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• NCTN: Treatment of Children with All Stages of Hepatoblastoma with Temsirolimus (NSC#683864) Added to High Risk Stratum Treatment (AHEP0731)

  Study ID: AHEP0731 NCT Number: NCT00980460Children's Oncology Group (COG) Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: Treatment of Children with All Stages of Hepatoblastoma with Temsirolimus (NSC#683864) Added to High Risk Stratum Treatment (AHEP0731)Trial Description: This phase III trial studies the side effects and how well risk-based therapy works in treating younger patients with newly diagnosed liver cancer. Surgery, chemotherapy drugs (cancer fighting medicines), and when necessary, liver transplant, are the main current treatments for hepatoblastoma. The stage of the cancer is one factor used to decide the best treatment. Treating patients according to the risk group they are in may help get rid of the cancer, keep it from coming back, and decrease the side effects of chemotherapy. Clinical data presented in the following publication(s): PMID 28211941PMID 30975630 PMID 34762296PMID 35810020PMID 37073741Disease type(s): Gastrointestinal Neoplasm - Liver and Hepatobiliary Cancer Clinical Dataset(s) included: • NCT00980460-D1 (PMID 28211941): There are three datasets (-D1 through -D3) for the AHEP0731 publication 28211941, reporting on the high-risk cohort who received Vincristine and Irinotecan. This dataset provides the information for baseline characteristics, PRETEXT grouping, surgery details, changes in AFP levels, response, relapse site, and surgical outcome plus event-free and overall survival for all evaluable patients as reported in the manuscript. Information is only provided for evaluable patients (analysiset = 1). Variables were left blank for the patients who were not evaluable (analysiset = 0). There is one row per patient. NCT00980460-D2 and -D3 contain toxicity data for this high-risk cohort. • NCT00980460-D2 (PMID 28211941): There are three datasets (-D1 through -D3) for the AHEP0731 publication 28211941, reporting on the high-risk cohort who received Vincristine and Irinotecan. This dataset provides the information for the specific toxicities that occurred during cycles 1 through 10 for evaluable patients. Evaluable patients are defined in NCT00980460-D1 (analysiset = 1). There are multiple rows per patient depending on whether they had multiple cycles submitted. NCT00980460-D1 contains baseline characteristics and outcome data and NCT00980460-D3 contains nausea and neuropathy toxicity events for this high-risk cohort. • NCT00980460-D3 (PMID 28211941): There are three datasets (-D1 through -D3) for the AHEP0731 publication 28211941, reporting on the high-risk cohort who received Vincristine and Irinotecan. This dataset provides the information for nausea and neuropathy that occurred during cycles 1 and 2 for evaluable patients. Evaluable patients are defined in NCT00980460-D1 (analysiset = 1). There is one row per patient. NCT00980460-D1 contains baseline characteristics and outcome data and NCT00980460-D2 contains toxicities from cycles 1 through 10 for this high-risk cohort. • NCT00980460-D4 (PMID 30975630): There are two datasets (-D4 and -D5) for the AHEP0731 publication 30975630, reporting on the low-risk cohort. This dataset provides the information for eligibility, baseline characteristics, disease stage, PRETEXT grouping, surgery details, changes in AFP levels, surgical outcome event-free survival, and overall survival. Information is only provided for eligible patients (analysis01 = 1). There is one row per patient. NCT00980460-D5 contains toxicity data for the low-risk cohort. • NCT00980460-D5 (PMID 30975630): There are two datasets (-D4 and -D5) for the AHEP0731 publication 30975630, reporting on the low-risk cohort. This dataset provides the information for the specific toxicities that occurred during protocol therapy. Evaluable patients are defined in NCT00980460-D4 (analysis01 = 1). There is one row per patient/toxicity term. Each row has the maximum grade of the particular toxicity term observed during the patient's protocol treatment. NCT00980460-D4 contains baseline characteristics and outcome data for the low-risk cohort. • NCT00980460-D6 (PMID 34762296): There are three datasets (-D6 through -D8) for the AHEP0731 publication 34762296, reporting on the intermediate-risk cohort. This dataset provides the information for all intermediate-risk patients who were enrolled on AHEP0731, up to 02/10/2020, both eligible and ineligible. It contains data presented in Figure 1 (the consort diagram), Figure 2 (Event-Free and Overall Survival of Patients with Unresectable non-Metastatic Hepatoblastoma), Table 1 (Patient Demographics for Patients with Intermediate-risk Hepatoblastoma), and the baseline characteristics, relapse sites, PRETEXT grouping, changes in AFP levels, surgery type, and evaluability for toxicity analyses. There is one row per patient. There are 105 patients in this dataset. NCT00980460-D7 contains mean percentage of target dose delivered data and NCT00980460-D8 contains toxicity data for the intermediate-risk cohort. • NCT00980460-D7 (PMID 34762296): There are three datasets (-D6 through -D8) for the AHEP0731 publication 34762296, reporting on the intermediate-risk cohort. This dataset, NCT00980460-D7, provides the information for all eligible intermediate-risk patients enrolled on AHEP0731, up to 02/10/2020. It contains data on the mean percentage of the target dose delivered for chemotherapy. There are 195 observations in this dataset, multiple rows per patient, with proportion of target dose delivered for cisplatin, 5-FU, doxorubicin and vincristine. NCT00980460-D6 contains baseline characteristics and outcome data and NCT00980460-D8 contains toxicity data for the intermediate-risk cohort. • NCT00980460-D8 (PMID 34762296): There are three datasets (-D6 through -D8) for the AHEP0731 publication 34762296, reporting on the intermediate-risk cohort. This dataset, NCT00980460-D8, provides the information for adverse events recorded for all eligible intermediate-risk patients enrolled on AHEP0731, up to 02/10/2020. It contains data on Table 2 (Toxicities (Grade 3, 4, and 5) of Patients with Intermediate-risk Hepatoblastoma), and the information on adverse events and toxicities in the Results section of the manuscript. There are 723 observations, one for each toxicity type per patient per cycle, included in this dataset. The number of rows per patient is dependent on the number of adverse events submitted. NCT00980460-D6 contains baseline characteristics and outcome data and NCT00980460-D7 contains mean percentage of target dose delivered data for the intermediate-risk cohort. • NCT00980460-D9 (PMID 35810020): There is one dataset for the AHEP0731 publication 35810020, reporting on the very low-risk cohort. NCT00980460-D9 provides the information for the 8 very low-risk hepatoblastoma patients who were enrolled on AHEP0731. The dataset contains baseline characteristics, α-fetoprotein levels, pretext group, vascular involvement, surgical details and tumor histology from local and central review, as well as outcome data as reported in the manuscript. It is used to generate all the tables in the manuscript, (Table 1. Patient Characteristics for Children with Very Low-Risk Hepatoblastoma and Table 2. Clinical and Surgical Traits for Children with Very Low-Risk Hepatoblastoma), and Figure 2. Event-free Survival and Overall Survival of Patients with Very Low Risk Hepatoblastoma Resected at Diagnosis. There are 8 patients in this dataset. There is one row for each patient. • NCT00980460-D10 (PMID 37073741): There are two datasets (-D10 and -D11) for the AHEP0731 publication 37073741, reporting on the high-risk cohort who received Vincristine, Irinotecan, and Temsirolimus. This dataset, NCT00980460-10, provides the information of baseline characteristics, α-fetoprotein levels, α-fetoprotein and RECIST response, as well as details on recurrent disease, metastatic disease, and surgery for the 40 high-risk hepatoblastoma patients who were enrolled on AHEP0731. Tumor histologic information and pretext classification from central review are also included as well as outcome data as reported in the manuscript. It is used to generate Table 1. Characteristics of eligible patients with high-risk hepatoblastoma treated with upfront vincristine/irinotecan/temsirolimus window therapy, Table 2. Response of patients to upfront vincristine/irinotecan/temsirolimus window therapy, Table 3. Surgical outcomes for patients treated with vincristine/irinotecan/temsirolimus upfront window therapy, Figure 1. Alpha-fetoprotein (AFP) decline after two cycles of VIT (vincristine/irinotecan/temsirolimus) therapy, and Figure 2. Event-free and overall survival of patients with high-risk hepatoblastoma treated with VIT (vincristine/irinotecan/temsirolimus). There are 40 patients in this dataset. There is one row for each patient. NCT00980460-D11 contains toxicity data for this high-risk cohort. • NCT00980460-D11 (PMID 37073741): There are two datasets (-D10 and -D11) for the AHEP0731 publication 37073741, reporting on the high-risk cohort who received Vincristine, Irinotecan, and Temsirolimus. This dataset, NCT00980460-D11, provides all grade 3 and 4 adverse events while on protocol therapy for the 36 eligible high-risk hepatoblastoma patients enrolled on AHEP0731 (Supplemental Table 3. Selected Grade 3 and 4 Toxicities) as well as selected grade 3 and 4 adverse events while on protocol therapy (Table 4. Selected grade 3 and 4 toxicities for patients treated with vincristine/irinotecan/temsirolimus upfront window therapy followed by cisplatin/5-fluorouracil/vincristine/doxorubicin.). The number of rows per patient is dependent on the number of adverse events submitted. NCT00980460-D10 contains baseline characteristics and outcome data for this high-risk cohort. 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 phs004135

• The Vaginal Microbiome, Maternal Response, and Preterm Birth

  An estimated 13 million preterm births (PTBs) occur annually worldwide, and PTB is the single most significant contributing factor to neonatal morbidity and mortality. Mechanisms underlying PTB are unknown hampering development of effective prediction and prevention strategies. PTB is linked to local and distant infections and recent data suggests that vaginal bacterial microbiome early in pregnancy is associated with subsequent PTB. Viral infections behave differently during pregnancy, with common viral infections such as varicella and influenza causing much more severe disease during pregnancy and human papillomavirus, the causative virus in cervical cancer, associated with a 2-fold increased risk for PTB. However, comprehensive assessment of vaginal viral communities during pregnancy has not been performed. Lastly, although maternal inflammation is one of the leading triggers for PTB, the precise constellation of inflammatory signals is not known. We propose that examining microbial communities or host response alone is incomplete, but that their combination will lead to refined definitions of appropriate and inappropriate microbe-maternal biology and shed new light on the old problem of PTB. Our central hypothesis is that PTB can be estimated by a combination of three criteria: vaginal bacterial communities, vaginal eukaryotic viral communities, and maternal inflammatory response. We have an interdisciplinary team assembled including perinatologists, epidemiologists, virologists, and genomics informatics experts, leveraging the unique capabilities of The McDonnell Genome Institute at Washington University in St. Louis, a well-established pregnancy bio-specimen and clinical data infrastructure, and a high-PTB burdened racially diverse patient population to test this novel hypothesis. The aims of this project are: 1) to determine the ability of bacterial and viral communities in the vagina and their dynamics over time to predict PTB, and 2) to determine the ability of the host inflammatory response in the vagina in the context of microbial communities to predict PTB. The proposed research is innovative, for the first time, comprehensively characterizing the eukaryotic vaginal virome simultaneously with vaginal bacterial communities and longitudinally capturing the maternal response to these communities. We employ an efficient study design, a well-established research infrastructure, and renowned genome sequencing expertise to test a physiologically plausible but uninvestigated paradigm that bacterial and viral communities in concert with the maternal host response can predict PTB.

  Study phs003875

• A Translational, Pharmacodynamic and Pharmacokinetic Phase IB Clinical Study of Everolimus in Resectable Non-Small Cell Lung Cancer

  This phase IB clinical trial studied the pharmacodynamic changes induced by everolimus in patients with previously untreated, resectable non small cell lung cancer. Using a combination of in vivo and ex vivo assessments with FDG PET, immunohistochemistry and genomic assays, evidence of mTOR pathway perturbation was assessed in patients treated with everolimus, an allosteric mTOR inhibitor. Untreated patients served as controls for comparison. Key results from this work include a dose-dependent biologic effect of everolimus, signal of activity in RAS mutant tumors as well as near complete metabolic and pathologic response in a case of sarcomatoid lung cancer. These findings represent novel translational insights that can guide future development of mTOR inhibitors in lung cancer and other tumor types. Additionally, metabolic response and anatomic tumor shrinkage observed in a significant proportion of patients following a short of duration of therapy with everolimus suggests potential clinical utility of this agent in carefully-selected lung cancer patients.

  Study phs000829

• Health Information National Trends Survey-SEER (HINTS-SEER)

  HINTS-SEER is a cross-sectional survey that sampled cancer survivors from three different SEER cancer registries. Sampling frames of survivors from each registry were stratified by time since diagnosis and race/ethnicity, with non-malignant tumors and non-melanoma skin cancers excluded. Respondents who consented completed a self-administered questionnaire sent through the mail and resulted in a total sample of 1,234 respondents. The goal of HINTS-SEER was to better understand the communication needs and practices, information preferences, risk behaviors and cancer knowledge of cancer survivors using a modified version of the Health Information National Trends Survey (HINTS) specifically designed for cancers survivors. Demographic information on the survivors showed that over 60% of the sample was 10 or more years since diagnosis with the most common cancers being male reproductive (24.6%), female breast (23%) and melanoma (9.6%) and gastrointestinal (8.6%). De-identified data is available in SAS, SPSS, and STATA formats, as part of a data package that also includes a history document, methodology report, data analysis recommendations, and a codebook.

  Study phs004065

• Center for Common Disease Genomics (CCDG) - Cardiovascular: Multiethnic Cohort

  The genetic basis of cardiovascular disease in individuals of non-European ancestry remains largely unknown. Availability of ethnically diverse study populations is essential to investigate the underlying causes of disease.The National Human Genome Research Institute (NHGRI) has funded the Centers for Common Disease Genomics (CCDG), a collaborative large-scale genome sequencing effort to comprehensively identify rare risk and protective variants contributing to multiple common disease phenotypes and to better understand the general principles of genomic architecture underlying common, complex, inherited diseases. The Multiethnic Cohort (MEC) of the University of Hawaii Cancer Center and the University of Southern California comprises primarily five ethnic groups: Caucasians, Japanese Americans, Native Hawaiians, African Americans and Latinos. This study contains whole genome sequence data derived from participants in the MEC cohort identified as having early onset coronary artery disease.

  Study phs003499

• Proteogenomic Studies to Understand Mechanisms and Drivers of Resistance to Immunotherapies

  Immune checkpoint inhibitors (ICIs) targeting programmed death (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) produce durable responses in advanced cutaneous melanoma, yet reliable predictive biomarkers remain elusive. We performed a multi-cohort proteogenomic investigation of pre-treatment formalin-fixed paraffin-embedded (FFPE) biopsies from patients with metastatic cutaneous melanoma who later underwent either dual PD-1+CTLA-4 ICI therapy or PD-1 ICI monotherapy. Melanoma metastases of the lung, lymph node, and skin from the 3 cohorts were collected from 12 study sites in the United States, Europe, and Australia, comprising two separate PD-1+CTLA-4 ICI-treated discovery and validation cohorts ("Discovery Cohort" and "Validation Cohort 1", n=164 samples), and one PD-1 ICI monotherapy-treated validation cohort ("Validation Cohort 2", n=44 samples). Comprehensive genomic profiling was performed across the Discovery and two Validation Cohorts (across 180 individual samples) using Ribo-Erase total RNA sequencing (RNA-seq) (data generated for 173 samples), low-pass whole-genome sequencing (lpWGS) for the purpose of detecting somatic copy-number alterations (data generated for 177 samples), and a custom melanoma-focused targeted DNA sequencing panel (comprised of 86 genes, ~0.75Mb) designed to maximize the sensitivity of detecting recurrent and clinically actionable mutations (data generated for 175 samples). Pathway-level proteomic clustering identified three tumor subtypes; ICI-sensitive (immune-inflamed), ribosome-high (translationally active), and epithelial-mesenchymal transition (EMT)-like (stromal-enriched) that were reproducibly validated and showed significant PFS differences (p = 0.02–0.03) across cohorts. Subtype–outcome associations were consistent with previous immunotherapy datasets, with pooled hazard ratios ~0.5–0.8 for immune-enriched tumors. Additionally, we identified a 127-protein classifier that outperformed previously reported genomic signatures, suggesting that proteomic subtyping captured clinically relevant biology not accessible via genomics or transcriptomics alone. Our results identify potential new therapeutic vulnerabilities and lay the foundation for biomarker-driven patient stratification in combination ICI trials. Proteomic data will be made available through the National Cancer Institute's Proteomic Data Commons repository.

  Study phs004511

• A Therapeutic Vaccine for Fibrolamellar Hepatocellular Carcinoma

  Fibrolamellar hepatocellular carcinoma (FLC) is a rare form of liver cancer affecting 33 children and young adults that is driven by a chimeric protein, DNAJ-PKAc. We conducted a phase 1 clinical trial of a therapeutic vaccine targeting DNAJ-PKAc 38 (FLC-Vac), in combination with nivolumab and ipilimumab, in children and adults with advanced FLC. Among 16 patients enrolled, 12 completed the vaccine priming phase and were evaluable for both immunological and clinical endpoints. Grade 3 treatment-related adverse events were reported by six patients (37.5%). DNAJ43 PKAc-specific T cell responses were detected in 9/12 patients after treatment. In the subset of patients who completed the initial priming phase the disease control rate (DCR) was 75% (9/12), with three partial responses (25%). All patients with clinical responses also had DNAJ-PKAc specific T cell responses, from which we identified multiple class II-restricted T cell receptors (TCRs) with specificity for DNAJ-PKAc. Correlates of response included both functional neoantigen reactivity and changes in TCR repertoire features over time. Immune escape in two patients corresponded with immune exhaustion rather than neoantigen escape or HLA loss.

  Study phs003970

• NCTN: A Phase III Randomized Trial of Adjuvant Chemotherapy With or Without Bevacizumab for Patients With Completely Resected Stage IB (>= 4 cm) - IIIA Non-small Cell Lung Cancer (NSCLC) (E1505)

  Study ID: E1505NCT Number: NCT00324805ECOG-ACRIN Cancer Research Group Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: A Phase III Randomized Trial of Adjuvant Chemotherapy with or without Bevacizumab for Patients with Completely Resected Stage IB (>= 4 cm) - IIIA Non-small Cell Lung Cancer (NSCLC) (E1505) Trial Description: This randomized phase III trial studies chemotherapy and bevacizumab to see how well they work compared to chemotherapy alone in treating patients with stage IB, stage II, or stage IIIA non-small cell lung cancer that was removed by surgery. Drugs used in chemotherapy 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 more than one drug (combination chemotherapy) may kill more tumor cells. Monoclonal antibodies, such as bevacizumab, may interfere with the ability of tumor cells to grow and spread. Bevacizumab also may stop the growth of non-small cell lung cancer by blocking the growth of new blood vessels necessary for tumor growth. It is not yet known whether chemotherapy is more effective with or without bevacizumab in treating non-small cell lung cancer. Clinical data presented in the following publication(s): • PMID 29129443 Disease type(s): Lung, Mediastinal and Pleural Neoplasm - Non-Small Cell Lung Cancer Clinical dataset(s) included: • NCT00324805-D1 (PMID 29129443): There are four different datasets for PMID 29129443 (trial NCT00324805). This dataset, NCT00324805-D1, contains baseline characteristics, stratification factors, treatment, resection type, site of recurrence, and efficacy data. • NCT00324805-D2 (PMID 29129443): There are four different datasets for PMID 29129443 (trial NCT00324805). This dataset, NCT00324805-D2, contains grade 2 toxicity data presented in Table 2 of the manuscript. • NCT00324805-D3 (PMID 29129443): There are four different datasets for PMID 29129443 (trial NCT00324805). This dataset, NCT00324805-D3, contains grades 3-5 toxicity data presented in Table 3 of the manuscript. • NCT00324805-D4 (PMID 29129443): There are four different datasets for PMID 29129443 (trial NCT00324805). This dataset, NCT00324805-D4, contains worst grade toxicity information and can be used to derive the number of patients with worst degree 1/2 toxicities (bottom row of Table 2); and the worst degree grade 3-5 events in Table 3 and Supplement. 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 phs004246

• 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

• Evaluation of the Effects of Endocrine Therapy and Abemaciclib on Host and Tumor Immune Cell Repertoire/Function in Advanced ER+/HER2- Breast Cancer

  To characterize the advanced and metastatic breast tumor immune landscape and the impact of CDK4/6 inhibition on its composition and function, we used scRNA-seq to analyze tumor biopsies pre- and post- treatment with ET and the CDK4/6i, abemaciclib. Patients with ER+/HER2- advanced or metastatic breast cancer starting first- or second-line CDK4/6i with ET were enrolled in the “Impact of Endocrine Therapy and Abemaciclib on Host and Tumor Immune Cell Repertoire/Function in Advanced ER+/HER2-Breast Cancer” (NCT04352777) trial. For each patient, the same lesion was biopsied prior to treatment (T1 = baseline, pretreatment) and following four weeks of continuous abemaciclib and ET (T2 = 4 weeks post-treatment). A total of 26 pre- and post-treatment tumor biopsies from diverse sites (recurrent breast and bone, liver, and lymph node metastases) from 13 patients who had varying responses to treatment were analyzed. Following tissue dissociation, positive selection of CD45+ cells was used to enrich for tumor-infiltrating immune cells. We find that genes associated with interferon response are downregulated in T cell populations and genes associated with antigen presentation were upregulated in macrophages and dendritic cells following treatment. Raw single-cell sequencing data from the 10 patients that consented to data sharing will be made available through dbGaP.

  Study phs004470