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• Combined Targeting of CDK4/6 and HER2 Signaling in Orthotopic Patient-Derived Xenografts of HER2-Positive Breast Cancer Brain Metastases

  Patients with metastatic HER2-positive (HER2+) breast cancer will frequently develop brain metastases (BCBMs). Here, we report that p16INK4A, a tumor suppressor, is deficient in the majority of HER2+ BCBMs. Furthermore, p16INK4A deficiency, as measured by protein immunohistochemistry, can be a predictive marker associated with response to combined treatment with tucatinib and abemaciclib in our orthotopic patient-derived xenografts (PDXs) models of HER2+ BCBMs. Our findings provide the rationale for a biomarker-driven clinical trial of combined treatment with CDK4/6- and HER2-targeted agents for patients with HER2+ BCBM.  

  Study phs002482

• NHLBI TOPMed - NHGRI CCDG: The Vanderbilt AF Ablation Registry

  The Vanderbilt Atrial Fibrillation Ablation Registry (VAFAR) was founded in 2011. Patients with AF referred for AF ablation are prospectively enrolled. A detailed clinical history is recorded, along with imaging data (cardiac MRI or CT). Blood samples are obtained for DNA extraction at the time of ablation. Details of the ablation procedure are recorded. Patients are longitudinally followed to monitor for AF recurrence. VAFAR contributed 171 samples submitted to dbGaP for WGS: 115 were from male subjects, of which 113 were white/non-Hispanic and 2 were Hispanic; 56 were from females, of which all 56 were white/non-Hispanic.

  Study phs000997

• Analysis of the Genetic Basis of Height in Large Jewish Nuclear Families

  This is a family based study of the genetic basis of height, which focused on very large nuclear families (10 siblings or more, average of 12), all from a founder (Jewish) population. All participants have completed their growth. This study design increases the frequency of some genetic variants that are rare in a cosmopolitan population but segregate in our cohort. Participants were genotyped with a ~630,000 SNP array (Affymetrix Axiom Biobank), and their standing height, sitting height and arm span were measured with high accuracy (±0.1 cm, with 4 technical repeats). All genomic coordinates refer to genome build hg19.

  Study phs001852

• Merkel Cell Carcinoma Tissue and Data Repository

  Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine skin cancer with increasing incidence in the United States. In this study we performed the first whole genome sequencing of three Merkel cell carcinomas with their matched normal tissues for somatic variant calling. From these data we describe the likely mechanism of Merkel cell polyomavirus integration and focal host genomic amplifications in two tumors and the dominance of UV-mediated mutagenesis in a virus-negative tumor. We also performed poly-A RNA sequencing on a total of six Merkel cell carcinomas to address expression differences between virus-positive and virus-negative MCC.

  Study phs002189

• RNA-Seq of Whole Blood from Pediatric Sickle Cell Anemia (SCA) Patients

  The aim of this study is to define the immune cell transcriptome by next generation RNA sequencing in blood from individuals with SCA, in comparison to healthy African American controls. This study has a cross-sectional case-control design. We will compare the transcriptome profiles of blood mononuclear cells from healthy age-matched African American children without cardiovascular disease or risk factors (“Controls”) to those of children with SCA, age 5 -21 years, who are not receiving chronic red blood cell transfusions or hydroxyurea therapy to identify genes that are differentially expressed in SCA. 

  Study phs002687

• The UC San Diego Chronic Lymphocytic Leukemia (CLL) Study

  The UC San Diego Chronic Lymphocytic Leukemia Study is designed to identify genetic, epigenetic, and transcriptional changes important for CLL. This data release consists of samples collected to 1) identify genomic changes associated with CLL progression using serially collected tumor samples; 2) characterize the transcriptional consequences of SF3B1 mutation through RNA-seq; and 3) characterize the expression profiles of ROR1+ vs. ROR1- tumors. The samples were collected from participants at the University of California, San Diego Moores Cancer Center and the data was generated at UC San Diego or in collaboration with the BC Cancer Agency Genome Sciences Centre.

  Study phs000767

• Type I Interferon and Cycling Lymphocytes in Macrophage Activation Syndrome

  We performed immune profiling of peripheral blood mononuclear cells from patients with Still's disease and macrophage activation syndrome (MAS) using bulk RNA sequencing and single-cell RNA sequencing. Three groups were included in the study: healthy controls, patients with Still's disease without macrophage activation syndrome, and patients with Still's disease and macrophage activation syndrome. We found that macrophage activation syndrome is associated with transcriptomic signatures of interferon upregulation and cell cycling. We identified cycling lymphocytes within T cell and NK cell populations that are correlated with MAS disease activity. All sequencing data are available through dbGaP.

  Study phs003310

• Circulating RNAs in Acute Heart Failure (CRUCIAL)

  The purpose of this American Heart Association-funded and NIH-funded study is to examine circulating RNAs in the acute congestive heart failure (CHF) setting, and how they change with decongestive therapy, and their function in vitro and in vivo. The investigators are testing the hypothesis that ex-RNA levels change significantly during decongestion therapy and can be used as a marker of those individuals who respond to CHF therapy (in terms of cardiac structure or outcome). Additionally, the translational research design allows the investigators to assay the effects of these RNAs on tissue phenotypes in vitro.

  Study phs003403

• Joint Addiction, Aging, and Mental Health Data Access Committee General Research Use Datasets (GSR Restricted) Collection

  This collection contains the Joint Addiction, Aging, and Mental Health Data Access Committee's authorized individual-level genomic datasets currently in dbGaP that are approved for General Research Use (GRU) and have no further limitations beyond those outlined in the model Data Use Certification Agreement. The public posting of Genomic Summary Results are not allowed. Access to this study collection will include additional authorized individual-level GRU datasets that become available. Renewal of this study collection is required annually. To request access to this study collection, select phs003421 in the dbGaP Authorized Access System.

  Study phs003421

• "BaTwa" populations from Zambia retain ancestry of past hunter-gatherer groups

  We genotyped and analyzed over two million genome-wide SNPs from two BaTwa populations (40 individuals by population), and from three comparative farming populations (10 to 21 individuals by population) in order to: (i) determine if the Zambian BaTwa carry any genetic material linking them to past hunter-gatherer-groups, and (ii) characterize the genetic affinities of past Zambian hunter-gatherer-groups. We found that both BaTwa populations harbor a hunter-gatherer- like genetic component, representing ∼19% (Bangweulu) and ∼31% (Kafue) of their genetic ancestry, while the rest of their ancestry is similar to western Africans.

  Study EGAS50000000378