Search Results - EGA European Genome-phenome Archive

Analysis of Epigenomes and Genome Topology in Colorectal Cancer

When diagnosing cancer, pathologists use nuclear morphology as a hallmark of tumor cells, but the topological changes linked to alterations in the shape of the nucleus were poorly understood. To uncover the molecular changes that occur in the 3D structure of cancer genomes, we integrated topological maps for colon tumors and normal colon tissues with epigenetic, transcriptional, and imaging data. We characterized tumor-associated changes in chromatin loops, topologically associated domains (TADs), and large-scale compartments. We found that chromatin loop rewiring contributes to oncogenic gene expression programs. Whereas TAD structures are largely stable, the spatial partitioning of the open and closed genome compartments is compromised in tumors and is accompanied by hypomethylation and histone mark rearrangements. We also identified a compartment that is reorganized in tumors and is at the interface between the canonical A and B compartments. Similar changes were evident in non-malignant cells that had accumulated excessive cellular divisions. Our analyses suggest that these compartment changes repress stemness and invasion programs while inducing immunity genes, and they may therefore restrain malignant progression.

Study phs002288

NCTN: A Randomized Phase III Post-operative Trial of Platinum Based Chemotherapy vs. Capecitabine in Patients with Residual Triple-Negative Basal-Like Breast Cancer following Neoadjuvant Chemotherapy (EA1131)

Study ID: EA1131 NCT Number: NCT02445391 ECOG-ACRIN Cancer Research Group Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: A Randomized Phase III Post-operative Trial of Platinum Based Chemotherapy vs. Capecitabine in Patients with Residual Triple-Negative Basal-Like Breast Cancer following Neoadjuvant Chemotherapy (EA1131) Trial Description: This randomized phase III trial studies how well cisplatin or carboplatin (platinum based chemotherapy) works compared to capecitabine in treating patients with remaining (residual) basal-like triple-negative breast cancer following chemotherapy after surgery (neoadjuvant). Drugs used in chemotherapy, such as cisplatin, carboplatin and capecitabine, 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. It is not yet known whether cisplatin or carboplatin is more effective than capecitabine in treating patients with residual triple negative basal-like breast cancer. Clinical data presented in the following publication(s): PMID 34092112 Disease type(s): Breast Neoplasm - Breast Cancer - Invasive Clinical dataset(s) included: NCT02445391-D1 (PMID 34092112): There are three datasets for PMID 34092112. This dataset, NCT02445391-D1, contains baseline characteristics, stratification factors, treatment, second primary cancer, cause of death and efficacy data. The data reflect the study database as of April 7, 2021. All patients who were randomized to one of the three arms were included in the database (NCT02445391-D1). Accrual was open to arm A (observation) and arm B (platinum) prior to Amendment #3, and accrual to arm A was permanently closed and accrual to arm C (capecitabine) was opened in Amendment #3. NCT02445391-D2 (PMID 34092112): There are three datasets for PMID 34092112. This dataset, NCT02445391-D2 contains data on dose modification. The data reflect the study database as of April 7, 2021. NCT02445391-D3 (PMID 34092112): There are three datasets for PMID 34092112. This dataset, NCT02445391-D3, contains toxicity data. The data reflect the study database as of April 7, 2021. All treatment-related AEs were included in the database, and only the worst degree was reported in the paper. You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

Study phs004236

Long-Read Sequencing of Ovarian Cancer Organoids

Two patient-derived organoids were derived from separate ascites fluid collections from a patient diagnosed with high-grade mullerian carcinoma, that could not be confidently subclassified based on the limited specimen. Long-read sequencing whole genome sequencing (WGS) was performed on the organoids, OC104 and OC109, using the Oxford Nanopore Technologies PromethION24 with V14 ligation kit. Information from genomic findings and further pathology on organoids suggests refining the diagnosis to mucinous ovarian carcinoma.

Study phs004795

Childhood Cancer Data Initiative (CCDI): Pediatric In Vivo Testing Program – Sarcomas and other Solid Tumors

The primary goal of this project involves the comprehensive molecular profiling of patient-derived xenograft (PDX) mouse tumor models. Molecular profiling of each PDX model will include whole exome sequencing (WES), RNAseq, MethylEPIC arrays, CytoSNP array, and DNA fingerprint for quality control. Limited clinical demographic data (e.g. diagnosis, disease site, disease status) will be obtained. This data can be utilized to validate PDX models with matched patient tumors and can be used to guide model selection for downstream preclinical drug testing.

Study phs003161

Childhood Cancer Data Initiative (CCDI): Integrating Longitudinal Clinical, Sociodemographic and Genomic Data into the NCCR

The goal of this study is to contribute clinical and genomic data from a large institutional cohort of pediatric cancer patients who had tumor genomic profiling between 2013 and 2019 at Dana-Farber/Boston Children's Hospital Cancer and Blood Disorders Center. Clinical data include demographics, diagnosis (classified according to the International Classification of Diseases for Oncology (ICD-O-3.2), stage, and biospecimen associated data. Tumors were sequenced with OncoPanel, a targeted next-generation DNA sequencing panel of up to 447 cancer genes for detection of single-nucleotide variants (SNV), insertions, and deletions, and copy number alterations (CNA), as well as selected intronic regions for up to 60 genes for the detection of structural variants (SV). This dataset includes a patient and sample identifier (GENIE ID) that can be used to link the genomic data included in this dataset to additional longitudinal clinical cancer data on a subset of patients that was submitted to the National Childhood Cancer Registry (NCCR).

Study phs002677

Whole Exome and RNA Sequencing of 22 Patient-Derived Xenografts from Estrogen Receptor-Positive Breast Cancers

We performed RNA and whole exome sequencing on 22 patient-derived xenografts (PDX) from estrogen receptor-positive (ER+) breast cancers, in the presence and absence of estradiol (E2) supplementation. Exome coverage across more than 3,500 clinically relevant genes that previously were covered below 20X (~2.72Mb) was achieved. On average, 11.2Gb of unique sequence data were generated with 95.3% of the bases in the exome design covered to 20x read depth or greater. RNA sequencing was generated from xenograft tumors. Between 50 and 85M total reads were performed. The average strand-specificity and rRNA rate was 98% and 1.5%, respectively. Transcripts for 17,000 to 27,087 genes were detected in these samples.

Study phs003324

NCTN: Randomized Phase III Study of Maintenance Therapy With Bevacizumab, Pemetrexed, or a Combination of Bevacizumab and Pemetrexed Following Carboplatin, Paclitaxel and Bevacizumab for Advanced Non-Squamous NSCLC (E5508)

Study ID: E5508NCT Number: NCT01107626ECOG-ACRIN Cancer Research Group Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: Randomized Phase III Study of Maintenance Therapy with Bevacizumab, Pemetrexed, or a Combination of Bevacizumab and Pemetrexed following Carboplatin, Paclitaxel and Bevacizumab for Advanced Non-Squamous NSCLC (E5508) Trial Description: RATIONALE: Drugs used in chemotherapy, such as paclitaxel and carboplatin, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Monoclonal antibodies, such as bevacizumab, can block tumor growth in different ways. Some block the ability of tumor cells to grow and spread. Others find tumor cells and help kill them or carry tumor-killing substances to them. Bevacizumab may also stop the growth of non-small cell lung cancer by blocking blood flow to the tumor. Pemetrexed disodium may stop the growth of tumor cells by blocking some enzymes needed for cell growth. It is not yet known whether giving bevacizumab or pemetrexed disodium alone or in combination is more effective in treating non-squamous non-small cell lung cancer. PURPOSE: This randomized phase III trial is studying bevacizumab and pemetrexed disodium alone or in combination after induction therapy to see how well they work in treating patients with advanced non-squamous non-small cell lung cancer. Clinical data presented in the following publication(s): PMID 31361535 Disease type(s): Lung, Mediastinal and Pleural Neoplasm - Non-Small Cell Lung Cancer Clinical dataset(s) included: NCT01107626-D1 (PMID 31361535): There are two different datasets for PMID 31361535 from trial E5508. This dataset, NCT01107626-D1, contains baseline characteristics, treatment assignment, prior treatment, metastatic sites and efficacy data. Pemetrexed or bevacizumab is used for maintenance therapy of advanced no squamous non-small cell lung cancer (NSCLC). The combination of bevacizumab and pemetrexed has also demonstrated efficacy. This study contains two step registration, induction therapy step and maintenance therapy. All patients who were registered to at least one of the steps are included. Due to data cleaning efforts, data may contain slight discrepancies from that reported in Table 1 and Table 2 in the publication (PMID 31361535). The number of each metastatic site is incorrect in the publication: The data in this dataset is correct.NCT01107626-D2 (PMID 31361535): There are two different datasets for PMID 31361535 from trial E5508. This dataset, NCT01107626-D2, contains toxicity data. Pemetrexed or bevacizumab is used for maintenance therapy of advanced no squamous non‐small cell lung cancer (NSCLC). The combination of bevacizumab and pemetrexed has also demonstrated efficacy. This study contains two step registration, induction therapy step and maintenance therapy. All patients who were registered to at least one of the steps are included.You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

Study phs004240

International Cancer Proteogenome Consortium (ICPC): Proteogenomics of Oral Squamous Cell Carcinoma in Taiwan

Oral cavity squamous cell carcinoma (OSCC) is the major subtype (~90%) of oral cancer, which is leading cancer with high mortality worldwide. The environmental risk factors associated with OSCC are quite different in Taiwan as compared to other populations. In most non-Taiwanese populations, OSCC is often associated with tobacco chewing, cigarette smoking, alcohol drinking, or human papillomavirus (HPV) infection. In Taiwan, in contrast, the OSCC occurs mainly in males aged 30 years or older who have habitual betel nut chewing, cigarette smoking, and alcohol drinking. To uncover molecular mechanisms and identify new therapeutic strategies of oral squamous cell carcinoma, this study recruited 112 treatment-naïve OSCC patients and generated multi-omics data, including WES, RNA-Seq, TMT-labeled proteomes, and phosphoproteomes from paired normal/tumor tissues. We have investigated our multi-omics data, covering molecular characterizations such as mutation signatures, impacts of mutations on RNA/protein/phosphoprotein, RNA-protein correlation, somatic copy number alteration, and the relationship with RNA & protein, proteome, and phosphoproteome analysis (T vs NAT), novel peptides (somatic variants, neoantigens, CT antigens, T cell receptors, etc.), as well as molecular subtyping (& pathway analysis). Notably, we have discovered a higher frequency of APOBEC3B deletion polymorphism in the Taiwanese population, and APOBEC3A is a potential prognostic biomarker. Our proteogenomic data enable us to further stratify patients into four groups based on APOBE3A expression level, which is found inversely correlated with EGFR expression. Therefore, the patients with high EGFR and low APOBEC3A expression may benefit from anti-EGFR therapy, while those with low EGFR and high APOBEC3A expression may benefit from immunotherapy. To clarify if there is an interaction between genetic polymorphisms and betel nut chewing habit in Taiwanese OSCC, we plan to concurrently evaluate the effect of habitual betel nut chewing on the gene mutation pattern, the dysregulated protein/phosphoproteins as novel biomarkers and/or therapeutic targets, and the molecular subtyping of patients for effective treatments. 

Study phs002580

Evolution of Structural Rearrangements in Prostate Cancer Intracranial Metastases

Intracranial metastases in prostate cancer are uncommon but clinically aggressive. We sought to characterize prostate cancer intracranial metastases in order to improve our understanding of their pathogenesis and to promote the search for new treatment strategies. We evaluated the clinical and molecular characteristics of 36 patients with metastatic prostate cancer to either the dura or brain parenchyma. We performed whole genome sequencing (WGS) on samples from 21 patients. The WGS samples include 10 intracranial prostate cancer metastases, as well as WGS of primary prostate tumors from men who later developed metastatic disease (n=6) and non-brain prostate cancer metastases (n=26).

Study phs003357

Genetic Factors Associated with Anthracycline-Induced Cardiomyopathy (COG-ALTE03N1)

We investigated the genetic mechanisms underlying anthracycline-induced cardiomyopathy, a serious long-term complication among childhood cancer survivors. We focused on the role of DNA damage response and repair (DDR) genes, which had not been previously studied in this context. A gene-based and pathway-based approach was applied to assess both the main effects and gene-by-anthracycline interaction effects of DDR genes on cardiomyopathy risk. The analysis was conducted using a matched case-control design within the COG-ALTE03N1 study, including 113 cases and 226 controls, all of whom were non-Hispanic White childhood cancer survivors exposed to anthracyclines. For each case, we randomly selected 1-3 childhood cancer survivors with no cardiomyopathy, matched on primary cancer diagnosis, year of diagnosis (±10y), and race/ethnicity. The selected controls had to have a longer duration of follow-up compared with time from cancer diagnosis to cardiomyopathy for the corresponding case. Participants provided blood or saliva for germline DNA isolation and genotyping. Genotyping was performed using Illumina HumanOmniExpress-12 v1.0 (709,358 SNPs) and IlluminaOmni5Exome-4 v1.3 arrays (4,293,368 SNPs), with merging of genotype data from the two arrays (683,781 overlapped SNPs) and quality control (QC) using PLINK. Of the 220 genes in the MD Anderson DDR gene website, 187 genes with 2,220 single nucleotide polymorphisms [SNPs] identified on our array data were included in the analyses. A total of 2,170 SNPs were retained in the final gene-based and pathway-based analysis in 339 anthracycline-exposed non-Hispanic White (NHW) patients (113 cases; 226 controls). Key findings included significant associations for FANCC and XRCC5 with cardiomyopathy risk (main effect), and a significant gene-environment interaction involving MGMT. The study also confirmed the involvement of DDR-related biological pathways through both genetic association and interaction analyses.Data Available Through dbGaP: • Genotype data (GWAS) for all study participants • Phenotype data: age at primary cancer diagnosis, sex, race/ethnicity, case-control status This dataset supports further research into genetic susceptibility to chemotherapy-induced adverse outcomes and enables cross-cohort comparisons in cardio-oncology.

Study phs003792

The Role of E2F4 in Controlling Resistance to Irinotecan (CPT-11) in Human Colon Cancer

This study reports the results of RNA sequencing (RNA-seq) experiments performed on three isogenic clones of the human HT29 colon cancer cell line, genetically engineered to achieve the selective inactivation of the adenovirus early 2 (E2) gene transcription factor 4 (E2F4) protein, a key functional component of the multimeric transcriptional repression complex known as the dimerization partner (DP), retinoblastoma-like (RB-like), E2F and multi-vulva class B (MuvB) complex (DREAM). In previous studies, we identified E2F4 as a key regulator of colorectal cancer (CRC) resistance to irinotecan (CPT-11), a cytotoxic agent that stands at the backbone of multiple chemotherapy regimens for the treatment of metastatic CRCs. The molecular mechanisms linking E2F4 to irinotecan resistance, however, remain poorly understood. The present study was designed to identify which genes are under the transcriptional control of E2F4, either at baseline or following exposure to SN38 (i.e., the active metabolite of irinotecan, generated in vivo by biotransformation in the liver) in order to clarify the role played by E2F4 in shaping colon cancer resistance to chemotherapy. The cell line used for this study (HT29) is aneuploid and contains three copies of the E2F4 gene, because of a trisomy of chromosome 16, where the E2F4 gene is located (Kawai et al., Genes, Chromosomes & Cancer, 34:1-8, 2002; PMID: 11921276). HT29 cells were infected with lentivirus vectors encoding for CRISPR/Cas9 constructs designed to selectively inactivate the E2F4 gene, using three distinct guide-RNAs (gRNAs), each targeting a different sequence within the proximal exons of the E2F4 gene (exon 1, exon 2). Lentivirus-infected cells were sub-cloned by single-cell fluorescence-activated cell sorting (FACS), based on the differential expression of a fluorescent reporter (EGFP) expressed in tandem with the gRNAs. Isogenic clones (EGFP+) were then screened to identify those with a tri-allelic knock-out, as revealed by both genetic sequencing of the E2F4 gene (revealing the presence of three distinct frameshift mutations) and Western blot (revealing complete loss of E2F4 protein expression). The study includes twelve (n=12) RNA-seq experiments, representative of 3 experimental replicates (i.e., three distinct isogenic clones of the HT29 cell line, each displaying complete loss of E2F4 expression) and 3 negative controls (i.e., three independent preparations of the parent HT29 cell line, infected with a lentivirus vector encoding for a non-targeting gRNA) exposed to 2 distinct in vitro cell culture conditions: a) treatment with SN38 resuspended in dimethyl sulfoxide (DMSO); or b) treatment with DMSO alone (negative control). The in vitro treatment regimen used for SN38 (32 nM, 24 hours) was designed so that the exposure to SN38 experienced in vitro by HT29 cells would mirror the exposure to SN38 experienced in vivo by malignant tissues, as measured, for example, in metastatic CRC patients receiving a standard dose of irinotecan (180 mg/m2) administered by intravenous infusion over 90 minutes (Deyme et al., Cancer Chemotherapy and Pharmacology, 88:247-258, 2021; PMID: 33912999).

Study phs003560

Proteogenomic Characterization Unveils Biomarkers Associated With Chemoresistance in Muscle Invasive Bladder Cancer

Cisplatin-based neoadjuvant chemotherapy (NAC) combined with radical cystectomy has been used as a standard of care for patients with clinically non-metastatic muscle invasive urothelial bladder cancer, but 40-50% patients will benefit from the treatment. Molecular subtypes of muscle invasive bladder cancer (MIBC) provide a possible biomarker roadmap that may help identify patients who may or may not respond to NAC. Recently, by integrating Mass Spectrometry-based proteomics, proteogenomic studies from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) have demonstrated the potential of this approach in prioritizing candidate driver genes and facilitating understanding of the chemotherapy resistance mechanisms. To demonstrate the proteogenomic workflow for investigating the mechanisms underlying chemotherapy resistance in MIBC, we conducted proteogenomic characterization of 46 pre- and 14 post- treatment tumors, including whole exome sequencing (WES), mRNA sequencing, Tandem Mass Tag (TMT)-proteomics, or TMT-phosphoproteomic. These samples were selected from an initial cohort of 143 MIBC tissues and filtered by tumor purity, clinical history, pathological response, and proteomic quality control metrics. The final cohort comprised samples from 53 patients, including 45 with both genomic and proteomic data and 8 with genomic data only.Our multi-omics-based clustering reveals subtypes associated with chemotherapy sensitivity. Protein abundance of a short isoform of ATAD1 and RAF family proteins were identified as biomarkers of chemosensitivity which highlights the importance of proteomics data. Integration of proteomic and phosphoproteomic data reveals Wnt signaling via GSK3B-S9 phosphorylation and the JAK/STAT pathway as potential targets to overcome chemoresistance. Correlations between PD-L1 and TROP-2/NECTIN-4 indicate an additive benefit of combination therapy targeting these proteins. Our data analysis clearly demonstrates that proteogenomic plays an important role in uncovering potential resistance mechanisms that operate only at protein and Post-Translational Modification (PTM) levels. Proteomics data can be accessed through PRIDE with ID PXD060290. RNA-seq and whole-exome sequencing (WES) FASTQ files are archived in the dbGaP database.

Study phs004049

Blood and Marrow Clinical Trials Network Trial of Non-Myeloablative Conditioning and Transplantation of Umbilical Cord Blood For Hematologic Malignancies (BMT CTN-0604-BioLINCC)

Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To examine the safety and effectiveness of a non-myeloablative stem cell transplant using umbilical cord blood as a treatment option for patients with leukemia or lymphoma and no suitable related donor.Background: Chemotherapy is a common treatment option for patients with aggressive forms of the blood cancers leukemia and lymphoma, but other treatment methods may need to be considered if the cancer does not respond well to chemotherapy, or if the cancer returns. In such cases, it may be recommended that the patient receive a stem cell transplant, commonly using donated bone marrow. A first degree relative is likely to be the best candidate for donation if the human leukocyte antigen (HLA) markers are a sufficient match. For patients lacking a HLA-matched related donor, it is routine to initiate an unrelated donor search. However some patients, particularly ethnic minorities, experience disease progression while awaiting identification of a suitably HLA-matched donor. Recently, stem cell transplants using umbilical cord blood have become a viable alternative option to treat these types of cancers.Typically patients undergoing a stem cell transplant receive high doses of chemotherapy before the transplant to prepare their bodies to accept the donor stem cells. In this study, participants received a type of stem cell transplant called a non-myeloablative transplant, which is a reduced intensity conditioning (RIC) method of transplantation that does not require high doses of chemotherapy. RIC can be preferable in patients that are older and less clinically fit, and therefore less able to withstand the chemotherapeutic agents' toxicity levels.The BMT CTN 0604 study was one of two parallel multicenter phase 2 studies; the other of which was BMT CTN 0603, which used partially HLA-mismatched related bone marrow (Haplo-marrow) transplantation. The goal of these studies was to generate pilot multicenter data to support a future phase 3 randomized clinical trial.Participants: Patients less than 71 years of age with acute leukemia or lymphoma and lacking a suitable HLA-matched related donor were eligible to participate. Patients less than 22 years of age were eligible if they were ineligible for the BMT CTN 0501 trial. Acute leukemia was required to be in morphologic complete remission. Large-cell, mantle-cell, and Hodgkin lymphomas were required to have achieved at least a partial remission with treatment before allogeneic hematopoietic cell transplantation. Low-grade lymphoma patients were required to have failed two prior chemotherapy regimens. Patients who had undergone prior autologous transplantation were not excluded as long as three months had elapsed since the procedure. Participants were also required to have adequate organ function, including a left ventricular ejection fraction of at least 35% and specific liver, kidney, pulmonary, and physical functioning scores within acceptable ranges. A total of 54 individuals were enrolled in the study and 50 were included in the analysis.Design: Participants underwent a reduced intensity conditioning regimen prior to receiving the double umbilical cord blood (dUCB) transplant, which included two chemotherapeutic agents, cyclophosphamide and fludarabine, and a small dose of radiation. Cyclophosphamide was administered intravenously at 50 mg/kg six days before the transplant. Fludarabine was administered intravenously at 40 mg/m2 (adjusted for creatinine clearance) each day for five days before the transplant. A single dose of 200 cGy total body irradiation was performed one day prior to transplantation. Participants also received cyclosporine and mycophenolate mofetil (MMF) beginning three days before the transplant as prophylaxis for graft-versus-host-disease (GVHD). Participants could receive tacrolimus instead of cyclosporine.At transplantation, patients received two partially HLA-matched umbilical cord blood units from unrelated donors. The maximum allowable mismatch between the UCB unit and the recipient, or between the UCB units, was 2 of 6 HLA loci. Each unit contained a minimum of 1.5 × 107 nucleated cells, or 2.0 × 107 for units that were not red cell depleted, per kilogram of recipient weight. Units were thawed and infused per institutional practice after validation using methods approved by the study. After transplantation, filgrastim, a granulocyte-colony stimulating factor, was initiated at 5 μg/kg a day and continued until the absolute neutrophil count was at least 2000/μL for three consecutive days. Participants continued to receive MMF for 30 days after the transplant or 7 days after engraftment, whichever was later, and cyclosporine or tacrolimus until 180 to 200 days after the transplant. Supportive care, including blood product administration, prophylaxis, therapy for infection, and treatment of GVHD, was at the discretion of treating physicians and transplantation center practices.The primary outcome was participant survival from the time of transplant to 180 days. Secondary end points included progression-free survival and cumulative incidences of hematopoietic recovery, acute or chronic GVHD, relapse, and non-relapse mortality.Conclusions: Survival at 180 days after double umbilical cord blood transplant was 74%. Collectively, the results of BMT CTN 0603 and 0604 confirm the utility of dUCB and Haplo-marrow as alternative donor sources for reduced intensity conditioning hematopoietic cell transplantation, providing a rationale for an additional clinical trial to assess the relative efficacy of these two strategies.

Study phs004890

A Phase II Study: CRS207/GVAX Plus Anti-PD1 and Anti-CTLA4 Recruits Mesothelin- and KRAS-Specific T cells into PDAC

This study examined immunologic correlatives from a phase II study evaluating CRS207/GVAX vaccines in combination with anti-PD1 and anti-CTLA4 in metastatic pancreatic cancer (NCT03190265). Arm A received CRS207/GVAX with anti-PD1 and anti-CTLA4 therapy; Arm B received CRS207 with anti-PD1 and anti-CTLA4 therapy. Patients undergoing treatment in this trial had peripheral blood mononuclear cells (PBMCs) and tumor tissue biopsied serially at pre-treatment and on-treatment timepoints. Single-cell RNA/TCR sequencing was employed on PBMCs. Bulk RNA/TCR sequencing was employed on tumor tissues. We identified treatment-enriched inflammatory pathways as well as T cell repertoires.

Study phs003798

Correlative Studies in Protocol GU16-287, which Studied Gemcitabine + (Carboplatin or Oxaliplatin) + Nivolumab in Metastatic Urothelial Cancer, which Included Collaboration with CIMAC-CIDC (Cohort 1 of 3)

Purpose: Oxaliplatin has demonstrated the ability to sensitize tumors to immune checkpoint blockade through its immunomodulatory properties in model systems of cancer. This randomized trial aimed to evaluate gemcitabine/oxaliplatin and gemcitabine/carboplatin, each combined with nivolumab, in cisplatin-ineligible metastatic urothelial carcinoma (mUC) patients. Patients and Methods: Cisplatin-ineligible patients with mUC were randomized 1:1 to gemcitabine/carboplatin plus nivolumab or gemcitabine/oxaliplatin plus nivolumab for up to 6 cycles, followed by nivolumab monotherapy. A pick-the-winner design was employed with objective response rate (ORR) as the primary endpoint. Secondary endpoints included progression-free survival (PFS) and overall survival (OS). Exploratory analyses evaluated plasma protein analytes, circulating immune cell populations, and circulating tumor cells. Results: Forty-nine patients were enrolled (carboplatin arm, N = 25; oxaliplatin arm, N = 24). The ORR was 69.6% (95% confidence interval [CI] 0.48–0.87) for the carboplatin arm and 33.3% (95% CI 0.15–0.57) for the oxaliplatin arm. Median OS was 24.74 months and 16.43 months for the carboplatin group and oxaliplatin arms, respectively (hazard ratio 1.99, 95% CI 0.94–4.22; p = 0.07). Exploratory biomarker analyses revealed sustained adaptive immune activation in the carboplatin arm and features suggestive of tumor-promoting inflammation in the oxaliplatin arm. Conclusions:Oxaliplatin-based chemo-immunotherapy, versus carboplatin-based chemo-immunotherapy, did not yield a higher response rate, challenging assumptions based on preclinical data.

Study phs004060

Durvalumab and Cediranib with and without Olaparib in Recurrent Ovarian Cancer: A phase II Proof-of-Concept Study

We report the efficacy and translational research findings of durvalumab, olaparib, and cediranib (D+O+C) and durvalumab and cediranib (D+C) therapies from the recurrent epithelial ovarian cancer (EOC) cohort within a single center, multi-arm, non-randomized, multi-cohort phase I/II trial (NCT02484404). Sixty-eight patients were enrolled (39 in D+O+C, 29 in D+C). The objective response rate (ORR) was 19.4% (95% CI, 9.5-43.5) for D+O+C and 29.6% (95% CI, 13.8-46.9) for D+C. Median progression-free survival (PFS) was 4.5 months in both arms, with each arm including four exceptional responders (PFS ≥ 12 months). Pre-treatment biopsies and paired normal peripheral blood mononuclear cells (PBMC) samples for whole exome sequencing (WES) were available for 31 patients in the D+O+C and 24 in the D+C, the remaining 13 patients were not biopsied due to safety concerns or being off treatment. WES was conducted to explore genomic profiles for potential correlations with clinical benefit (CB; partial response or stable disease [SD] with PFS ≥ 4 months) or no clinical benefit (NCB; progressive disease or SD with PFS TP53 mutations were found in most cases in both D+O+C and D+C arms. Overall, no consistent associations between baseline genomic alterations and CB were observed.

Study phs004519

NCTN: A Double Blind Randomization to Letrozole or Placebo for Women Previously Diagnosed with Primary Breast Cancer Completing Five Years of Adjuvant Aromatase Inhibitor either as Initial Therapy or after Tamoxifen (NCIC-MA.17R)

Study ID: NCIC-MA.17RNCT Number: NCT00754845 Canadian Cancer Trials Group (CCTG)Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Double Blind Randomization to Letrozole or Placebo for Women Previously Diagnosed with Primary Breast Cancer Completing Five Years of Adjuvant Aromatase Inhibitor either as Initial Therapy or after Tamoxifen (NCIC-MA.17R)Trial Description: RATIONALE: Estrogen can cause the growth of breast cancer cells. Hormone therapy using letrozole may fight breast cancer by lowering the amount of estrogen the body makes. It is not yet known whether letrozole is more effective than a placebo in treating in women with breast cancer who have already received 5 years of aromatase inhibitor therapy.PURPOSE: This randomized phase III trial is studying letrozole to see how well it works compared with a placebo in treating women with primary breast cancer who have received 5 years of aromatase inhibitor therapy. Clinical data presented in the following publication(s):PMID 27264120 Disease type(s): Breast Neoplasm - Breast Cancer - InvasiveClinical Dataset(s) included:NCT00754845-D1 (PMID 27264120): There is one dataset for NCIC-MA.17R's primary publication 27264120. This dataset contains number of major protocol violations, time from diagnosis to randomization, baseline characteristics, hormone receptor status, sites of recurrence, survival, toxicity, stratification factors, cause of death, and QOL data.You are encouraged to view the PDF data dictionaries found in the “Documents” tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

Study phs004248

Somatic Evolution in Li-Fraumeni Syndrome

In this study, we used ultradeep duplex sequencing (~15,000× depth) to measure somatic evolution in blood samples from a family of three individuals with Li-Fraumeni Syndrome (LFS) caused by an inherited TP53 pathogenic variant (p.R181H), and compared them to a cohort of unaffected controls using a set of genes related to Clonal Hematopoiesis of Indeterminate Potential (CHIP)/Acute Myeloid Leukemia (AML), as well as a mutagenesis panel designed to examine mutagenic processes. We found that individuals inheriting a single mutated copy of TP53 may experience less positive selection for subsequent TP53 mutations, as evidenced by a deficit of coding TP53 mutations, reduced dN/dS, and low predicted pathogenicity among the TP53 somatic mutations that do occur. However, the overall degree of mutagenesis in genomic regions without strong selection was higher in LFS patients. In addition, we investigated how LFS affects clonal evolution across multiple tissue contexts in one individual carrying p.R181H who succumbed to metastatic esophageal cancer.The data available through dbGaP includes BAM files, MAF files (mutation data), and genomic MUT files (showing per-position depth of sequencing), from ultradeep duplex sequencing of multiple tissues from a LFS patient as well blood samples from family members and controls.

Study phs004484

Prostate Cancer Upgrading Reference Set

This study aimed to investigate clinical, demographic, and molecular features of men diagnosed with low-risk prostate cancer [ISUP Grade Group 1 (GG1)] at biopsy who underwent radical prostatectomy, and for whom an increased tumor grade (ISUP Grade Group 2 or above) was subsequently detected in the resected prostate. This phenomenon is termed upgrading. In collaboration with the Early Detection Research Network (EDRN), a blinded reference set was established to facilitate upgrading biomarker detection and validation. A prospective, multi-institutional, cohort of men with the GG1 prostate cancer and intention to undergo prostatectomy was recruited. Biospecimens (blood, urine) were collected and this biorepository comprises the official EDRN Upgrading Reference Set (URS). Recording of case-control status (case = upgrading at prostatectomy, control = no upgrading at prostatectomy) was coordinated by the Data Management and Coordinating Center (DMCC) of the EDRN, who ensured blinding of all participating researchers. A subset of the reference set (n = 192) was chosen to undergo whole genome sequencing (WGS) for the investigation of a germline genomic biomarker of upgrading. Variant calls from all sequenced URS whole genomes are available through dbGaP, with the exception of one sample for which sequencing was not successful. Among investigated clinical features, prostate-specific antigen (PSA) density and percent of cancer in pre-prostatectomy positive biopsy cores were significantly associated with upgrading. Two polygenic risk score-based biomarkers were computed in the genetic sub-cohort and tested against case-control status. Neither was predictive of upgrading.

Study phs003670

Improved Cardiovascular Risk Reduction to Enhance Rural Primary Care (ICARE-BioLINCC)

Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To evaluate whether a centralized, remote clinical pharmacy service could improve guideline adherence and secondary measures of cardiovascular risk in primary care offices in rural and small communitiesBackground: More than 2200 Americans die of cardiovascular disease every day. Team-based care and medication therapy management have become useful strategies to reduce gaps in the delivery of guideline-concordant therapy for cardiovascular therapy. Physician offices, especially in rural and smaller communities, lack the resources to implement team-based care with pharmacists who can provide medication therapy management. The ICARE trial developed a physician-pharmacist collaborative model to provide virtual clinical pharmacy services from a central location to 12 family medicine offices in Iowa to evaluate whether a centralized, remote clinical pharmacy service could improve outcomes.Participants: Subject inclusion involved 3 separate processes. First, subjects were required to be an English-speaking male or female over the age of 50 who had been seen in the clinic/practice at least once in the past 24 months. Second, subjects were required to have at least one of the following conditions: uncontrolled diabetes (hemoglobin A1c > 7.5%); low-density lipoprotein cholesterol (LDL-C) > 110 mg/dl for patients with a history of peripheral artery disease, coronary artery disease, stroke, transient ischemic attack, or diabetes, elevated blood pressure with systolic BP ≥ 140 mmHg or diastolic BP ≥ 90 mmHg in persons with diabetes or chronic kidney disease, or systolic BP ≥ 150 mmHg or diastolic BP ≥ 90 mm Hg in persons with uncomplicated hypertension. Third, subjects were required to additionally have three or more of the following cardiovascular conditions or risk factors: history of myocardial infarction, coronary artery disease, stroke, transient ischemic attack, atrial fibrillation, peripheral vascular disease/claudication, current smoker, or obesity with BMI > 30.Exclusion criteria included diagnosis of primary pulmonary hypertension, a cancer diagnosis with a life expectancy of less than 2 years, residence in a nursing home or diagnosis of dementia, no telephone access or a hearing impairment that prevented telephone use, or patient had plans to move from the area or transfer care to a different clinic in the next 12 months.In total, there were 302 subjects enrolled in the ICARE trial. Of these, 259 subjects completed the 12-month visit.Design: The study included 11 private physician offices and one Federally Qualified Health Center. Offices were identified from the Iowa Research Network and screened for their ability to conduct the trial, enroll subjects, and meet quality control measures. A Study Coordinator employed in each office identified, screened, and recruited subjects. All subjects and physicians in a given office received either the intervention or usual care.Blood pressure, hemoglobin A1c, and LDL cholesterol were collected at baseline and 12 months regardless of whether the subject had a diagnosis of hypertension, diabetes, or hyperlipidemia. Baseline data were collected on case report forms by Study Coordinators and entered centrally by the research team.Three clinical pharmacy specialists located within the research offices of the principal investigator provided the intervention. Pharmacists were required to have a Doctor of Pharmacy degree and a minimum of one year of clinical residency (or equivalent practice experience). The pharmacists travelled to each intervention office to be introduced to the providers and facilitate team-building before the intervention started. These sessions explored the providers' preferred methods and frequency of communication with the pharmacists based on other telemedicine studies. Pharmacists had access to the baseline data, including BP and laboratory values, which they used to reconcile medications and update the medical records. Pharmacists monitored blood glucose values, BP readings, laboratory values, and potential adverse events from the EMR or from the patient in order to recommend medication changes to the treating medical provider. Interventions for physicians were directed at improving guideline adherence for reducing CV risk and preventive care based on the Guideline Advantage (GA) criteria.Each subject was assigned to one of the three pharmacists to maintain continuity. Subjects were assigned to the pharmacists in the order they were enrolled into the study, independent of medical office. Subjects were primarily contacted by telephone and counseled by the pharmacists about beneficial health behavior changes related to tobacco use, diet, physical activity, and alcohol consumption. Medications and dosages were reconciled. The pharmacists identified problems related to poor disease control, subject misunderstandings, poor medication adherence or failure to receive preventive health services, adverse effects, drug interactions, and cost. Pharmacists provided patient education when problems were identified and developed a plan for follow-up contacts, generally every 1-2 weeks by telephone if there were continuing problems or medication issues. The primary outcome measure was adherence to the GA criteria.Conclusions: There was no improvement in the GA score from baseline to 12 months in the control group. There was a statistically significant improvement in the intervention group in the GA score plus several criteria were significantly better for intervention subjects including appropriate statin therapy, body mass index (BMI) screening and alcohol screening. Only 13.7% of subjects with diabetes had hemoglobin A1c at goal at baseline and this increased to 30.8% and 21.0% in the intervention and control groups, respectively, at 12 months.The improvements in outcomes were modest and not statistically significant, due to higher-than-anticipated baseline guideline adherence and greater inter-office variability than anticipated.

Study phs004679

Epigenomics of Neurocognitive Function in Breast Cancer

This study harnessed the data and biospecimens from the Exercise Program in Cancer and Cognition (EPICC) study (parent study) that collected data on cognitive function, demographics, other symptoms and biospecimens at two time points (T1: enrollment, T2: six months later) within the context of a six-month randomized controlled trial of a moderate intensity aerobic exercise intervention. This study collected genome wide DNA methylation data from T1 and T2 and conducted epigenome-wide association-based analyses to find genes and biological pathways explaining variability in cognitive function and explaining how exercise mitigates cognitive decline. Our initial findings identified cg10331779 near CTNND2 (p-value=9.65×10-9) associated with processing speed and cg25906741 in MLIP (p-value=2.01×10-8) associated with subjectively measured cognitive function. Additionally, differentially methylated regions were identified near SLC6A11, PRKG1/CSTF2T, and FAM3B for processing speed and near PI4KB and SGCE/PEG10 for mental flexibility.

Study phs003959

Human GPR15 Deficiency Reveals CD8+ T Regulatory Cell-Macrophage Crosstalk in Intestinal Inflammation

Inflammatory bowel disease (IBD) causes lifelong suffering from gastrointestinal inflammation and dysfunction with severe complications including colon cancer. The disease is increasing in global prevalence, and current therapies are insufficient, highlighting an urgent need to understand its pathogenic mechanism. We reported multiple patients with GPR15 deficiency which result in severe early-onset IBD. GPR15, a G protein-coupled receptor (GPCR), expressed in immune cells and previously described as an entry co-factor for human and simian immunodeficiency viruses, is a crucial marker and homing receptor for a unique subset of intramucosal GPR15-guided regulatory CD8+ T lymphocytes (CD8+ TIGR). These cells potently kill macrophages that become aggressively activated in response to intestinal damage or disease. Thus, our identification of CD8+ TIGR cells yields new insights into organ-specific immune regulation and potential treatment strategies for IBD.

Study phs003950

Combined PDCD1, BRAF and MAP2K7 Inhibition in BRAFV600E Colorectal Cancer: A Phase 2 Trial

In this study, we evaluated the clinical efficacy of combined PDCD1, BRAF, and MAP2K7 inhibition in metastatic BRAFV600E Colorectal Cancer (CRC) patients (NCT03668431). We performed bulk whole exome sequencing (WXS) and bulk RNA sequencing (RNA-Seq) in 35 pre-treatment tumor biopsies and matching germline for tumor mutational burden (TMB), BM1/BM2 transcriptional subtypes, and consensus molecular subtypes (CMS) analysis, which were previously reported to affect prognosis and response to therapy (PMIDs: 32047001, 27354468, and 26457756). Analysis of bulk data showed that TMB, BM1/BM2 subtypes, and CMS did not correlate with clinical response in this study. Analysis of single cell RNA sequencing (scRNA-Seq) data of tumor epithelial cells from 23 paired day 0 and day 15 tumor biopsies revealed greater induction of tumor cell-intrinsic immune programs and more complete MAPK inhibition in patients with better clinical outcome.

Study phs003178

Childhood Cancer Data Initiative (CCDI): Single-Cell Atlas of NF1 Nerve Sheath Tumors

The worst outcome of NF1 is the development of the aggressive and highly metastatic malignant peripheral nerve sheath tumors (MPNST), which transform from benign plexiform neurofibroma (PN) and lack effective treatment. In this study, we performed single-cell RNA sequencing of 63 clinically annotated NF1-associated peripheral nerve sheath tumors, including 24 PN, 34 premalignant atypical neurofibromas, and 5 MPNSTs. These results improve the ability of identifying high-risk neurofibromas and provide a unique opportunity for early detection of MPNST.

Study phs003519

Single Cell RNA-Sequencing of BCG Naive and Recurrent Non-Muscle Invasive Bladder Cancer Reveals a CD6/ALCAM-Mediated Immune-Suppressive Pathway

Non-muscle invasive bladder cancer (NMIBC) represents 70–80% patients with newly diagnosed bladder cancer, and Bacillus Calmette-Guerin (BCG) remains a cornerstone treatment for intermediate- and high-risk NMIBC to prevent disease recurrence and progression. However, a significant number of patients experience recurrence after their first course of BCG, posing significant challenges in the management of the disease. We conducted single cell RNA sequencing (scRNA-Seq) on freshly collected NMIBC samples, distinguishing between those naive to BCG treatment and those that recurred post-BCG treatment. We observed a clear activation of inflammatory pathways across cell types during recurrence, but these were not associated with canonical immune checkpoint or T cell exhaustion phenotypes. Analysis of cell-to-cell communication revealed enhanced interactions between T cells and urothelial cells in BCG-recurrence, predominantly modulated by CD6 and activated leukocyte cell adhesion molecule (ALCAM). Furthermore, we found CD6hi T cells to be immunosuppressed and enriched in recurrent samples, suggesting a potential role for CD6 as an immune evasion signal in NMIBC.

Study phs003742

6048 results for "canc*"

in 37.92 milliseconds.