical outcomes and genomic, epigenomic and protein alterations in a
 cohort of 200 patients. Tumor samples from the pathology department and the Cancer Center at
 UC Christus healthcare network at Pontificia Universidad Católica de Chile will be analyzed
 using a panel of 143 known cancer genes (Oncomine Comprehensive Assay) at the Center of
 Excellence of Precision Medicine (CEMP) in Santiago, Chile. Additionally, gene promoter
 methylation will be performed and selected clinically relevant proteins (e.g. PD-L1, Erb-2,
 VEGFR2 among others) will be assessed by Tissue Microarray, Epstein-Barr virus (EBV) status
 will also be assessed. Observations will be correlated to 120 clinical parameters, including
 general patient information, cancer history, laboratory studies, comorbidity index,
 chemotherapy, targeted therapies, efficacy and follow-up.

 Discussion. The development of a clinically meaningful classification that encompasses
 comprehensive clinical and molecular parameters may improve patient treatment, predict
 clinical outcomes, aid patient selection for clinical trials and offer insights into future
 preventive and/or therapeutic strategies.
Participating entities: The Chilean Gastric Cancer Task Force (GCTF) is a collective effort
 between two principal identities: 1- The Center of Excellence of Precision Medicine (CEMP),
 which was established through a joint funding by the government agency for economic
 development (Corporacion de Fomento de la Produccion, CORFO) and Pfizer Chile and 2- The
 Center UC for Investigation in Oncology (CITO) based at the Pontificia Universidad Católica
 de Chile. Both entities are non-profit research organizations aimed at enhancing public
 education and implementing strategies to improve clinical outcomes in oncology treatment and
 cancer prevention.

 Primary objective: To stratify Chilean GC patients into prognostic subgroups, and to
 correlate therapy response according to clinical, protein, epigenetic and genetic alterations
 in a cohort of 200 GAC patients.

 Secondary objectives

 -  To determine the mutation profile in Chilean GC patients.

 -  To assess the percentage of Chilean GC patients that could benefit from currently
 available druggable targets (actionable genes).

 -  To correlate EBV presence to clinical parameters.

 -  To assess the expression levels of proteins associated with molecular stratifications
 and currently targeted therapies (eg. PD-L1 and antiangiogenics)

 -  To determine the profile of SNPs in the DPYD and TYMS genes in Chilean GC patients and
 their correlation with adverse events.

 Study design

 Ethics approval The GCTF is a non-interventional, collaborative, prospective non-concurrent
 study that seeks to stratify GAC patients based on their prognosis and therapy response. The
 study will strictly adhere to all legal requirements, regulations and general principles
 established by international agencies governing the ethical conduct in biomedical research on
 human subjects, following the good clinical practices and the declaration of Helsinki. The
 GCTF study protocol has been approved by the Ethics Committee of the University hospital
 (Pontificia Universidad Catolica de Chile , CEC MED UC approval number 16-046, resolution
 dated April 21st, 2016).

 Patient recruitment & characteristics Diagnosed GC patients will be recruited from the Red UC
 Christus network in Santiago, Chile. Patient recruitment and signing of informed consent
 forms, maintenance and monitoring of patient medical records, biological material and sample
 extractions will be managed by CITO.

 Patient and treatment history reveals that besides surgery and chemotherapy, approximately
 10% of patients received Trastuzumab (ERBB2 targeted therapy, also called Herceptin), another
 10% received immunotherapy including pembrolizumab and Ipilimumab (checkpoint inhibitors).
 Finally approximately 5% of patients received antiangiogenic therapy (consisting of VEGFR2
 targeted therapy with Ramucirumab). Additionally, histological analysis showed that
 approximately 50% of patients were classified as intestinal type, 30% as diffuse, and 20%
 were either mixed or undetermined.

 Inclusion criteria

 -  Adult male or female, aged >18 years

 -  Diagnosed with gastric cancer (histological or cytological)

 -  Attending health centers of the Red UC Christus network for at least 3 months with
 clinical follow-up

 -  Capable to read and speak Spanish

 -  Willing and able to provide written informed consent to the study that should be dated
 and signed at the time of enrollment.

 Exclusion criteria

 Patients:

 -  With small biopsy samples insufficient for analysis.

 -  Whose medical records cannot be collected or are unavailable.

 -  Without signed informed consent.

 Clinical data Clinical data from patients will be obtained by healthcare providers and
 entered into an online electronic platform. Samples will be coded and patient identity known
 only to the attending physician. Clinical variables are divided into sections: General
 Patient Information, Cancer History, Laboratory Studies, Comorbidity (Charlson) Index,
 Chemotherapy, Efficacy & Follow Up and Toxicity. Patient chemotherapy will be classified by:
 regime, number of cycles & time of treatment and chemotherapy dose-intensity during the first
 6 months. Chemotherapy regimens representing the first line chemotherapy prescribed to the
 patients. Full chemotherapy dose intensity during the first 6 months will be obtained through
 patient interviews and entered directly into the online platform. Finally, efficacy &
 follow-up and toxicity data obtained from patients.

 Main clinical outcomes Main outcomes will be inferred from obtained clinical data, these
 include overall survival, progression-free, and recurrence-free survival rates.

 Biological samples & Oncomine Comprehensive Assay Biological materials obtained at the Red UC
 Christus will be transported to CEMP in Santiago de Chile under standardized protocols. A
 total of 200 patient tumor samples will be obtained from archived Formalin Fixed Paraffin
 Embedded (FFPE) samples. Nucleic acids will be extracted using the RecoverAll kit (Thermo
 Fisher Cat #AM1975) and analyzed using the commercially available Oncomine Comprehensive
 Assay kit. This assay simultaneously analyzes DNA and RNA from samples allowing the
 assessment of 73 gene hotspots (based on DNA), 49 focal copy number variations (CNVs, DNA
 based), 26 full coding sequences (for mutations and CNV loss), and 22 gene fusion drivers
 (RNA). Notably, 72 of these genes are drug targets. Genomic raw data obtained (.vcf and .pdf
 files) will be stored and backed up in a local Data Center for subsequent genomic analysis.
 Upon publication of the findings of this study, the Oncomine results along with clinical
 classification of individual tumors will be made publicly available.

 Tissue Micro Array (TMA) Analysis The following genes will be further analyzed by a TMA using
 specific antibodies against: PD-L1 (Dako, Cat # SK00521), PD-L2 (Thermo Cat# B7-DC/CD273),
 Phosphorylated mTOR (Abcam Cat#AB118815), p53 (Cat # 5278074001), VEGFR2 (Abcam Cat
 #AB39256), Phosphorylated Akt (Thermo Cat #473), HER2 (Roche, Cat # 05278368001), p16 (Roche,
 Cat # 06695221001), Met (Abcam Cat #AB51067), HA-4 (Abcam Cat #AB24480) and four
 microsatellite markers (all from Roche): MLH1 (Cat # 06472966001), MSH2 (Cat # 05269270001),
 MSH6 (Cat # 5929911001), PMS2 (Cat # 06419216001). Manual TMA will be prepared as described
 previously. Briefly, paraffin blocks will be obtained and cut and stained by Hematoxylin &
 Eosin (H&E) in order to select the best histological area. Subsequently selected tissue area
 will be placed into the TMA by circling the identified area in the corresponding block.
 Cylindrical core biopsies will be extracted from each paraffin block using a 1 mm stylet and
 placed into a new recipient block. Selected adequate cases had tumors that occupied at least
 10% of the core area. Each case will be processed in triplicate to prevent tissue loss during
 cutting. Sections from each tissue array block will be cut, de-paraffinized and dehydrated
 for H&E and immunohistochemical procedures.

 Gene methylation Promoter gene methylation on six selected genes that have previously shown
 promoter regulation by methylation associated with GC will be assessed. Methylation analysis
 will include the reprimo gene and other mRNAs associated with GC progression. Analysis will
 be performed by bisulfite sequencing as described previously using the EZ DNA methylation
 Gold kit (Zymo Research) with minor modifications. Briefly, bisulfite treated DNA is
 amplified using specific PCR primers, with PCR products subsequently cloned and sequenced.

 EBV identification EBV subtypes in patient samples will be assessed using the chromogenic in
 situ hybridization (CISH) method with minor modifications.

 Single Nucleotide Polymorphism (SNP) analysis A significant proportion of GC patients can
 develop serious toxicity from 5-FU treatment including bone marrow suppression, neuropathy,
 low white blood cell numbers, fever, infections, nausea, vomiting, severe diarrhea, mouth and
 digestive tract inflammation, all of which are recorded in the patient history of other
 cohorts. Subtle personal and population changes in DNA, called SNPs can account for increases
 in the risk of 5-FU toxicity; 5-FU metabolism is predominantly hepatic, where the enzyme DPYD
 is responsible for metabolizing >80% of the drug, producing the inactive metabolite 5,6
 dihydroxy-5-FU. It is widely documented that a decreased DPYP activity is associated with
 severe toxicity. Non-metabolised fraction of 5-FU (20%) is transformed by a series of enzymes
 (e.g TP, TK), producing the active metabolites that will cause TYMS inhibition, thereby
 promoting DNA/RNA damage. Variations in TYMS and MTHFR genes (related to reduced folate
 synthesis, increased 5-FU effect), have been associated with toxicity by treatment with 5-FU.
 The approach that was used to select the genetic variants consisted of a search in the
 database, PharmGKB. A total of six non-synonymous SNPs will be analyzed: four of them
 comprise the DPYD gene, one for TYMS and one for MTHFR. Analysis will be performed using
 TaqMan™ SNP Genotyping Assay technology (Applied Biosystems™). SNPs will be assessed in DNA
 isolated from paraffin embedded patient samples.

 Sample size and statistical analysis

 The minimum sample number will be calculated in order to ensure the goals of the project are
 fully accomplished. Considering that approximately 90% of GC cases are indeed GAC, at 5%
 error rate and at 95% confidence interval the investigators originally projected a sample
 size of 200 patients. However the investigators have also considered a 15% rate of sample
 loss (defective samples or patient drop-out), which gave a total of 230 patients to be
 recruited.

 Standard descriptive statistics will be utilized to analyze qualitative and quantitative
 variables, such as relative and absolute frequencies, frequency tables, average, median,
 standard deviation, range and quartiles. A 95% confidence will be considered appropriate for
 analysis. Descriptive statistics will also be used to characterize the most relevant clinical
 parameters measured. The association of categorized variables will be performed by chi-square
 or Fisher's exact tests. One arm Analysis of Variance will compare continuous variables among
 groups. Survival outcome studies will be accomplished using the Kaplan-Meier method.
 Prognostic factors will be evaluated according to the Cox proportional hazards regression
 model.

 Principal component analysis (PCA) of the genes variants will be conducted and the
 association of the first principal components with a small pre-defined set of genomic
 alteration signatures will be assessed. To define molecular subgroups, the investigators will
 utilize unsupervised clustering. The correlation of the molecular subtypes with clinical data
 (e.g. age, gender, Lauren class) and clinical outcomes (e.g. overall survival, response rate)
 will be assessed. Moreover, supervised classification will be performed based on clinical
 outcomes and the resulting groups of both approaches will be compared with other reported
 molecular subtypes.

 Patient protection/written informed consent forms

 All parties guarantee the protection of the patients' personal records. Patient names are not
 included in any form in sheet-reports, publications, or in any type of publishable document
 derived from the study with the exception of documents required by law. Informed consent
 forms are elaborated strictly following legal and local regulations. The written informed
 consent forms, including all changes made throughout the study must be prospectively approved
 by the Internal Review Board/independent Ethics Committee, and CEMP prior to be incorporated
 into the study.

 The investigators, representatives or healthcare providers will obtain written informed
 consent forms from every patient or a legal representative before any specific activity of
 the study is performed.
Inclusion Criteria:

 -  Diagnosed with gastric cancer (histological or cytological) Attending health centers
 of the Red UC Christus network for at least 3 months with clinical follow-up.

 Capable to read and speak spanish Willing and able to provide written informed consent to
 eh study that should be dated and signed informed consent

 Exclusion Criteria:

 -  With small biopsy samples insufficient for analysis. Whose medical records cannot be
 collected or are unavaible Without signed informed consent.