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• Single Cell Genome Variation Induced by Mutational Processes in Cancer - HGSOC Trios Study

  Mutational signatures derived from whole genome sequencing have potential prognostic significance. Identification of high grade serous ovarian cancer patients with deficiency in homologous recombination repair pathways could identify a subset of patients that would benefit from homologous recombination deficiency-specific treatments independent of identification of a pathological BRCA1/2 gene mutation. Clinical protocols rely on a pathologist's assessment of formalin-fixed paraffin-embedded (FFPE) tissues, and thus FFPE tissue samples are readily available. However, the bulk of mutational signature analyses have been performed on fresh frozen tissues. In this study, we aimed to assess the reliability of whole genome sequencing, variant calling, and mutational signature analysis from FFPE tissue samples.

  Study phs003036

• Single-Cell Profiling of Premature Neonate Airways Reveals a Continuum of Myeloid Differentiation

  We set out to develop a reference single-cell transcriptomic profile of airway aspirate samples from extremely premature neonates (collected within an hour of birth). In this study, we profiled samples from 10 subjects. We identified cells in the airways of premature neonates representing a continuum of myeloid differentiation, including fetal monocytes, differentiating myeloid cells, and macrophages. Trajectory analysis identified two trajectories consistent with interstitial and alveolar macrophages, and a bridging trajectory providing an alternative route between these terminal states. We defined 259 alveolar-specific genes, 666 interstitial-specific genes, and 285 bridging-specific genes providing the first single-cell transcriptional map of differentiating airway macrophages in humans.

  Study phs003427

• PGRN-Leducq: Identification of the KCNE1 D85N Polymorphism as a Possible Modulator of Drug-Induced Torsades de Pointes

  The goal of this study was to search for genetic variants that could be responsible for modifying the risk of drug-induced long QT syndrome (diLQTS). diLQTS is a relatively common adverse drug event and has been a leading cause for drug relabeling and withdrawal from the market. Our hypothesis, that variants in genes which regulate electrical properties in the heart modify the risk of diLQTS, was tested by genotyping patients of European descent at 1424 single nucleotide polymorphisms (SNPs) in 18 candidate genes. We found that the SNP KCNE1 D85N was highly predictive of diLQTS with an odds ratio of 9.0 (95% confidence interval: 3.5-22.9).

  Study phs000617

• NHLBI TOPMed: Rare Variants for Hypertension in Taiwan Chinese (THRV)

  The THRV-TOPMed study consists of three cohorts: The SAPPHIRe Family cohort (N=1,271), TSGH (Tri-Service General Hospital, a hospital-based cohort, N=160), and TCVGH (Taichung Veterans General Hospital, another hospital-based cohort, N=922), all based in Taiwan. 1,271 subjects were previously recruited as part of the NHLBI-sponsored SAPPHIRe Network (which is part of the Family Blood Pressure Program, FBPP). The SAPPHIRe families were recruited to have two or more hypertensive sibs, some families also with one normotensive/hypotensive sib. The two Hospital-based cohorts (TSGH and TCVGH) both recruited unrelated subjects with different recruitment criteria (matched with SAPPHIRe subjects for age, sex, and BMI category).

  Study phs001387

• Phenotyping and Therapeutic Approaches for Patients with Sellar/Suprasellar Disorders

  The goal of the study is to phenotype and genotype patients with rare hypothalamic and pituitary disorders and identify biomarkers of disease diagnosis, presentation, and progression. We are investigating genetic mechanisms of pituitary tumorigenesis as well as genomic/transcriptomic markers of disease presentation and severity. Patients with suspected or confirmed hypothalamic and/or pituitary disorders and their family members are recruited. Biospecimens including peripheral blood, urine, tumor tissue (as available), and/or stool are collected. Genetic analysis may include a variety of techniques including peripheral blood or tumor tissue targeted Sanger sequencing of one or few genes, peripheral blood or tumor tissue whole exome sequencing, and other as applicable.

  Study phs003245

• Malnutrition and Enteric Disease Network (Mal-ED) Case-Control Study in Brazil

  The Malnutrition and Enteric Disease Network (Mal-ED) Case-Control Study enrolled children in the age range 6-24 months between 2010 and 2014 in Fortaleza, Ceará, Brazil.The aim of the study was to understand the etiology and pathogenesis of malnutrition. Children were prospectively enrolled cases defined as weight for age Z Score (WAZ) <-2 and age and neighborhood matched controls defined as WAZ>-1.This submission includes genetic and associated phenotypic data on a subset of 336 participants. More information on this project and its related projects can be found here: Studies of diarrheal susceptibility, growth, and development, in pediatric populations in Northeastern Brazil

  Study phs003173

• Genomic Characterization of Pediatric Low-Grade Gliomas

  Pediatric low-grade gliomas (PLGGs) are the most common pediatric brain-tumor, with more than ten histologic subtypes recognized by the World Health Organization. We performed a genomic analysis of 230 PLGGs of which 73 had whole genome/RNA sequencing performed and show that MYB-QKI fusions define the seizure associated tumor, Angiocentric Glioma (AG). MYB-QKI fusions present in AGs contribute to tumorigenesis through three mechanisms: MYB activation by truncation, enhancer translocation driving aberrant MYB-QKI expression, and hemizygous loss of QKI, a tumor suppressor gene. Such interplay between three oncogenic mechanisms has diagnostic and therapeutic implications in AGs, and illustrates the functional complexity associated with rearrangements in cancer.

  Study phs001054

• Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors

  Most pancreatic neuroendocrine tumors (PNETs) do not produce symptoms of hormonal excess and are hence considered “non-functional”. Their clinical behaviors vary widely, emphasizing the need for a robust classification with prognostic power. Using enhancer maps to infer regulatory programs, we find that the large majority of non-functional PNETs fall into two major sub-types that reflect alpha and beta endocrine cell ontogeny, respectively. Tumors of the different subtypes have similar clinical presentations and histology, but express distinct lineage-specifying transcription factors, ARX or PDX1. Here we provide the raw ChIP-seq and RNA-seq data of the PNET cohort in this study, as well as ChIP-seq data of ileal carcinoids.

  Study phs001910

• Multiethnic Cohort Adiposity Phenotype Study (MEC-APS)

  A total of 1,861 healthy men and postmenopausal women aged 60-77 years with body mass indexes (BMIs) of 17.1-46.2 kg/m2 were enrolled into the study. Stratified sampling was conducted based on sex, race/ethnicity, and six BMI categories (18.5-21.9, 22-24.9, 25-26.9, 27-29.9, 30-34.9, and 35-40 kg/m2) to balance the sample size across the wide range of BMI and optimize adjustment for total adiposity in populations with different BMI distributions. Study participants underwent body composition assessment, in person interview, blood collection, and completed a self-administered questionnaire. A genome-wide association study of obesity phenotypes was conducted among five racial/ethnic groups of the Multiethnic Cohort Study.

  Study phs001689

• Genomic landscape of Neutrophilic Leukemias of Ambiguous Diagnosis

  Chronic neutrophilic leukemia (CNL), atypical chronic myeloid leukemia (aCML), and unclassified myelodysplastic syndrome/myeloproliferative neoplasms (MDS/MPN-U) are a group of rare, heterogeneous myeloid disorders. There is strong morphologic resemblance amongst these distinct diagnostic entities as well as lack of specific molecular markers and limited understanding of disease pathogenesis, which has made their diagnosis challenging. Treatment has remained empirical, resulting in dismal outcomes. We, therefore, performed whole exome and RNA-sequencing on a cohort of over 100 cases of these rare hematologic malignancies and present the most complete survey of the genomic landscape of these diseases to date. [Abstract from manuscript currently under review so copyright not yet determined]

  Study phs001799