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dbGaP phs000841 Tyrosine Kinase Mutations in Endometrial Cancer - pht004420.v1.p1

- 1/29/25 - 5 forms, 1 itemgroup, 5 items, 1 language
Itemgroup: pht004420
Principal Investigator: Daphne W. Bell, PhD, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Endometrial Carcinomas https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000841 The purpose of the original study was to search for somatic mutations in the tyrosine kinome of serous and clear cell endometrial carcinomas (human). The study was conducted in two phases. Phase 1: A mutation discovery screen, in which ~577 exons encoding the catalytic domains of 86 tyrosine kinases were PCR-amplified and bidirectionally Sanger sequenced from 24 serous, 11 clear cell, and 5 mixed histology endometrial tumors. This was followed by alignment of sequence reads to the human reference sequence and subsequent nucleotide variant calling to identify potential somatic (tumor-specific) mutations. Potential somatic mutations were confirmed by re-amplification and sequencing of the relevant tumor DNA as well as matched non-tumor ("normal") DNA from the same case. Phase 2: A mutation prevalence screen, in which the non-catalytic regions two tyrosine kinase genes, TNK2 and DDR1, were PCR-amplified and sequenced from the 40 discovery screen tumors, and all coding exons of TNK2 and DDR1 were PCR-amplified and sequenced from another 10 clear cell, 21 serous, and 41 endometrioid endometrial tumors, in an effort to identify additional somatic mutations in each gene. Exons encoding the exonuclease domain of POLE were also sequenced to document somatic mutations.

pht004421.v1.p1

1 itemgroup 4 items

pht004422.v1.p1

1 itemgroup 12 items

Eligibility

1 itemgroup 4 items

pht004419.v1.p1

1 itemgroup 3 items

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

- 11/27/24 - 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 phs000893 Genome-Wide Association Study of Endometrial Cancer in E2C2 - pht005501.v1.p1

- 4/2/24 - 6 forms, 1 itemgroup, 3 items, 1 language
Itemgroup: pht005501
Principal Investigator: Immaculata De Vivo, PhD, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA and Harvard TH Chan School of Public Health, Boston, MA, USA MeSH: Carcinoma, Endometrioid,Endometrial Neoplasms,Uterine Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000893 Endometrial cancer, the most common gynecological malignancy in the United States, has both an environmental and genetic component. To this end, we conducted a genome-wide association study to identify genes involved in endometrial cancer using studies from the NCI-supported Epidemiology of Endometrial Cancer Consortium (E2C2). For the discovery stage we included samples from 6 cohort and 7 case control studies through 2007. The total number of cases genotyped were 2,307, white women of European descent, and 2,307 matched controls using the Illumina HumanOmniExpress platform. We conducted the replication using the Infinium HumanExome BeadChip, which successfully genotyped 177,139 variants in 1055 cases and 1778 controls from four ethnically diverse studies that are part of the Epidemiology of Endometrial Cancer Consortium (E2C2). The overall goal is to determine whether certain genotypes are predictive of future endometrial cancer risk, and whether the genotypes interact with established endometrial risk factors.

pht005502.v1.p1

1 itemgroup 15 items

pht005503.v1.p1

1 itemgroup 8 items

pht005504.v1.p1

1 itemgroup 4 items

Eligibility

1 itemgroup 2 items

pht005500.v1.p1

1 itemgroup 4 items

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

- 11/6/23 - 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 phs001127 Genomic Analysis of Paired Endometrial Cancer Primaries and Metastases - Eligibility

- 6/19/23 - 5 forms, 1 itemgroup, 1 item, 1 language
Itemgroup: IG.elig
Principal Investigator: Rameen Beroukhim, MD, PhD, Dana-Farber Cancer Institute, Boston, MA, USA, Brigham and Women's Hospital, Boston, MA, USA, Broad Institute of MIT and Harvard, Cambridge, MA, USA MeSH: Endometrial Neoplasms,Neoplasm Metastasis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001127 Formation of metastases is the major cause of cancer related deaths. Recent studies have sequenced primary endometrial carcinomas yielding data for a single entity in the progression from the birth of a progenitor tumor cell to metastatic disease. However, the progression of these tumors to metastases has not been characterized. We performed whole-exome sequencing of 98 tumor biopsies including complex atypical hyperplasias, primary tumors and paired abdominopelvic metastases to survey the evolutionary landscape of endometrial cancer. We expanded and reanalyzed TCGA-data, identifying novel recurrent alterations in primary tumors, including mutations in the estrogen receptor cofactor *NRIP1* in 12% of patients. We found that likely driver events tended to be shared by primary and metastatic tissue-samples, with notable exceptions such as *ARID1A* mutations. Phylogenetic analyses in cases with multiple metastases indicated these metastases typically arose from one lineage of the primary tumor. These data indicate extensive genetic heterogeneity within endometrial cancers and relative homogeneity across metastatic sites.

pht005525.v1.p1

1 itemgroup 2 items

pht005526.v1.p1

1 itemgroup 3 items

pht005527.v1.p1

1 itemgroup 7 items

pht005528.v1.p1

1 itemgroup 5 items

dbGaP phs001152 Somatic Mutational Analysis by Exome Sequencing Endometrial Carcinosarcomas - Eligibility

- 6/14/23 - 5 forms, 1 itemgroup, 4 items, 1 language
Itemgroup: IG.elig
Principal Investigator: Daphne W. Bell, PhD, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Endometrial Neoplasms,Carcinosarcoma https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001152 The purpose of this study was to identify somatic (tumor-specific) mutations in endometrial carcinosarcoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 14 de-identified primary tumor DNAs and matched non-tumor DNAs.

pht005534.v1.p1

1 itemgroup 3 items

pht005535.v1.p1

1 itemgroup 3 items

pht005536.v1.p1

1 itemgroup 2 items

pht005537.v1.p1

1 itemgroup 8 items

dbGaP phs001153 Somatic Mutational Analysis by Exome Sequencing Late-Stage Endometrioid Endometrial Carcinoma - pht005695.v1.p1

- 6/5/23 - 5 forms, 1 itemgroup, 3 items, 1 language
Itemgroup: pht005695
Principal Investigator: Daphne W. Bell, PhD, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Endometrial Neoplasms,Carcinoma, Endometrioid https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001153 The purpose of this study was to identify somatic (tumor-specific) mutations in advanced stage endometrioid endometrial carcinoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 19 de-identified primary tumor DNAs, from advanced stage tumors, and matched non-tumor DNAs.

pht005696.v1.p1

1 itemgroup 2 items

pht005697.v1.p1

1 itemgroup 8 items

pht005694.v1.p1

1 itemgroup 3 items

Eligibility

1 itemgroup 5 items

dbGaP phs000559 PAGE: Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project - Eligibility

- 12/12/22 - 5 forms, 1 itemgroup, 20 items, 1 language
Itemgroup: IG.elig
Principal Investigator: Dana Crawford, PhD, Vanderbilt University, Nashville, TN, USA MeSH: Neoplasms,Breast Neoplasms,Colorectal Neoplasms,Endometrial Neoplasms,Lung Neoplasms,Lymphoma, Non-Hodgkin,Ovarian Neoplasms,Melanoma,Prostatic Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000559 As part of Population Architecture using Genomics and Epidemiology PAGE study (Phase I), the Epidemiologic Architecture using Genomics and Epidemiology (EAGLE I) project accessed both epidemiologic- and clinic-based collections. The epidemiologic-based collection of EAGLE I included the National Health and Nutritional Examination Surveys (NHANES), ascertained between 1991-1994 (NHANES III), 1999-2002, and 2007-2008. NHANES is a population-based cross-sectional survey now conducted every year in the United States to assess the health status of Americans at the time of ascertainment and to assess trends over the years of survey. Genetic NHANES consists of 19,613 DNA samples linked to thousands of variables including demographics, health and lifestyle variables, physical examination variables, laboratory variables, and exposures. NHANES is diverse with almost one-half of the samples (46.4%) coming from self-reported Mexican Americans and non-Hispanic blacks. In contrast to NHANES, BioVU is a clinic-based collection of 150,000 DNA samples from Vanderbilt University Medical Center linked to de-identified electronic medical records (EMRs). Approximately 12% of BioVU's overall DNA sample collection is from African American, Hispanic, and Asian patients. The overall goals of PAGE I and EAGLE I were broad and several-fold:- Replicate genome-wide association study (GWAS)- identified variants in European Americans; - Identify population-specific and trans-population genotype-phenotype associations; - Identify genetic and environmental modifiers of these associations. NHANES is an excellent resource for the study of quantitative traits associated with common human diseases. However, given that the age range of NHANES spans childhood to late adulthood and not all diseases are surveyed, NHANES is less useful for the study of adult-onset diseases such as major cancers. Therefore, under American Recovery and Reinvestment Act (ARRA) funding, EAGLE as part of PAGE I defined eight major cancers sites for genetic analysis in BioVU, Vanderbilt's biorepository linked to de-identified EMRs. The eight major cancers defined for this study included melanoma, breast, ovarian, prostate, colorectal, lung, endometrial, and Non-Hodgkin's lymphoma (NHL). Cancer cases were defined using a combination of ICD-9 codes and tumor registry entries. Controls include BioVU participants without cancer and encompassing the age and gender distributions of cancer cases. Targeted genotyping of GWAS-identified variants for these diseases (124 SNPs) and ancestry informative markers (128 AIMs) was performed by the Center for Human Genetics Research Vanderbilt DNA Resources Core. After quality control, a total of 116 cancer-associated SNPs and 122 AIMs were available for downstream analyses.

pht003614.v1.p1

1 itemgroup 2 items

pht003615.v1.p1

1 itemgroup 3 items

pht003616.v1.p1

1 itemgroup 58 items

pht003617.v1.p1

1 itemgroup 5 items

Eligibility NCT00334295 Metastatic Endometrial Carcinoma - Eligibility

- 9/20/21 - 1 form, 2 itemgroups, 8 items, 2 languages
Itemgroups: Inclusion Criteria, Exclusion criteria
ODM derived from http://clinicaltrials.gov/ct2/show/NCT00334295?term=NCT00334295&rank=1

Endometrial Cancer NCT01210222 Pre-Study - GOG-0229L: Fast Fact Sheet for Protocol 0229L (Endometrium) - 3184152v1.0 - GOG-0229L: Fast Fact Sheet for Protocol 0229L (Endometrium)

- 9/17/21 - 1 form, 3 itemgroups, 88 items, 1 language
Itemgroups: Patient Information, Eligibility 1, Provide comments about this Fast Fact Sheet
GOG-0229L: Fast Fact Sheet for Protocol 0229L (Endometrium) AMG 386 in Treating Patients With Persistent or Recurrent Endometrial Cancer Source Form: NCI FormBuilder: https://formbuilder.nci.nih.gov/FormBuilder/formDetailsAction.do?method=getFormDetails&formIdSeq=9A223983-7B94-E221-E040-BB89AD437E30

Endometrial Cancer NCT00265759 Registration - ACOSOG-Z1031 OPEN Registration Worksheet - 3014513v1.0 - ACOSOG-Z1031 OPEN Registration Worksheet

- 9/17/21 - 1 form, 6 itemgroups, 45 items, 1 language
Itemgroups: Header Module, Demography Section, General Information, Inclusion Criteria, Exclusion Criteria, Treatment Arm
ACOSOG-Z1031 OPEN Registration Worksheet Exemestane, Letrozole, or Anastrozole in Treating Postmenopausal Women Who Are Undergoing Surgery for Stage II or Stage III Breast Cancer Source Form: NCI FormBuilder: https://formbuilder.nci.nih.gov/FormBuilder/formDetailsAction.do?method=getFormDetails&formIdSeq=8036B060-D675-EB4B-E040-BB89AD434531

Endometrial Cancer NCT01225887 Pre-Study - GOG-0229K: Fast Fact Sheet for Protocol 0229-K (Endometrium) - 3183206v1.0 - GOG-0229K: Fast Fact Sheet for Protocol 0229-K (Endometrium)

- 9/17/21 - 1 form, 3 itemgroups, 91 items, 1 language
Itemgroups: Patient Information, Eligibility 1, Provide comments about this Fast Fact Sheet
GOG-0229K: Fast Fact Sheet for Protocol 0229-K (Endometrium) BIBF 1120 in Treating Patients With Recurrent or Persistent Endometrial Cancer Source Form: NCI FormBuilder: https://formbuilder.nci.nih.gov/FormBuilder/formDetailsAction.do?method=getFormDetails&formIdSeq=99D51BE9-A450-39B5-E040-BB89AD43255D

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