6048 results for "canc*"

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• Genomic Profiling of Pediatric B-cell Acute Lymphoblastic Leukemia

  Pediatric leukemia is the most common type of childhood cancer and, despite tremendous progress in treatment, remains the second leading cause of cancer deaths in children. B-cell acute lymphoblastic leukemia (B-ALL) is the most common type of pediatric leukemia. Recent studies using transcriptional profiling of large cohorts of pediatric B-ALL have shown that patients can be grouped into transcriptional subtypes that are often defined by specific driver mutations. Interestingly, many of these mutational subtypes are defined by gene fusions or rearrangements that drive altered expression of transcription factors (ETV6-RUNX1, PAX5, DUX4, TCF3-PBX1, ZNF384) or in chromatin regulatory machinery (KMT2A), suggesting that transcriptional dysregulation is a major driver of B-ALL. While the transcriptional distinctions are clear, the relationship between patients in terms of their chromatin regulatory landscape remains unclear. To address this, we profiled gene expression, open chromatin, and 3D genome folding in patient derived B-ALL samples. We identified that at the level of 3D genome organization, many chromatin interactions and looping events are shared across mutational subtypes, suggesting that shared transcriptional programs, in addition to group specific driver mutations, possibly regulate the chromatin landscape in B-ALL. Using RNA-seq and ATAC-seq data, we were able to identify "latent" signatures of expression related to non-mutant transcription factors (TFs) that also contribute to expression heterogeneity across TF subtypes. These are related to patient specific patterns of 3D genome folding, and in some cases, are predictive of disease outcomes. This study helps shed light on the chromatin landscape in B-ALL and furthers our understanding of the interactions between diverse mutant TFs that drive B-ALL and non-mutant TFs that help shape the B-ALL chromatin landscape.

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• Patient-Derived Breast Cancer Organoid Study

  This study uses normal and tumor tissues from breast cancer patients to derive 3D cell culture models called organoids. Organoid technology is an innovative platform that can be used to study a patient's tumor in a dish ex-vivo. As part of this study we have comprehensively characterized these models using next-generation sequencing for: 1) pathogenic SNVs in a targeted gene panel 2) copy number alterations 3) transcriptome analysis using RNA sequencing and 4) single-cell RNA sequencing

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• NCTN: Radiation Therapy and Cisplatin with or without Cetuximab in Treating Patients with Stage III or Stage IV Head and Neck Cancer (RTOG-0522)

  Study ID: RTOG-0522NCT Number: NCT00265941 NRG OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Randomized Phase III Trial of Concurrent Accelerated Radiation and Cisplatin vs Concurrent Accelerated Radiation, Cisplatin, and Cetuximab (C225) [followed by Surgery for Selected Patients] for Stage III and IV Head and Neck Carcinomas (RTOG-0522)Trial Description: RATIONALE: Radiation therapy uses high-energy x-rays to kill tumor cells. Drugs used in chemotherapy, such as cisplatin, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Cisplatin may also make tumor cells more sensitive to radiation therapy. Monoclonal antibodies, such as cetuximab, 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. Giving radiation therapy and cisplatin together with cetuximab may kill more tumor cells. It is not yet known whether radiation therapy and cisplatin are more effective with or without cetuximab in treating head and neck cancer.PURPOSE: This randomized phase III trial is studying radiation therapy, cisplatin, and cetuximab to see how well they work compared to radiation therapy and cisplatin in treating patients with stage III or stage IV head and neck cancer. Clinical data presented in the following publication(s):PMID 25154822 Disease type(s): Head and Neck Neoplasm - Squamous Cell CarcinomaClinical Dataset(s) included:NCT00265941-D1 (PMID 25154822): There are two datasets for RTOG-0522's primary publication 25154822 (-D1 and -D2). This dataset, NCT00265941-D1, contains reasons for exclusion, treatment received, treatment discontinuation reasons, baseline characteristics, p16 status, EGFR expression, survival, distant metastases, and use of feeding tube data.NCT00265941-D2 (PMID 25154822): There are two datasets for RTOG-0522's primary publication 25154822 (-D1 and -D2). This dataset, NCT00265941-D2, contains adverse event data. This dataset is limited to grade 1-4 adverse events that were attributed as definitely, probably, or possibly related to protocol treatment and occurred in at least 10% of patients in either arm. The acute and late periods are defined as 90 days or fewer and > 90 days, respectively, from the start of radiation therapy.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).

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• Single-Cell ATAC and RNA Sequencing of Human Breast Cancer Reveals Salient Cancer-Specific Enhancers

  Matched single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq) were performed for 12 human breast tumor samples, 4 normal human mammary reduction samples, and 4 human breast cancer cell lines (HCC1143, SUM149PT, MCF7, and T47D). Both scATAC-seq and scRNA-seq assays resolved the underlying cellular heterogeneity in chromatin accessibility and transcriptional output for each patient sample. In this work, we quantitatively linked variation in chromatin accessibility to gene expression across malignant and non-malignant cell types from patient samples. We then showed that our findings were recapitulated in the breast cancer cell line samples. These data will serve as an important resource for the single-cell genomics and breast cancer research communities.

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• HINTS Geo-Coded Data 2018 (HINTS 5 Cycle 2)

  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 second round of data collection for HINTS 5 (Cycle 2) was conducted from January 26 through May 2, 2018 with a goal of obtaining 3,500 completed questionnaires. A total of 3,504 respondents are included in the final sample.

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• Molecular Profiling of Head and Neck Squamous Cell Carcinomas

  This study performed targeted DNA sequencing of key NF-κB signaling pathway regulatory genes in matched tumor and normal tissues from patients with HPV-associated head and neck squamous cell carcinoma (HNSCC). A custom Ion Torrent AmpliSeq panel was designed to interrogate ten genes whose products regulate NF-κB activity and are frequently altered in the NF-κB-active subtype of HPV+ HNSCC: TRAF3, CYLD, TRAF2, NFKBIA, TNFAIP3, TRAF6, BIRC2, BIRC3, MYD88, and MAP3K14. The panel comprised 250 overlapping amplicons in a 2-primer pool format, achieving 93.65% coverage across the 24.86 kb target region. Genomic DNA was isolated from formalin-fixed paraffin-embedded (FFPE) macro-dissected tumor and matched normal tissues at the UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab. This sequencing was performed as part of a study developing a clinical assay to identify HPV+ HNSCC subtypes defined by NF-κB activity for the purpose of risk stratification and de-escalation of radiation therapy.

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• Prediction of Resistance and Sensitivity to HER2 Targeted Therapy in the Neoadjuvant Setting

  Women with breast cancers that overexpress HER2 are at greater risk for disease progression and death than women whose tumors do not overexpress HER2. Trastuzumab, a recombinant humanized monoclonal antibody against the extracellular domain of the HER2 protein blocks downstream signaling of HER2 and substantially improves the efficacy of chemotherapy in women with metastatic and early-stage HER2-positive breast cancers. Because resistance to trastuzumab eventually results in progressive disease in the metastatic setting and contributes to recurrence following adjuvant trastuzumab-based therapy, it is important to develop agents other than trastuzumab that target HER2 signaling through different mechanisms of action. Lapatinib is an oral, small molecule, dual tyrosine kinase inhibitor of HER2 and EGFR. Lapatinib has shown a lack of cross-resistance with trastuzumab in preclinical studies and activity in women with HER2-positive, metastatic breast cancer that has progressed during trastuzumab treatment. Trastuzumab blocks the downstream signaling of HER2 by binding to the extracellular domain of the receptor. Lapatinib binds to the intracellular domains of HER2 and EGFR and prevents activation of downstream signaling pathways. Because of this different mechanism of action, lapatinib may be effective in trastuzumab-resistant disease. The study will also provide important safety information on trastuzumab and lapatinib combinations immediately following anthracycline exposure, and also provide an initial direct comparison of cardiac effects of trastuzumab and lapatinib when incorporated into a standard sequential adriamycin and cyclophosphamide (AC) followed by weekly paclitaxel neoadjuvant regimen. Availability of a second agent that can interrupt HER2-signaling pathways through completely different mechanisms than those of trastuzumab offers the potential for further improvement in the management of patients with HER2-overexpressing breast cancer in both the adjuvant and metastatic setting. Co-administration of both trastuzumab and lapatinib with chemotherapy may be important in improving outcomes in subsets of HER2-positive breast cancers. However, use of two inhibitors of the HER2 pathway will increase costs and may increase toxicity, so it will be important to identify the subsets of patients who would benefit from the dual therapy. Inhibition of HER2 with a single agent clearly is sufficient for many patients as evidenced by the results of the trastuzumab trials. Therefore, co-administration to unselected populations of women with HER2-positive breast cancers would not represent an optimal approach. Given the activity of lapatinib, it is likely that it will also be sufficiently active in inhibiting HER2-pathway activation in some patients to allow for its use as the sole inhibitor of the HER2 pathway. Different populations may also derive greater benefit from one of the HER2-blocking agents relative to the other. Identification of potential predictive factors for pathologic complete response to the combination or to either agent administered alone in neoadjuvant trials would provide important information for adjuvant trials designed to definitively address these important issues. This study will compare 3 combined chemotherapy regimens: AC followed by paclitaxel plus trastuzumab and lapatinib, AC followed by paclitaxel plus lapatinib, and AC followed by paclitaxel plus trastuzumab given before surgery to patients with HER2-positive breast cancer.Tumor samples were collected prior to and post-treatment, and RNA sequencing was performed with this version.

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• NCTN_NCORP: The Men's Eating and Living (MEAL) Study: A Randomized Trial of Diet to Alter Disease Progression in Prostate Cancer Patients on Active Surveillance (CALGB-70807)

  Study ID: CALGB-70807NCT Number: NCT01238172 Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN_NCORP: The Men's Eating and Living (MEAL) Study: A Randomized Trial of Diet to Alter Disease Progression in Prostate Cancer Patients on Active Surveillance (CALGB-70807)Trial Description:RATIONALE: Eating a diet high in vegetables may slow down disease progression in patients with prostate cancer.PURPOSE: This randomized clinical trial is studying how well diet works in altering disease progression in patients with prostate cancer on active surveillance. Clinical data presented in the following publication(s):PMID 31935026 Disease type(s): Reproductive System Neoplasm, Male - Prostate CancerClinical Dataset(s) included:NCT01238172-D1 (PMID 31935026): Dataset NCT01238172-D1 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains baseline characteristics, including baseline serum PSA values.NCT01238172-D2 (PMID 31935026): Dataset NCT01238172-D2 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for the consort diagram (inclusion/exclusion status, treatment arm).NCT01238172-D3 (PMID 31935026): Dataset NCT01238172-D3 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains survival and time to alternative treatment data.NCT01238172-D4 (PMID 31935026): Dataset NCT01238172-D4 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for patient off treatment reasons.NCT01238172-D5 (PMID 31935026): Dataset NCT01238172-D5 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for the dietary patterns analysis included in Table 2 and the eTable.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).

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• The Haplotype-Resolved Genome and Epigenome of the Aneuploid HeLa Cancer Cell Line

  The genomic architecture of HeLa remains largely unexplored beyond its karyotype, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq and ENCODE Project data sets to phase the HeLa epigenome. This revealed strong, haplotype specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes. Reprinted from Adey et. al. 2013, Nature, with permission from Nature Publishing Group.

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• Study of Novel Approaches for Prevention (SNAP-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.ObjectivesTo compare two self-regulation interventions versus control in reducing weight gain in young adults over an average follow-up of 3 years.BackgroundWeight gain occurs commonly throughout adulthood and has been associated with many adverse health outcomes. Weight gain in adults aged 18 – 35 years had stronger negative associations with critical outcomes such as cancer risk and mortality compared to weight gain at later ages. Developing effective approaches to reduce weight gain in young adults was therefore an important public health priority and focus of the SNAP study.ParticipantsSNAP targeted an enrollment of 600 participants (25% men and 25% racial / ethnic minorities), age 18–35, with a BMI of 21–30.9 kg/m2. Eligibility requirements focused on ability to participate in the program (e.g., internet access, English speaking), safety (no history of eating disorders, ability to walk for activity) and completion of screening and baseline assessment visits.Potential subjects were excluded due to pregnancy, diabetes, alcohol or substance dependence, psychiatric disorders, and any medical problem that could cause unintentional weight change.A total of 599 subjects were enrolled and randomly assigned into one of three treatment arms. 202 participants were enrolled in the control group, 197 assigned to the large changes group, and 200 assigned to the small changes group.DesignThe Study of Novel Approaches to Weight Gain Prevention (SNAP) was a 3-armed randomized controlled clinical trial that compared self-regulation with small daily behavior changes (Small Changes), self-regulation with large periodic behavior changes (Large Changes), and a minimal treatment control.The Control group attended one face-to-face meeting where they were introduced to the issue of weight gain, the concept of self-regulation, and an overview of both Small and Large Change approaches to potentially prevent weight gain.The Small and Large Changes interventions both began with 10 face-to-face group meetings over 4 months. Participants in Small Changes were taught to make daily small changes (approximately 100 kcal/day) in both diet and physical activity. Participants were given pedometers and instructed to add 2000 steps per day above their baseline activity level.Large Changes focused on losing weight during the initial four-month program to create a buffer against subsequent weight gain. To achieve this, participants were prescribed a calorie goal based on a 500- 1000 kcal deficit from baseline to use during the initial 8 weeks. They were also encouraged to gradually increase moderate intensity physical activity to a goal of 250 minutes/week, the level recommended for weight loss maintenance.All participants were scheduled to complete assessments at baseline, month 4, year 1 and year 2. To encourage self-regulation, participants were instructed to weigh themselves daily and submit their weight via the study website, text message or email. They received monthly email feedback on their weight, which was based on a color-coded system and either reinforced their success, encouraged problem-solving, or recommended additional strategies to help reverse weight gain. Each year, participants were invited to join two 4-week online refresher campaigns reinforcing the behaviors taught during the initial program. All participants received identical quarterly newsletters and personalized feedback reports on their assessment data, including the Control group.The primary outcome was the mean weight gain over an average follow-up of 3 years. Secondary outcomes were the proportion of participants gaining ≥1 pound (chosen to represent a stringent criterion of weight gain over baseline) and the incidence of obesity (BMI≥30 kg/m2) over the 3 years.ConclusionsSelf-regulation interventions involving small or large changes were both effective in reducing the mean weight gain relative to control over an average follow-up of 3 years. The Large Changes intervention successfully decreased the proportion of participants who experienced weight gains ≥1 pound over the follow-up, and both interventions reduced the incidence of obesity during follow-up by almost 50% relative to Control, representing a clinically significant reduction in risk of developing obesity.Wing RR, Tate DF, Espeland MA, et al. Innovative Self-Regulation Strategies to Reduce Weight Gain in Young Adults: The Study of Novel Approaches to Weight Gain Prevention (SNAP) Randomized Clinical Trial. JAMA Intern Med. 2016;176(6):755-762. doi:10.1001/jamainternmed.2016.1236

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