Neoplasms

Digestive System Diseases

All Conditions

Symptoms and General Pathology

Rare Diseases

Stomach Neoplasms

Atrophy

Gastritis, Atrophic

Gastritis

Pathological Conditions, Anatomical

Gastroenteritis

Gastrointestinal Diseases

Stomach Diseases

Gastrointestinal Neoplasms

Digestive System Neoplasms

Chronic Graft Versus Host Disease

Stomach Cancer

Corpus-dominant chronic atrophic gastritis was characterized by a PGI/PGII ratio of less than 3.

Healthy participants in the TwinGene cohort were included.

Metabolomic profiling using serum samples was performed based on Nightingale Blood Biomarker Analysis platform; Proteomic profiling will be performed by both Scanning SWATH and OLINK® Explore 384 Oncology panel.

Metabolomic profiling

The overall aim is to utilize multi-omics approach to identify novel etiopathogenesis and early detection biomarkers for stomach cancer precursor lesions. To achieve this aim, first the investigators will use stored serum samples to perform metabolomics profiling among 12,599 twin subjects, among whom 1034 were deemed to have chronic atrophic gastritis based on measured pepsinogen I and II levels. Logistic regression will be used to search for metabolites related to the risk of chronic atrophic gastritis. Second, the investigators will further measure serum proteome by using two quantitatively precise proteomics assays, among the above-mentioned twin subjects. Identified protein biomarkers will be combined with metabolomics biomarkers to create a prediction model for chronic atrophic gastritis. The results will hopefully improve our understanding of the etiological factors and provide promising early detection biomarkers for stomach cancer precursor lesions.

The study population is part of the Swedish Twin Registry (STR), which has since its establishment in the late 1950s collected questionnaire data from all twins born after 1886. The data in this specific study is a subset of the Screening Across the Lifespan (SALT) study within the STR, in which all twins born between 1911-1958 were interviewed between 1998-2002. The subcohort named TwinGene was set-up between the years 2004 and 2008 when participants were invited to respond to a questionnaire on common diseases and provide a blood sample. Samples were collected from 12,618 twins born 1958 or earlier, of which blood sample from 12,609 were available. After excluding 10 samples which were unable to link to the available environmental data, a total of 12,599 blood samples were analyzed. Corpus-dominant CAG was characterized by a PGI/PGII ratio of less than 3. Metabolomic profiling using serum samples has been performed based on Nightingale Blood Biomarker Analysis platform. Proteomic profiling will be performed by both Scanning SWATH and OLINK® Explore 384 Oncology panel. History of H. pylori infection is examined by measuring serum IgG antibodies against H. pylori, using ELISA. Detailed lifestyle information collected by questionnaires includes education, smoking, snuff dipping, alcohol drinking, drug use, diet, and height/weight, etc. Metabolites will be log transformed prior to analyses, due to its usually skewed distribution. For each metabolite, firstly, CAG patients will be compared with all the CAG-free controls. Wilcoxon-Mann-Whitney test or Kruskal-Wallis test will be used for comparing differences of protein expressions between CAG and non-CAG groups, and multiple comparisons will be adjusted using Bonferroni correction. Generalized estimation equation (GEE) models with the robust option will be fitted to estimate the odds ratios (ORs). Second, in the comparison with MZ co-twin controls and DZ co-twin controls, only complete twin pairs with discordant CAG will be included in the study. Specifically, conditional logistic regression models will be used to control for the matching within co-twin pairs. The investigators will further combine metabolomics and proteomics data, and try to build up a CAG prediction model. Covariates will include age, sex, H. pylori seropositivity, education level, smoking, snuff dipping, and alcohol drinking. Joint effects of different metabolites and interaction with other covariates will also be examined.

Participants from TwinGene provided blood samples.

Multi-omics Analyses on Etiology and Early Detection of Stomach Cancer Precursor Lesions

Multi-omics Approach for Identification of Etiopathogenesis and Early Detection Biomarkers of Stomach Cancer Precursor Lesions

Karolinska Institutet

Professor

Blood and Lymph Conditions

Hematologic Neoplasms

Hematologic Diseases

Patients on this study must have either a suspected or confirmed solid tumor or hematological cancer. The intervention performed in this study is the molecular analysis of cancer. The samples will be taken at the time of the patient's planned diagnostic or staging procedure. If the patient is scheduled for surgery a sample of tissue not required for their diagnosis will be obtained and used for this research study. If the patient has undergone a previous diagnostic procedure, some of the stored tissue from that procedure will be submitted for molecular analysis as well.

The intervention performed in this study is the molecular analysis of cancer. Samples to be tested for genetic alterations will be collected during the course of a routine diagnostic procedure such as a surgery or tumor biopsy. Samples that have been stored from previous diagnostic procedures will be analyzed as well. This testing will be performed by the Department of Pathology at Rhode Island Hospital or an outside laboratory designated by Rhode Island Hospital. The extent of molecular testing will be different in each individual case. For example, in some cases, study of genetic alterations will start with whole genome or exome sequencing and will be confirmed by targeted Sanger resequencing, single nucleotide polymorphism, and transcriptome analysis. In other cases targeted multigene panel sequencing or targeted amplicon Sanger sequencing will be the initial and only step.

Molecular Analysis of Cancer

Andrew Schumacher, M.S.

Allison Jean, B.A.

Priscilla Merriam, M.D.

Howard Safran, M.D.

Maria Constantinou, M.D.

Anthony Mega, M.D.

Kimberly Perez, M.D.

Amy Pilotte, N. P.

Humera Khurshid, M.D.

Evgeny Yakirevich, M.D.

Murray Resnick, M.D.

James Butera, M.D.

Mary Anne Fenton, M.D.

Lucia Fontes-Bortes, N.P.

Peter Quesenberry, M.D.

Matthew Quesenberry, M.D.

John Reagan, M.D.

Eric Winer, M.D.

Thomas DiPetrillo, M.D.

Jaroslaw Hepel, M.D.

Kara Lynne Leonard, M.D.

David Tracey, P.A.

Inna Yakirevich, N.P.

Sharon Benson, N.P.

Heinrich Elinzano, M.D.

Timothy Kinsella, M.D.

Thomas Ng, M.D.

Maureen Jean, R.N.

Diane Martel, R.N.

Jennifer Collins, N.P.

Irene Kolberg, N.P.

Jodi Layton, M.D.

Fred Schiffman, M.D.

Edward Wittles, M.D.

Angela Taber, M.D.

Camille Higel-McGovern, N.P.

Amy Pilotte, N.P.

Xristin Maestri, N.P.

The purpose of this study is to discover genetic changes associated with different cancers. With the information from this study the investigators hope to provide better ways to prevent, detect and treat many cancers.

Many diseases can result from changes in a person's genetic material that causes cells to not work properly. Currently, researchers and doctors know some of the genetic changes that can cause disease, but they do not know all of the genetic changes that can cause disease.

This project is designed to identify genetic changes that can cause cancer in humans. Specimens will be collected from a scheduled diagnostic or routine (i.e. blood draw for counts) procedure and may include samples from the tissue itself (surgery), bone marrow, blood, saliva, urine, spinal fluid, sputum, joint fluid, seminal fluid, ascites (a fluid that fills up in the abdomen), and/or pleural fluid (fluid in the lung cavity), to either confirm the diagnosis of cancer or to help to decide how best to treat cancer or other illness. Additionally archived tissue may be analyzed. Samples may be stored for future use in later experiments. The Department of Pathology at Rhode Island Hospital will store the samples.

Information from the medical record, such as responses to treatments or family history of cancer, will be collected.

Complex, progressive, multigenic, somatic mutations of the genome are now widely accepted as the primary driving force in the evolution of cancer initiation, growth, metastasis and pharmacoresistance. Different types of tumors are associated with mutations in distinct sets of genes, and there is a pressing need for a sequencing-based method of analyzing panels of candidate genes that differ for each tumor type.

Traditional approaches to sequence analysis employing capillary electrophoresis-based Sanger sequencing are widely used to guide therapy for patients with lung and colorectal cancer and for melanoma, sarcomas, leukemias and lymphomas. This technology is limited in throughput, scalability, speed, and resolution. The emerging technology such as next-generation sequencing (NGS) - holds a number of advantages over traditional methods, including the ability to fully sequence large numbers of genes in a single test and simultaneously detect deletions, insertions, copy number alterations, translocations, and exome-wide base substitutions in all known cancer-related genes.

Sequencing the whole genome is financially prohibitive for many potentially valuable applications. One alternative to whole genome methods is target enrichment, such as exome sequencing, which captures and sequences only protein coding regions. The exome represents 1-2% of the human genome; however contains the vast majority of disease causing alterations. In addition to exome sequencing, full-length transcriptome (mRNA) sequencing offers a fast and inexpensive alternative. It is an easier method to identify coding sequences and capture variants in genes that are expressed, as well as to generate additional information, such as gene expression level and splicing patterns.

The goal of this study is to investigate genomic, transcriptomic and proteomic alterations in human solid cancers and hematologic malignancies.

Patients \>18 y.o. diagnosed with cancer (including any solid tumor or hematologic malignancy) or patients who are undergoing a procedure for the diagnosis of a presumed cancer are eligible.

The research analysis will be performed by the department of pathology or the division of hematology oncology. The body/blood tissue analyzed will be from extra tissue/blood that is not needed for diagnosis or evaluation of the patient's cancer. All samples will be de-identified. Samples will be stored for an indefinite period of time or until all samples are utilized.

Molecular Testing of Cancer by Integrated Genomic, Transcriptomic, and Proteomic Analysis

MOLECULAR TESTING OF CANCER BY INTEGRATED GENOMIC, TRANSCRIPTOMIC, AND PROTEOMIC ANALYSIS

Rhode Island Hospital

Adenocarcinoma

Esophageal Neoplasms

Barrett Esophagus

Carcinoma

Neoplasms, Glandular and Epithelial

Neoplasms by Histologic Type

Precancerous Conditions

Esophageal Diseases

Head and Neck Neoplasms

Esophageal Cancer

Piet Pattyn, MD, PhD

Annouck Philippron, MD

This study is designed to perform a explorative search of the transcriptome to detect new circulating diagnostic sensitive and specific biomarkers in patients with Barrett's esophagus or esophageal adenocarcinoma.

By developing new tools for risk-assessing of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) in a population at risk, the investigators expect that diagnosis can be done in an earlier stage resulting in an improved 5-year survival. A proof-of-concept RNA profiling study will be done in 20 BE and EAC patients where 2 biomaterials (tissue and plasma) and 2 RNA biotopes (micro RNA and messenger RNA) will be compared. Previously validated methodology on small RNA and messenger RNA capture sequencing on both tissue and plasma will be used to obtain high-quality data. Differential expression analysis will be done on tissue and plasma sample data. Additional in-depth data-mining will be done, amongst other focusing on structural information encoded in the transcriptome and building a multifeature classifier. These findings will be validated in a large validation cohort, followed by development of a clinical-grade quantitative Polymerase Chain Reaction (qPCR) test, ready for testing in an independent cohort.

Barrett's Esophagus and Esophageal Adenocarcinoma, Searching for Reliable Diagnostic RNA Plasma-based Biomarkers

Liquid Biopsies in Esophageal Adenocarcinoma: Barrett's Esophagus and Esophageal Adenocarcinoma, Searching for Reliable Diagnostic RNA Plasma-based Biomarkers

Identification of micro RNAs in plasma and tissue of patients with (non-)dysplastic Barrett's esophagus and EAC that are differentially abundant, compared to healthy plasma (healthy volunteers) or healthy tissue (patient-matched healthy esophagus biopsies).

Identification of messenger RNAs in plasma and tissue of patients with (non-)dysplastic Barrett's esophagus and EAC that are differentially abundant, compared to healthy plasma (healthy volunteers) or healthy tissue (patient-matched healthy esophagus biopsies).

Identification of a set of messenger RNAs that change during treatment (using longitudinally collected plasma samples) and that separate responders from non-responders to neo-adjuvant radiochemotherapy.

After development and validation on an independent cohort, this test should be evaluated in a second external cohort

Universitaire Ziekenhuizen KU Leuven

University Hospital, Ghent

Carcinogenesis

Neoplastic Processes

Patients with atypical hyperplasia of endometrium

The goal of this observational study is to draw the characteristic maps of imaging omics, genomics, transcriptome, proteomics, pathological omics, metabolomics, etc. of the dynamic evolution of endometrial carcinogenesis in 100 patients with normal endometrium, 100 patients with atypical endometrial hyperplasia, and 100 patients with endometrial cancer; and then to explore the underlying molecular mechanism, and establish the database system for the dynamic evolution of endometrial carcinogenesis.

A Multiomics Study Based on the Dynamic Evolution of Endometrial Carcinogenesis

RenJi Hospital

Disease Susceptibility

This pediatric oncology study proposing a global approach integrating trio-based whole exome sequencing, somatic DNA and RNA analysis will improve the recognition of genetic predisposition and the characterization of target therapies in children with cancer.

Exome sequencing in pediatrics cancers

Pascal Pujol, PU-PH

Background. Cancer is the leading cause of death by disease in children. Most pediatric tumors differ from adult tumors in terms of biological and clinical characteristics. In children, the part of genetic determinism could be higher since the role of environmental factors may be less pronounced than in adults and that a young age at onset is a main feature of genetic cancer predisposition. Recent studies suggested that a number of genetic predisposition remains to be characterized.

Methods. Trio-Based whole exome sequencing of germline DNA from patients (children and adults diagnosed with cancers between 0 and 17 years) and parents will be performed prospectively in a multicentric study including 40 unselected cases of malignant tumor. Participating hospitals will include the CHU of Montpellier, the CHU de Nice and the AP-HP. Tumor analysis will include whole exome analysis and transcriptome for the identification of therapeutic target and contribute to confirm potential link between constitutive mutations and tumor phenotype (such as loss of expression, loss of heterozygosity).

Perspectives. This pediatric oncology study proposing a global approach integrating trio-based whole exome sequencing, somatic DNA and RNA analysis will improve the recognition of genetic predisposition and the characterization of target therapies in children with cancer.

Analyse of Tumour and Constitutional DNA for the Study of the Determinism in Child Neoplasia

A blood sample will be taken from patients and their parents in order to carry out genetic analyses.

New generation NGS Exome sequencing in trio (patient and 2 healthy parents) on an Illumina HiSeq 2000 platform using the SureSelectXT Human All Exon 50Mb, V5 kit.

Bioinformatics analysis of the data. Confirmation of mutations by Sanger sequencing (gold standard).

In case of identification of mutations in candidate genes confirmed by Sanger sequencing, we will perform functional and clinical-genetic studies.

Soroptimist association of Monaco

University Hospital, Montpellier

Cell Transformation, Neoplastic

The HPV integration status will be checked by GWAS.

A multi-omics analysis including genome-wide association study, whole exome sequencing, transcriptomics and metabolomics.

A multi-omics analysis

Lei Li, M.D.

Lei Li, MD

This study aims to analyze the multi-omics results between uterine cervical adenocarcinoma patients with and without human papillomavirus (HPV) infections. The multi-omics profiles include genome wide association study (GWAS), whole exome sequencing, analysis of transcriptomics and metabolomics. The HPV integration status is interpreted by GWAS. A comprehensive multi-omics will reveal the role of HPV integration in the molecular mechanism of tumorigenesis and prognosis of uterine cervical adenocarcinoma.

An 8 ml peripheral venous blood, and 50 μL cancer tissue and tissue adjacent to cancer will be collected from eligible patients.

HPV Integration and Tumorigenesis of Uterine Cervical Adenocarcinoma

A Multi-omics Study on the Human Papillomavirus Integration and Tumorigenesis of Uterine Cervical Adenocarcinoma

All data will be available to all researchers.

The differences of frequencies of somatic driving mutations will be compared between patients with and without HPV integration.

The alteration of patterns of RNA expression, including mRNA, miRNA, and lncRNA, will be compared between patients with and without HPV integration.

The alteration of patterns of protein expression and signal pathway will be compared between patients with and without HPV integration.

Progression-free survival between patients with differential expressed multi-omics will be compared.

Lei Li

The goal of this observational study is to draw the characteristic maps of genomics, transcriptome, proteomics, metabolomics, etc. in 600 patients with gynecological rare pathological types of malignant tumors. Then it is planned to explore the molecular mechanism and find some new targets for diagnosis and treatment, and design and establish the database system of the above rare tumors.

Prospective Multi-omics Observational Study of Gynecological Rare Pathological Tumors

Draw the characteristic maps of imaging omics, genomics, transcriptome, proteomics, pathological omics, metabolomics, etc. of patients with gynecological rare pathological types of malignant tumors, and explore the molecular mechanism thus finding some new targets for diagnosis and treatment.

Design and establish the database system of the above gynecological rare pathological types of tumors.

Integrate the characteristic maps of imaging omics, genomics, transcriptome, proteomics, pathological omics, metabonomics, etc. to study their possible relevance.

Study title	NCT ID	Conditions	Interventions	Eligibility	Organization
Multi-omics Analyses on Etiology and Early Detection of Stomach Cancer Precursor Lesions	NCT06267703	Chronic Atrophi...	Metabolomic pro...	46 Years - 97 Years	Karolinska Institutet
Molecular Testing of Cancer by Integrated Genomic, Transcriptomic, and Proteomic Analysis	NCT02213822	Solid Tumors Hematological M...	Molecular Analy...	18 Years -	Rhode Island Hospital
Barrett's Esophagus and Esophageal Adenocarcinoma, Searching for Reliable Diagnostic RNA Plasma-based Biomarkers	NCT05688176	Esophageal Neop...		18 Years -	University Hospital, Ghent
Molecular Testing of Cancer by Integrated Genomic, Transcriptomic, and Proteomic Analysis	NCT02213822	Solid Tumors Hematological M...	Molecular Analy...	18 Years -	Rhode Island Hospital
Multi-omics Analyses on Etiology and Early Detection of Stomach Cancer Precursor Lesions	NCT06267703	Chronic Atrophi...	Metabolomic pro...	46 Years - 97 Years	Karolinska Institutet
A Multiomics Study Based on the Dynamic Evolution of Endometrial Carcinogenesis	NCT06007300	the Dynamic Evo... Multiomics Anal...		18 Years -	RenJi Hospital
Analyse of Tumour and Constitutional DNA for the Study of the Determinism in Child Neoplasia	NCT04471961	Pediatric Tumor Familial Cancer Solid Tumor, Ch... Hematological T...	Exome sequencin...	-	University Hospital, Montpellier
HPV Integration and Tumorigenesis of Uterine Cervical Adenocarcinoma	NCT03742869	Cervical Adenoc... Human Papilloma... Genome-wide Ass... Whole Exome Seq... Transcriptome Metabolome Tumorigenesis Prognosis	A multi-omics a...	-	Peking Union Medical College Hospital
Prospective Multi-omics Observational Study of Gynecological Rare Pathological Tumors	NCT05985941	Rare Gynecologi... Multi-omics Ana...		18 Years -	RenJi Hospital
Molecular Testing of Cancer by Integrated Genomic, Transcriptomic, and Proteomic Analysis	NCT02213822	Solid Tumors Hematological M...	Molecular Analy...	18 Years -	Rhode Island Hospital

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