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• NCTN: A Phase 1/2 Study of CPX-351 (NSC# 775341) Alone followed by Fludarabine, Cytarabine, and G-CSF (FLAG) for Children with Relapsed Acute Myeloid Leukemia (AML) (AAML1421)

  Study ID: AAML1421NCT Number: NCT02642965 Children's Oncology Group (COG)Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Phase 1/2 Study of CPX-351 (NSC# 775341) Alone followed by Fludarabine, Cytarabine, and G-CSF (FLAG) for Children with Relapsed Acute Myeloid Leukemia (AML) (AAML1421)Trial Description: This phase I/II trial studies the side effects and best dose of liposome-encapsulated daunorubicin-cytarabine when given with fludarabine phosphate, cytarabine, and filgrastim and to see how well they work in treating younger patients with acute myeloid leukemia that has come back after treatment (relapsed) or is not responding to treatment (is refractory). Liposome-encapsulated daunorubicin-cytarabine is made up of two chemotherapy drugs, cytarabine and daunorubicin hydrochloride, and works to stop cancer cell growth by blocking the cells from dividing. Drugs used in chemotherapy, such as fludarabine phosphate and cytarabine, work in different ways to stop the growth of cancer cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. Filgrastim may increase the production of blood cells and may help the immune system recover from the side effects of chemotherapy. Giving liposome-encapsulated daunorubicin-cytarabine followed by fludarabine phosphate, cytarabine, and filgrastim may be a better treatment for patients with relapsed acute myeloid leukemia and may cause fewer side effects to the heart, a common effect of other chemotherapy treatments for acute myeloid leukemia. Clinical data presented in the following publication(s): PMID 32401633 Disease type(s): Hematopoietic Neoplasm/Leukemia - Acute Myeloid LeukemiaClinical Dataset(s) included: NCT02642965-D1 (PMID 32401633): There is 1 dataset for AAML1421's primary publication, PMID 32401633. The NCT02642965-D1 dataset is a patient level dataset (single row per patient) containing patient characteristics, cytogenetic categories, tumor response, survival, neutrophil count recovery, toxicity, residual disease status, and pharmacokinetic data for eligible pediatric acute myeloid leukemia (AML) patients enrolled on the AAML1421 clinical trial.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 phs004160

• Whole Genome Sequencing of Locally Advanced Esophageal Cancer

  We assembled a cohort of 36 patients with locally advanced esophageal cancer undergoing curative-intent therapy. Two ultrasensitive, tumor-informed, mutation enrichment sequencing tests were applied to serially collected blood samples to detect circulating tumor DNA (ctDNA), MAESTRO-Pool of the Broad Institute and the Oncodetect V2 assay (based on MAESTRO) of Exact Sciences. Both assays showed highly concordant results, with the Oncodetect V2 assay showing better sensitivity while maintaining high specificity. We found ctDNA detection postoperatively was strongly associated with disease recurrence and that most ctDNA-positive samples had variant allele fractions below 100 parts-per-million, the limit of detection of first-generation assays. Here we provide whole genome sequencing of matched tumor tissue and normal germline DNA from these 36 patients that were used to design individualized assays for MAESTRO-Pool and the Oncodetect V2 assay.

  Study phs004613

• NCI's Collection of Datasets for Pediatric and Adolescent and Young Adults Research

  This collection contains a compilation of NIH authorized individual-level datasets on childhood cancers currently in dbGaP with various data use limitations (DULs) such as Pediatric Cancer Research without the NPU modifier. The collection has been created to streamline access to pediatric, and adolescent and young adults (AYA) cancer datasets under the purview of NCI DAC and other NIH IC DACs with permission and will include any additional authorized individual-level datasets as they become available. To request access to this study collection, select phs003964 in the dbGaP Authorized Access System.

  Study phs003964

• Germline EGFR T790M and Lung Cancer Risk

  We performed germline whole-genome sequencing from peripheral blood of individuals carrying the EGFR T790M variant (n=53) and those who do not (n=206). This data is subset to chromosome 7 for all participants. For more information on study protocol please see NCT05587439.

  Study phs004412

• Genomic Sequencing of Ewing Sarcoma

  Pediatric Ewing sarcoma is a pediatric cancer that primarily arises from the bone. It is characterized by chimeric fusions of the EWS gene and an ETS family transcription factor. In this study, we performed massively parallel sequencing of a larger collection of Ewing sarcoma tumors to define the genomic landscape of this disease. We found that these tumors are among of the most genetically normal cancers currently characterized. There was also a marked absence of recurrent mutations in immediately targetable signaling transduction pathway genes. In this study we answer outstanding questions about ETS transcription factor expression, effects of treatment on mutational burden in Ewing sarcoma tumors, and describe patterns of tumor evolution. We also found that loss-of-function mutations in STAG2 were present in approximately 15% of Ewing sarcoma tumors and loss of STAG2 expression was associated with disease metastasis in this patient cohort.

  Study phs000804

• 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

• Somatic Mutations in 3,929 HPV-Positive Exfoliated Cervical Cell Samples

  We investigated the detection, timing, and HPV type specificity of cervical somatic hotspot mutations (i.e., previously reported cancer driver mutations) in 3,929 HPV-positive exfoliated cervical cell samples from individuals undergoing routine cervical screening in the U.S. using deep-targeted sequencing of 20 candidate genes. Our study included samples from 3,351 women with the following infection outcomes: 1,478 HPV16-, HPV18- and/or HPV45-positive controls (i.e., HPV infections that did not progress to precancer and/or subsequently cleared), 1,712 cervical precancers, and 161 invasive cervical cancers. We utilized residual exfoliated cervical cell samples from women routinely screened for cervical cancer precursors at Kaiser Permanente Northern California (KPNC) as part of the prospective KPNC-NCI HPV Persistence and Progression (PaP) cohort. We included 3,929 samples collected from these 3,351 women, including 974 serial sample from 396 women collected prior to their most recent screening visit to evaluate somatic hotspot mutation detection prior to diagnosis.

  Study phs003691

• Carolina Breast Cancer Study (CBCS)

  The Carolina Breast Cancer Study (CBCS), phase III, is a population-based study aiming to understand the social and molecular correlates of breast cancer outcomes, particularly among Black and young women. CBCS recruited first primary breast cancer cases from 44 North Carolina counties between 2008-2013. All cases were between age 20 and 74 and self-identified as female. Black women and young women were systematically oversampled by randomized recruitment such that the study includes approximately 50% Black women and approximately 50% women diagnosed before age 50. A total of 2,998 participants were enrolled. In the ten years following diagnosis, women completed surveys approximately every 1-2 years and diagnoses of subsequent distant local recurrence and second primary tumors were ascertained via linked medical records. We identified records of women who developed secondary breast tumors (including second primary tumors, contralateral breast cancers, and locoregional recurrences), and these participants were oversampled for targeted DNA sequencing using the UNCseq panel (~1200 genes).CBCS germline pathogenic mutations cannot be investigated because participants were consented between 2008 and 2013 with specific language prohibiting this. However, germline data can be used to call somatic mutations or to standardize somatic genomic data.For sharing of study data not included here, please visit unclineberger.org for instructions on submitting a data use agreement.

  Study phs003725

• Profiling Genome-Wide Circulating ncRNAs for the Early Detection of Lung Cancer

  Lung cancer remains the leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for approximately 85% of all cases. Although imaging techniques such as low-dose computed tomography (LDCT), combined with tissue biopsies, have improved early detection rates, current diagnostic approaches are often limited by high false-positive rates, invasiveness, and radiation exposure, which lead to misdiagnosis and increased patient burden. Therefore, there is an urgent need for minimally invasive, accurate, and safe diagnostic biomarkers, particularly those derived from liquid biopsies such as blood-based exosomal RNA.This dataset specifically focuses on plasma-derived exosomal small non-coding RNAs (sncRNAs).A total of 233 de-identified plasma samples were obtained from Rush University Medical Center, including 116 NSCLC patients and 117 non-cancer controls. Exosomes were isolated from plasma, RNA was extracted, and small RNA sequencing was performed using the Illumina NextSeq 500 platform. Data available through dbGaP include individual-level raw sequencing files (FASTQ) and basic phenotype annotations of the plasma cohort.A diagnostic model was initially developed using small RNA-seq data from 1,446 tissue samples obtained from TCGA and GEO, identifying a robust sncRNA signature that distinguished NSCLC from non-cancer samples with an AUC of 0.90 in hold-out tissue validation. This signature was subsequently validated in the plasma exosome cohort, achieving an AUC of 0.84 in independent validation. The model demonstrated consistent diagnostic performance across subgroups stratified by age, sex, smoking history, cancer stage, and NSCLC subtype. Survival and functional analyses further supported the clinical and biological relevance of the identified sncRNAs. It is hoped that this resource will contribute to a better understanding of the sncRNA expression landscape in NSCLC and promote the development of non-invasive biomarkers for early cancer detection. These data may be applied to the investigation of transcriptomic and other risk factors, provide insight into cancer screening, tumor progression mechanisms, and prognosis prediction, and ultimately support precision medicine for NSCLC.

  Study phs004166

• Cancer-Restricted Cryptic Antigens Are Targets for T Cell Recognition

  Subjects included patients with pancreatic cancer, at least 18 years of age, who were recruited from outpatient clinics and inpatient units at Dana-Farber Cancer Institute and Brigham and Women's Hospital.Bulk and single-cell transcriptomic profiling of human pancreatic cancer patient samples (direct from tumor or profiling of patient-derived organoids) was performed. Patient-derived pancreatic cancer organoids were profiled in the presence or absence of interferon-gamma stimulation. Healthy-donor CD8 T lymphocytes were ex vivo primed and expanded with candidate non-canonical (cryptic) peptide antigens. Single-cell transcriptomic profiling with paired T cell receptor (TCR) sequencing and molecularly-barcoded HLA tetramers enabled deconvolution and identification of cryptic antigen-reactive TCRs.

  Study phs003887