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dbGaP phs000942 Use of WGS for Diagnosis and Discovery in the Cancer Genetics Clinic - Eligibility

- 2024-11-27 - 5 forms, 1 itemgroup, 1 item, 1 language
Itemgroup: IG.elig
Principal Investigator: Theodora S. Ross, MD, PhD, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA, and Department of Cancer Genetics, UT Southwestern Medical Center, Dallas, TX, USA MeSH: Neoplasms,Breast Neoplasms,Ovarian Neoplasms,Peritoneal Neoplasms,Skin Neoplasms,Esophageal Neoplasms,Thyroid Neoplasms,Urinary Bladder Neoplasms,Endometrial Neoplasms,Fallopian Tube Neoplasms,Melanoma,Testicular Neoplasms,Bile Duct Neoplasms,Lung Neoplasms,Colonic Neoplasms,Adrenocortical Carcinoma,Carcinoma, Renal Cell,Colonic Polyps,Adenomatous Polyposis Coli,Lymphoma, Large B-Cell, Diffuse,Pheochromocytoma,Paraganglioma,Leiomyoma,Hemangioblastoma,Hyperparathyroidism,Pancreatic Neoplasms,Vulvar Neoplasms,Brain Neoplasms,Liver Neoplasms,Kidney Neoplasms,Prostatic Neoplasms,Glioblastoma,Oncocytoma, renal https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000942 Despite the potential of whole-genome sequencing (WGS) to improve patient diagnosis and care, the empirical value of WGS in the cancer genetics clinic is unknown. We performed WGS on members of two cohorts of cancer genetics patients: those with BRCA1/2 mutations (n = 176) and those without (n = 82). Initial analysis of potentially pathogenic variants (PPVs, defined as nonsynonymous variants with allele frequency 1% in ESP6500) in 163 clinically-relevant genes suggested that WGS will provide useful clinical results. This is despite the fact that a majority of PPVs were novel missense variants likely to be classified as variants of unknown significance (VUS). Furthermore, previously reported pathogenic missense variants did not always associate with their predicted diseases in our patients. This suggests that the clinical use of WGS will require large-scale efforts to consolidate WGS and patient data to improve accuracy of interpretation of rare variants. While loss-of-function (LoF) variants represented only a small fraction of PPVs, WGS identified additional cancer risk LoF PPVs in patients with known BRCA1/2 mutations and led to cancer risk diagnoses in 21% of non-BRCA cancer genetics patients after expanding our analysis to 3209 ClinVar genes. These data illustrate how WGS can be used to improve our ability to discover patients' cancer genetic risks. "Reprinted from doi:10.1016/j.ebiom.2014.12.003, with permission from EBioMedicine."

pht004834.v1.p1

1 itemgroup 5 items

pht004835.v1.p1

1 itemgroup 5 items

pht004836.v1.p1

1 itemgroup 16 items

pht004837.v1.p1

1 itemgroup 5 items

dbGaP phs000869 Barrett's and Esophageal Adenocarcinoma Genetic Susceptibility Study (BEAGESS) - pht004610.v1.p1

- 2024-03-16 - 5 forms, 1 itemgroup, 11 items, 1 language
Itemgroup: pht004610
Principal Investigator: Thomas Vaughan, MD, MPH, Fred Hutchinson Cancer Research Center, Seattle, WA, USA MeSH: Esophageal Neoplasms,Barrett Esophagus https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000869 BEAGESS is a genome-wide association study (GWAS) which takes advantage of the extensive data collected by investigators in the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON, http://beacon.tlvnet.net), representing many of the high-quality population-based and other epidemiologic studies of BE and EA in the world. The overall goal of our research is to evaluate the influence of genetic susceptibility on risk of EA and its main precancerous condition, BE. The primary aims of the study are to identify tagSNPs most strongly associated with risk of esophageal adenocarcinoma (EA) and Barrett's esophagus (BE). In the secondary aims we will evaluate the extent to which the most significant associations vary according to key environmental and host factors for these conditions, including gender, obesity and cigarette smoking. These results will guide additional exploratory analyses examining ways in which individual SNP results might be aggregated to shed light in the importance of specific pathways relevant to the etiology of BE and EA, and to identify possible epistatic effects.

pht004611.v1.p1

1 itemgroup 8 items

pht004607.v1.p1

1 itemgroup 5 items

pht004608.v1.p1

1 itemgroup 5 items

pht004609.v1.p1

1 itemgroup 5 items

dbGaP phs001003 Prospective Procurement of Solid Tumor Tissue to Identify Novel Therapeutic Targets - pht010322.v2.p1

- 2023-11-06 - 6 forms, 1 itemgroup, 2 items, 1 language
Itemgroup: pht010322
Principal Investigator: Steven A. Rosenberg, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Colonic Neoplasms,Ovarian Neoplasms,Stomach Neoplasms,Cholangiocarcinoma,Pancreatic Neoplasms,Rectal Neoplasms,Esophageal Neoplasms,Colorectal Neoplasms,Endometrial Neoplasms,Paraneoplastic Syndromes, Ocular https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001003 Recent advances and insights into the molecular pathogenesis of cancer have led to the development of novel molecular and biologic targeted therapies for the treatment of advanced cancer patients. A critical challenge in extending these studies involves the identification and validation of new therapeutic targets for future cancer therapies. In this study, we performed whole exome and RNA-Seq analysis metastases to determine the nature and frequency of somatic mutations.

pht010323.v2.p1

1 itemgroup 2 items

pht010324.v2.p1

1 itemgroup 4 items

pht010325.v1.p1

1 itemgroup 2 items

pht010326.v2.p1

1 itemgroup 5 items

Eligibility

1 itemgroup 9 items

dbGaP phs001214 DNA and RNA Profiling Using Simultaneous Sequencing (Simul-seq) - pht005875.v1.p1

- 2023-05-17 - 4 forms, 1 itemgroup, 4 items, 1 language
Itemgroup: pht005875
Principal Investigator: Michael P. Snyder, PhD, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA MeSH: Esophageal Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001214 Paired DNA and RNA profiling is increasingly employed in genomics research to uncover molecular mechanisms of disease and to explore personal genotype and phenotype correlations. We developed a novel simultaneous DNA and RNA sequencing approach (Simul-seq) that enables comprehensive genomic and transcriptomic profiles from small quantities of cells or tissues. In this study, Simul-seq was performed on patient-derived fibroblast cells as well as an esophageal adenocarcinoma tumor sample and compared with standard DNA and RNA-sequencing approaches.

pht005876.v1.p1

1 itemgroup 4 items

pht005877.v1.p1

1 itemgroup 3 items

pht005878.v1.p1

1 itemgroup 11 items

dbGaP phs000598 Exome Sequencing of Esophageal Adenocarcinoma - pht003322.v2.p2

- 2023-01-09 - 4 forms, 1 itemgroup, 2 items, 1 language
Itemgroup: pht003322
Principal Investigator: Adam Bass, Dana-Farber Cancer Institute, Boston, MA; Broad Institute, Cambridge MA; Brigham and Women's Hospital, Boston, MA, USA MeSH: Esophageal Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000598 The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. When coupled to the five-year survival rate of only 15% for this disease, identification of new therapeutic targets for EAC is of great importance. Here, we analyze the mutational spectra identified from the whole genome sequencing of 16 EACs and complete exome sequencing of 149 EAC tumors and matched germline samples. We identify a novel mutation signature marked by high prevalence of A to C transversions at AA*(N) trinucleotides. Notably, the development of EAC is preceded by pathologic intestinal metaplasia of the lower esophagus, Barrett's esophagus, itself a response to injury from gastric-esophageal reflux disease (GERD). Thus, we hypothesize to represent these AA*(N) mutations to a novel signature of GERD-induced mutagenesis. Analysis of the exome data identified 26 genes subject to statistically significant recurrent mutation. Of these 26 genes, only TP53, CDKN2A, SMAD4, and PIK3CA had been previously implicated in EAC. Novel mutations include those targeting chromatin modifying factors and novel candidate contributors to EAC: SPG20, TLR4, ELMO1 and DOCK2. Of these, ELMO1 and DOCK2 are notably direct dimerization partners that act to activate Rac1 to enhance cellular invasiveness, thus generating new hypotheses about the potential for the Rac1 pathway to be a novel target for therapy of EAC. "Reprinted from 'Unraveling the mutational complexity of esophageal adenocarcinoma', with permission from Nature Genetics."

pht003323.v2.p2

1 itemgroup 3 items

pht003324.v2.p2

1 itemgroup 3 items

pht003325.v2.p2

1 itemgroup 5 items

dbGaP phs000260 Foregut Microbiome in Development of Esophageal Adenocarcinoma - pht001256.v4.p2

- 2022-10-12 - 5 forms, 1 itemgroup, 2 items, 1 language
Itemgroup: pht001256
Principal Investigator: Zhiheng Pei, MD, PhD, NYU Langone Medical Center, New York, NY, USA MeSH: Esophageal Adenocarcinoma,Barrett's Esophagus,GERD https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000260 The distal esophagus is an important anatomical area where gastric acid reflux can cause reflux esophagitis (RE), Barrett's esophagus (BE) (intestinal metaplasia), and esophageal adenocarcinoma (EA). The incidence of EA has increased 6-fold in the U.S. since the 1970s, parallel to a significant increase in the prevalence of gastroesophageal reflux diseases (GERD). Although specific host factors might predispose one to disease risk, such a rapid increase in incidence must be predominantly environmental. The cause remains unknown. Our hypothesis is that changes in the foregut microbiome are associated with EA and its precursors, RE and BE in the GERD sequence. We will conduct a case control study to characterize the microbiome in every stage of the GERD sequence as well as analyze the trend in changes in the microbiome along disease progression toward EA. Specific Aim 1. To conduct a comprehensive population survey of the foregut microbiome and demonstrate its association with GERD sequence, by a 16S rRNA gene survey. We will analyze samples of the foregut microbiome at three anatomic loci: mouth, distal esophagus, and gastric corpus. Changes of the microbiota in the distal esophagus will be correlated with the phenotypes. Spatial relationship between the esophageal microbiota and upstream (mouth) and downstream (stomach) foregut microbiotas as well as temporal stability of the microbiome-disease association will also be examined. Specific Aim 2. To define distal esophageal metagenome and demonstrate its association with GERD sequence, by shotgun metagenomic analysis. We will first classify samples of the metagenome into metagenotypes by between-sample k-mer distance and correlate the metagenotypes with the four phenotypes. Subsequent detailed analyses will include pathway-disease and gene-disease associations. DNA viruses and fungi, if identified, also will be correlated with the phenotypes. A significant association between the foregut microbiome composition and GERD sequence, if demonstrated, will be the first step for eventually testing the causal hypothesis that an abnormal microbiome is required for the development of the sequence of phenotypic changes toward EA. If EA and its precursors represent a microbial ecological disease, treating the cause of GERD might become possible, for example, by normalizing the microbiome through use of antibiotics, probiotics, or prebiotics. Causative therapy for GERD could prevent its progression and reverse the current trend of increasing incidence of EA.

Eligibility

1 itemgroup 18 items

pht001257.v4.p2

1 itemgroup 3 items

pht001258.v4.p2

1 itemgroup 8 items

pht001259.v4.p2

1 itemgroup 7 items

dbGaP phs000361 Genome-Wide Association Studies in Upper Gastrointestinal Cancers (Asian) - pht002221.v1.p1

- 2022-10-12 - 4 forms, 1 itemgroup, 3 items, 1 language
Itemgroup: pht002221
Principal Investigator: Philip R. Taylor, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Squamous Cell Carcinoma,Esophageal Cancer,Gastric Cancer https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000361 This project aims to conduct genome-wide association studies (GWAS) in two anatomically different upper gastrointestinal (UGI) cancer sites in two populations with distinctly different disease rates and genetic profiles. One population has very high rates for both esophageal squamous cell carcinomas (ESCCs) and gastric cancers (GCs) and is comprised of Asians (*the "Asian UGI GWAS"*), while the other population has low rates of ESCC and GC and includes non-Asians from the Americas, Europe, and Australia (*the "Non-Asian UGI GWAS"*). Study participants for the Asian UGI GWAS reported here (Illumina 660W Quad chip) were drawn from 2 studies, the Shanxi Upper Gastrointestinal Cancer Genetics Project (Shanxi) and the Linxian Nutrition Intervention Trial (NIT), a prospective cohort, and included a total of 1898 ESCCs, 1625 GCs, and 2100 controls. For the 2nd phase (8 TaqMan SNPs), additional subjects from Shanxi and NIT as well as subjects from the Shanghai Men's Health Study (SMHS), the Shanghai Women's Health Study (SWHS), and the Singapore Chinese Health Study (SCHS) were also included (217 ESCCs, 615 GCs, 1202 controls). Altogether 2115 ESCCs, 2240 GCs, and 3302 controls were genotyped in this study.

pht002222.v1.p1

1 itemgroup 2 items

pht002223.v1.p1

1 itemgroup 5 items

Eligibility

1 itemgroup 3 items

Esophageal Cancer NCT00655876 Treatment - TF: Radiation Therapy Oncology Group Phase III Esophagus Systemic Treatment Summary Form - 2598533v1.0 - TF: Radiation Therapy Oncology Group Phase III Esophagus Systemic Treatment Summary Form

- 2021-09-27 - 1 form, 6 itemgroups, 56 items, 1 language
Itemgroups: MODULE 1, Summary of Systemic Treatment, Summary of Systemic Treatment, Protocol Specific Adverse Events Evaluation, REPORT ALL CONTINUING OR NEW ADVERSE EVENTS, Footer
TF: Radiation Therapy Oncology Group Phase III Esophagus Systemic Treatment Summary Form Paclitaxel, Cisplatin, and Radiation Therapy With or Without Cetuximab in Treating Patients With Locally Advanced Esophageal Cancer Source Form: NCI FormBuilder: https://formbuilder.nci.nih.gov/FormBuilder/formDetailsAction.do?method=getFormDetails&formIdSeq=2A02FE34-6EF5-5B5C-E044-0003BA3F9857

Esophageal Cancer NCT00551759 Eligibility - E2205 Registration Worksheet (step 1) - 2753343v1.0 - E2205 Registration Worksheet (step 1)

- 2021-09-17 - 1 form, 2 itemgroups, 34 items, 1 language
Itemgroups: Eligibility, Demographic Data Required For Patient Registration
E2205 Registration Worksheet (step 1) Chemotherapy, Radiation Therapy, and Cetuximab Followed by Surgery, Docetaxel, and Cetuximab in Treating Patients With Esophageal Cancer or Gastroesophageal Junction Cancer Source Form: NCI FormBuilder: https://formbuilder.nci.nih.gov/FormBuilder/formDetailsAction.do?method=getFormDetails&formIdSeq=4E4AEBDF-A595-00B2-E044-0003BA3F9857

Esophageal Cancer NCT00655876 Demographic - A0 HQ Confirmation - 2904861v1.0 - A0 HQ Confirmation

- 2021-09-17 - 1 form, 1 itemgroup, 29 items, 1 language
Itemgroup: Patient Information
A0 HQ Confirmation - PHASE III ESOPHAGEAL: RT/PACLITAXEL/CISPLATIN +/ Paclitaxel, Cisplatin, and Radiation Therapy With or Without Cetuximab in Treating Patients With Locally Advanced Esophageal Cancer Source Form: NCI FormBuilder: https://formbuilder.nci.nih.gov/FormBuilder/formDetailsAction.do?method=getFormDetails&formIdSeq=6D4170C3-6E1D-4980-E040-BB89AD435BA5

Esophageal Cancer NCT00757172 Registration - ACOSOG-Z4051 OPEN Registration Worksheet - 3013492v1.0 - ACOSOG-Z4051 OPEN Registration Worksheet

- 2021-09-17 - 1 form, 4 itemgroups, 65 items, 1 language
Itemgroups: Demography Section, General Information, Eligibility Checklist, Specimen Banking Consent
ACOSOG-Z4051 OPEN Registration Worksheet Panitumumab, Docetaxel, Cisplatin, Radiation Therapy, and Surgery in Treating Patients With Newly Diagnosed, Locally Advanced Esophageal Cancer or Cancer of the Gastroesophageal Junction Source Form: NCI FormBuilder: https://formbuilder.nci.nih.gov/FormBuilder/formDetailsAction.do?method=getFormDetails&formIdSeq=7FFA1514-8109-A58F-E040-BB89AD4376E5

Eligibility Localized Squamous Cell Carcinoma of the Esophagus NCT02017600

- 2020-07-02 - 1 form, 2 itemgroups, 17 items, 1 language
Itemgroups: Inclusion Criteria, Exclusion Criteria
A Phase II Trial of Induction Chemotherapy With ND-420, Cisplatin and Fluorouracil Followed by Surgery in the Treatment of Patients With Localized Squamous Cell Carcinoma of the Esophagus; ODM derived from: https://clinicaltrials.gov/show/NCT02017600

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