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• Sex Chromosome Aneuploidy Effects on Human Gene Expression

  Sex chromosome aneuploidy (SCA) syndromes are defined by the presence of a sex chromosome complement other than the typical XX for females and XY for males. SCAs are collectively common and increase risks for diverse immune, metabolic, and neuropsychiatric illnesses. Understanding genome-wide transcriptomic changes in SCAs is critical for clarifying the biological underpinnings of their clinical phenotypes. Assessments of sex chromosome dosage (SCD) effects on gene expression in humans have often been confined to the use of a few SCA subtypes (e.g., XO or XXY) - precluding analysis of the same SCD change in different contexts. Our study used RNA-seq data from lymphoblastoid cell lines in 197 individuals representing diverse SCA karyotypes (49 XX, 24 XXX, 39 XY, 39 XXY, 23 XXYY, 23 XYY) to assess expression changes for 25,075 genes in multiple pairwise SCD group comparisons. The paper reporting our findings has been cited below.

  Study phs003278

• A Phase 2 Study of Lamivudine in Patients with p53 Mutant Metastatic Colorectal Cancer

  This was an open-label, single-arm Phase II study of lamivudine in patients who had progressed on systemic therapy for advanced colorectal cancer with TP53 mutations. The phase II study had a two-stage design, with a target accrual of 20 evaluable patients for the first stage and a total of 32 patients for the whole study. The first 9 patients were treated with lamivudine at 150 mg PO bid continuously for 28-day cycles. Subsequent patients (10-32) received a higher dose of 600 mg PO bid continuously for 28-day cycles. Tumor assessments were performed every 8 weeks until documented disease progression by Response Evaluation Criteria in Solid Tumors (RECIST) or drug intolerance. Whole genome sequencing (WGS) and total RNA-seq were performed on pre- and post- treatment biopsies on this trial.

  Study phs002833

• The Prostate, Lung, Colon, Ovary Screening Trial (PLCO)

  The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a large population-based randomized trial designed and sponsored by the National Cancer Institute (NCI) to determine the effects of screening on cancer-related mortality and secondary endpoints in over 150,000 men and women aged 55 to 74. The screening component of the trial was completed in 2006. However, participants have been under follow-up for cancer incidence and mortality since that time. In addition, PLCO included a large biological sample biorepository which has served as a unique resource for cancer research, particularly for etiologic and early-marker studies. As part of these efforts, PLCO has been used for a large number of genome-wide association and exome sequencing studies for different types of cancer. Recently, a blood DNA methylation analysis was conducted in annexes case-controls study of breast cancer.

  Study phs001286

• From matrimonial practices to genetic diversity in Southeast Asian populations: the signature of the matrilineal puzzle

  This project aims at revisiting the "matrilineal puzzle" from a population genetics' point of view. The dataset consists of 719 individuals from 12 populations sampled in continental Southeast Asia and genotyped at 598764 loci. This dataset can only be accessed and used for non-commercial research purposes with a finality complying with the informed consent provided by donors. For accessing the data, please provide: 1. An explicit title for the project you wish to use the data for. 2. A detailed institutional affiliation of all recipients and users of the data. 3. A summary (500 words) of the research project, with emphasis on its scientific and societal finality, and predicted outputs. If access is granted by the DAC, data cannot be shared with a third party not initially involved in the project, without the third party officially applying for accessing the data.

  Study EGAS00001003727

• Whole Exome Sequencing for Familial Intracranial Aneurysm (FIA I-II) Study

  The goal of this study is to identify the genes underlying the risk of intracranial aneurysm (IA). The FIA Study initially recruited families appropriate for linkage analysis. Therefore, the recruitment focus was not only on probands with a family history of IA but also required that biological samples be obtained for at least two affected family members. Family members underwent detailed interviews for medical, social and family history, and provided blood samples for DNA extraction. Over 400 multiplex IA families were recruited and enrolled. The whole exome sequencing project aims to identify novel and rare (in the general population) genetic variants that are enriched in seven extended multiplex families with a strong familial aggregation of intracranial aneurysms.

  Study phs000636

• Helmholtz Centre for Infection Research, Centre for Individualised Medicine

  Dac EGAC00001002303

• DAC for Sarcopenia HNSCC

  Data access committee for Sarcopenia HNSCC study

  Dac EGAC50000000420

• A Multi-Omic Single-Cell Atlas of Human Gynecological Malignancies

  Matched single-cell transcriptomic sequencing (scRNA-seq) and single-cell chromatin accessibility sequencing (scATAC-seq) were performed for 11 fresh human tumors collected from the endometrium or ovary. More detailed information for each patient tumor will be provided in selected phenotype/attributes data. Both scRNA-seq and scATAC-seq assays revealed the underlying cellular heterogeneity in transcriptional output and in chromatin accessibility for each patient tumor specimen. In this work, we identified potential non-coding regulatory elements that mediate cell type-specific gene expression patterns. These data will serve as an important reference for the single-cell genomics and gynecologic oncology research communities.

  Study phs002340

• Mayo Clinic Adult Diffuse Glioma Illumina OncoArray SNP Data

  These data are from adult diffuse glioma subjects genotyped on the Illumina OncoArray. Data from this study were used for case control association studies and developing polygenic risk scores. Variants in D2HGDH and near FAM20C were identified that were associated with glioma subtypes (PMID: 32386320). Mutation and copy number data are included for select genes and chromosomes. IDH mutation and 1p/19q co-deletion are used in glioma diagnosis and are also prognostic markers. Data for additional prognostic genes and chromosomes are also included. RNA-seq and CHIP-seq data are available for select subjects from this cohort in GEO (GSE167806).

  Study phs003041

• Vitamin-D-Kids Asthma

  The Vitamin D Kids Asthma Study (VDKA) was a 48-week multicenter randomized, double-blinded, placebo-controlled trial of vitamin D3 for severe asthma exacerbations in children 6-16 years old, recruited from February 28, 2016 to September 20, 2019. An ancillary study for nasal sampling was conducted at the Pittsburgh site. Prior to randomization, participants completed questionnaires and underwent collection of nasal samples for gene expression studies. VDKA was approved by the IRBs of all participating institutions, and the ancillary study was approved by the IRB of the University of Pittsburgh. Written parental consent was obtained for participating children, from whom written assent was also obtained.

  Study phs004051