Search Results - EGA European Genome-Phenome Archive

Bulk ATAC and RNA Sequencing of Human Breast Cancer Metastasis Samples

Bulk RNA-Seq and ATAC-Seq were performed on a number of matched primary breast and metastatic lung/liver tissues; in addition, non-matched metastases and primaries were also sequenced. The goal of this study is to better understand the role that regulatory elements, such as enhancers, play in metastatic breast cancer.

Study phs003363

CIDR: Understanding the Increased Risk of Childhood Acute Lymphoblastic Leukemia in Latinos

This study aims to investigate the genetic contribution to the increased risk of acute lymphoblastic leukemia (ALL) in children of Hispanic/Latino ethnicity. Genome-wide single nucleotide polymorphism (SNP) genotyping was performed on childhood ALL cases and controls of self-reported Hispanic/Latino ethnicity from two studies: 1) the California Childhood Leukemia Study (CCLS), and 2) the Mexican Interinstitutional Group for the Identification of the Causes of Childhood Leukemia (MIGICCL). This study will provide genome-wide SNP array data from Hispanic/Latino children, contributing to studies of the genetic etiology of childhood ALL and cancer health disparities. It will also provide data from childhood ALL cases and controls from a Hispanic/Latino population outside of the United States (i.e., Mexico). Genetic data were generated by the Center for Inherited Disease Research. Samples were genotyped using the Illumina Global Diversity Array GDA-8v1-0. Individual level genotype data will be available through dbGaP. Note that for a small number of genotyped cases in the MIGICCL study, it was later found that these were not ALL cases but were either acute myeloid leukemia (AML) or non-acute leukemia. Additional available data include demographic and birth-related variables, and patient-related data including age-at-diagnosis and leukemia immunophenotype and molecular subtypes.

Study phs003953

Testicular Cancer Consortium WES

We have leveraged our previous collaborative research to better understand the genetic underpinnings of testicular germ cell tumor (TGCT), and have completed whole exome sequencing on the DNA of patients at high risk for TGCT. Specifically, we conducted a study of high-risk individuals using data from Penn Medicine and the NCI. We collected germline DNA from blood or saliva samples from men with bilateral TGCT, and a family history consisting of at least one first to third degree relative diagnosed with the disease. The goal of the study was to identify coding genomic variation associated with predisposition to TGCT. Whole exome sequencing and gene burden analyses were performed on 293 men with a family history of TGCT or bilateral disease. 228 unique families were represented in this sample. Our results found a missense variant in the hinge domain of proto-oncogene PIM1. Several more candidates were identified via gene burden association, including loss-of-function variants in NIN and QRSL1. We also identified an association with variants in CFTR using gene-specific analysis. There was no association with sex and germ cell development pathways or regions identified by GWAS previously. We identified associations with three major pathways including, mitosis/cell cycle, co-translational protein targeting, and sex differentiation. Our results showed associations with variants in several genes, which suggests a multigenic heritability. We also found potential association with CFTR, co-translational protein targeting, and chromosomal segregation in sex determination. Our results suggest potential drug targets for TGCT prevention or treatment, e.g., PIM1, and the co-translational targeting pathway. To our knowledge, our study is the largest to date of men with high risk TGCT.

Study phs003107

Uncovering Colorectal Cancer Etiology and Biology by Integrating Proteomics with Other Omics Data

This study included the expression profiling of approximately 10,000 proteins generated in normal colon tissue samples collected from 323 participants of European descent, paired with genome-wide genotype data obtained from blood samples. Using these proteomics and genotype datasets, we developed genetically prediction models for protein expression and conducted a proteome-wide association study (PWAS) of colorectal cancer (CRC) in European populations to identify proteins associated with CRC risk.

Study phs004089

MP2PRT: Discovering Biomarkers of Outcome: EBV DNA Quantification and the Relationship of EBV and LINE1 Retrotransposon Expression in Pediatric Patients With Nasopharyngeal Carcinoma (NPC) Enrolled on ARAR0331

Nasopharyngeal carcinoma (NPC) is a malignant neoplasm of epithelial cells. Plasma Epstein-Barr Virus (pEBV) DNA levels have been found to correlate with treatment response and survival in both pediatric and adult NPC. A completed Children's Oncology Group (COG) clinical trial, ARAR0331, treated pediatric NPC patients with induction chemotherapy followed by chemoradiotherapy with excellent survival. In this study, >95% of patients had EBV positive tumors. As a secondary objective of ARAR0331, plasma was collected at multiple time points throughout therapy to evaluate pEBV, but the analysis had not been completed as part of ARAR0331. ARAR0331 showed a higher proportion of adolescents and more Black patients, compared to White or Asian, providing a unique opportunity to compare racial subgroups. Unfortunately, patients treated on ARAR0331 had significant morbidity from treatment toxicity. Therefore, the next clinical trial will be aimed at reducing this toxicity. Discovering biomarkers of outcome is critical to correctly assigning patients to treatment groups. With support from the Cancer Moonshot Molecular Profiling to Predict Response to Treatment (MP2PRT) program, our primary analyses evaluated use of pEBV to predict outcomes or response to treatment using specimens from ARAR0331. In secondary analyses, we are evaluating EBV RNA expression using RNA in situ hybridization and LINE1 retrotransposon using immunohistochemistry. We are analyzing tumor mutations and investigation of L1TD1 and EBV insertion via whole genome sequencing (WGS). We also processed tumor specimens using single nuclei sequencing, RNA exome and multiplex immunofluorescence to evaluate immune response and spatial relationships of immune and tumor cells. Understanding NPC tumors and their immune microenvironment will help us improve future clinical trials.

Study phs003092

Reduction of Lethal Prostate Cancer Disparities in Underserved Hispanic/Latino Populations

This pilot study investigated the genomic underpinnings of prostate cancer in Puerto Rican Hispanic/Latino men, a group disproportionately affected by this disease, in terms of incidence, mortality and aggressiveness. By examining tumors from 35 patients for specific genetic mutations and gene expression patterns using cutting-edge genomic sequencing, we aimed to identify distinct genetic profiles that could influence the course of the disease and its treatment. Our initial findings suggest the presence of unique genomic characteristics in this population, offering a promising avenue for developing personalized treatments that could reduce the health disparities observed in these men. This study underscores the importance of including diverse ethnic groups in genomic studies to ensure that the published data required for personalized cancer care are available.

Study phs004487

Investigations of Genetic Variation in Families Affected by MUTYH-Associated Polyposis

Defects in the Base-Excision Repair gene, MUTYH, are known to increase colorectal cancer risk through a recessive Mendelian pattern and raise mutation rates in both normal somatic and germline mammalian cells. In this study, we employed whole genome sequencing (WGS) of fifteen human individuals (representing 4 related families) at 50X coverage to examine germline de novo mutation rates in a large family with pathogenic MUTYH mutations and a history of colorectal cancer. We used an in vitro cell line assay to determine the family's genotype (p. Y179C/V234M, transcript NM_001128425) partially attenuates MUTYH's function. The children of mothers affected by the biallelic pathogenic genotype were associated with a moderate increase in the C>A mutation rate, but this effect was determined to be lower than previously reported mutator effects for other biallelic pathogenic MUTYH genotypes. No similar mutation rate increase was found in children of fathers with the same genotype despite calculating that we should have adequate power to detect such a mutator effect, indicating that MUTYH's role in repairing oxidative stress might be more significant in female reproductive aging than in males. We used a combination of in vitro cell line assays and bioinformatics pipelines to assess the impact of the MUTYH genotype on germline mutation rates. The study design ensures that sufficient statistical power was available to detect mutator effects in both maternal and paternal lineages. The sequencing data generated from this study include single sample genotype files derived from WGS, focusing on germline DNA. The phenotypic data at individual level and sequence data can be accessed by authorized users, facilitating further exploration of the relationship between MUTYH pathogenic variants and colorectal cancer risk.

Study phs003554

HINTS Geo-Coded Data 2019 (HINTS 5 Cycle 3)

The Health Information National Trends Survey (HINTS) is a nationally representative survey which has been administered every few years by the National Cancer Institute since 2003. HINTS 5 includes four mail-mode data collection cycles over the course of four years. The third round of data collection for HINTS 5 (Cycle 3) was conducted from January 22 to April 30, 2019 with a goal of obtaining 3,500 completed questionnaires. A push-to-web pilot test was conducted alongside the fielding of Cycle 3 (referred to as the Web Pilot). The Web Pilot was conducted from January 29 to May 7, 2019 with a goal of obtaining 2,046 additional completed questionnaires. A total of 5,438 respondents are included in the final sample.

Study phs004216

A Phase Ib Study of Sapacitabine and Olaparib in Patients With BRCA1/2-Mutated (BRCA1/2m) Metastatic Breast Cancer

PARP inhibitors significantly extend progression-free survival (PFS), compared to chemotherapy in patients with germline BRCA1/2 (gBRCA1/2)-mutated HER2-negative metastatic breast cancer, but responses are not durable. Preclinical studies suggest that sapacitabine, an oral nucleoside analog, is synergistic with PARP inhibition in cell lines harboring homologous recombination repair (HRR) defects. To translate these findings, this phase Ib study combining sapacitabine and olaparib enrolled ten patients with gBRCA1/2-mutated HER2-negative metastatic breast cancer. The recommended phase 2 dose was not determined due to hematological toxicities, mainly neutropenia and anemia. Archival tumors from responders demonstrated evidence of HRR deficiency or of high replication stress. At progression, BRCA1/2 reversion mutations associated with a microhomology-mediated end-joining (MMEJ) signature and other acquired putative non-reversion mechanisms of resistance were identified. The median PFS observed of 9.7 months, with three patients experiencing clinical benefit greater than 15 months, suggests that the addition of sapacitabine to PARP inhibition merits further investigation.

Study phs004095

Randomized Phase 2 Study of Neoadjuvant Chemotherapy, Carboplatin and Paclitaxel, with or without Atezolizumab in Triple Negative Breast Cancer (TNBC)

This phase II trial studies how well carboplatin and paclitaxel, with or without atezolizumab, before surgery works in treating patients with newly diagnosed, stage II-III triple negative breast cancer. Immunotherapy with monoclonal antibodies, such as atezolizumab, may help the body's immune system attack the cancer, and may interfere with the ability of tumor cells to grow and spread. Drugs used in chemotherapy, such as carboplatin and paclitaxel, work in different ways to stop the growth of tumor cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. Giving carboplatin and paclitaxel with or without atezolizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed.

Study phs003296

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