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• Genomics and Methylation of Neuroendocrine Prostate Cancer from cfDNA (Cornell/Trento 2019)

  A subset of castration resistant prostate cancers develop small cell neuroendocrine prostate cancer (NEPC) as a mechanism of treatment resistance. Metastatic tissue biopsies to evaluate for NEPC transformation are invasive and challenging to perform serially. We performed whole exome and whole genome bisulfite sequencing of plasma cfDNA and matched tumor biopsy samples from 62 patients with metastatic prostate cancer along the disease spectrum to evaluate for NEPC associated genomic and epigenomic features. Multiple tissue biopsies and/or plasma time points were included for a subset of patients to characterize disease heterogeneity and dynamic changes. Computational analysis of clonality and allele specific quantification allowed for detailed comparison of matched tumor tissue and cfDNA data (CLONET v2). Methylation profiles detected from tissue and plasma data were compared and NEPC specific alterations were evaluated in cfDNA. The study supports the feasibility of a plasma based assay for the detection of NEPC.

  Study phs001752

• miRNA data for aSAH patients with or without subsequent vasospasm

  These files contain the normalized and raw count abundances miRNA for aSAH patients. These abundances were obtained using Next-Generation Sequencing after selection of the miRNA in the RNA biobank. In total, there are 28 VSP- and 28 VSP+ patients for two-time points. Normalized data were obtained by applying size factor and VSN normalizations as described in Pulcrano-Nicolas et al. Stroke 2018. Raw count data corresponding to the raw abundances of miRNA in aSAH patients.

  Dataset EGAD00001004185

• Genetic vulnerability of knockout cancer lines (2019-04-01)

  Genome-wide CRISPR/Cas9 library screen was performed in isogenic cell lines. Three biological replicates were used. Cells were harvested at initiation of screen and at specific time points following cell culture. Using this approach we aim to identify genes specifically important in cell survival in engineered cell lines. Please perform 72, instead of 36, PCR reactions as the screen performed at 200x coverage. . This dataset contains all the data available for this study on 2019-04-01.

  Dataset EGAD00001004881

• COVID-19 Challenge Project Single Cell Profiling

  Single-cell profiling of sero-negative and sero-positive humans that were inoculated with SARS-CoV-2. The cellular response during SARS-CoV-2 is profiled using single-cell transcriptomics, CITE-seq and single cell immune profiling, by sampling PBMCs and nasal swabs before and at multiple time points during SARS-CoV-2 infection. This one-of-a-kind cellular map will give unique temporal resolution of how nasal and immune cells respond to SARS-CoV-2 exposure and infection.

  Dataset EGAD00001012227

• NGS-based monitoring of the T cell receptor repertoire in living donor kidney transplant patients undergoing combination cell therapy

  Tolerance induction through mixed chimerism is a promising approach to achieve long term graft patency without or only low dose maintenance immunosuppression. In this phase I/IIa academic trial kidney transplant recipients in the case group were co-transplanted with bone marrow from the same donor and received an autologous cell product. The control group did not receive donor bone marrow or an autologous cell product. Peripheral blood mononuclear cells were collected at multiple timepoints before and after transplantation and the recipients native T-cell receptor (TCR) repertoire at time points 0, 1, 3 and 6 months after transplantation as well as their donor reactive TCR repertoire were analysed using NGS-based TCR sequencing.

  Study EGAS50000000210

• Count Me In (CMI): The Metastatic Prostate Cancer (MPC) Project (CMI-MPCproject)

  Count Me In - The Metastatic Prostate Cancer Project: A Patient-Driven Research Initiative to Accelerate Metastatic Prostate Cancer Research The Metastatic Prostate Cancer Project (MPCproject; http://mpcproject.org/) is a research study that empowers men with metastatic and advanced prostate cancer to partner directly with researchers by sharing their samples and clinical information, with the ultimate goal of accelerating scientific discoveries that have clinical impact. The MPCproject enables any man with metastatic or advanced prostate cancer in the US and Canada to participate in cutting-edge genomic and molecular research, regardless of where they live. Metastatic or advanced prostate cancer patients visit the project website and complete an online questionnaire of basic information about themselves and their cancer. Enrolled patients are mailed saliva and blood draw kits, which can be used to extract germline DNA and cell-free DNA (cfDNA), respectively. The study team contacts participants' healthcare institutions to obtain medical records and a portion of archived tumor samples. Whole exome sequencing is performed on tumor DNA, germline DNA, and cfDNA, and transcriptome sequencing is performed on tumor RNA. De-identified data, including linked genomic, clinical, and patient-reported data, are shared via public databases on a recurring pre-publication basis. Participants are regularly provided with updates on the study.

  Study phs001939

• Gynecology and Lubricant Effects (GALE) Study

  The GALE study is a longitudinal study of the association between lubricant use and the vaginal microbiota in women receiving transvaginal ultrasound (TVUS) at the Diagnostic Radiology and Nuclear Medicine Department at the University of Maryland School of Medicine. Participants undergo a clinical exam at enrollment (at least 5 days prior to TVUS) and self-collect daily, mid-vaginal samples in the week leading up to TVUS, including immediately before the procedure. At the TVUS appointment, the sonographer applies a single-use packet of Glide lubricating jelly to the probe. The product was selected for study as it was currently being used in the TVUS clinic at the University of Maryland Medical Center and is a clinical lubricant which is very similar in composition to many sex lubricants. Participants collect samples the evening after TVUS and present for a follow-up clinical exam within a week of TVUS. Participants continue to sample twice weekly for an additional 8 weeks (returning completed kits each week), complete daily health and behavior diaries, and attend one final clinical exam at week 10. The clinician evaluates participants for bacterial vaginosis (BV) at each clinical visit using Amsel's criteria, and also looks for signs of vulvovaginal candidiasis (VVC) and trichomonas using a wet mount.

  Study phs002211

• High-resolution testing of ctDNA dynamics predicts survival in metastatic NSCLC

  One of the great challenges of therapeutic oncology is determining who might achieve survival benefit from a particular therapy. Circulating tumor DNA (ctDNA) provides real-time assessments of patient prognosis and response to treatment using a simple blood draw. While ctDNA positivity is established as a poor prognostic factor, studies on longitudinal ctDNA dynamics have been small and non-randomized, with ctDNA assessments done at disparate time points. To address this, we performed high-sensitivity longitudinal ctDNA testing in 466 patients across 5 time points (1,954 samples total) in a randomized phase III study comparing different chemotherapy-immunotherapy combinations. We leverage machine learning to jointly model multiple ctDNA metrics to predict overall survival in a training/testing framework. _ . Treatment initiation correlated with reductions in ctDNA levels, and training of our machine learning model suggests that assessment of ctDNA dynamics at C3D1 (cycle 3 day 1) of chemo-IO treatment may be optimal to predict OS. The model performs well in the hold-back test data, enabling stratification of patients with Stable Disease (SD) into high-risk vs low-intermediate-risk (HR = 3.2 [2.0-5.3], p <0.001; median 7.1 versus 22.3 months respectively); similarly, the model stratifies patients with a Partial Response (PR) (HR =3.3 [1.7-6.4], p <0.001; median 8.8 versus 28.6 months). Importantly, the model validates well in an external cohort of patients in a different treatment setting and assayed with a different ctDNA technology, in which model predictions similarly identified high-risk patients (OS HR=3.73 [1.83-7.60], logrank p=0.00012). Simulations of clinical trial scenarios employing our ctDNA model further suggest that early ctDNA testing outperforms early radiographic imaging for predicting trial outcomes (increasing the rate of ‘True Go’ decisions by 5.2 - 22.8% depending on the drug combination). Overall, we show that measuring ctDNA dynamics during the course of therapy dramatically improves patient risk stratification, and may provide a means to differentiate between competing therapies at an early time point during clinical trials.

  Study EGAS00001006703

• Natural History and Structural Functional Relationships in Fabry Renal Disease

  Fabry disease is a rare genetic disease with deficient activity of an enzyme, which leads to accumulation of inclusions in different organs including kidney, heart and vessels. The purpose of the study is to conduct a cross-sectional investigation of the natural history of Fabry renal disease and measure renal function and renal structure in male and female Fabry's patients. The study will utilize the resultant cross-sectional information to determine the renal structural parameters or composite of parameters that most closely relates to the onset and progression of clinical renal disease in Fabry patients. This is an observational, cross-sectional study of 60 individuals with Fabry disease. Those participating in the study will be evaluated during a one day visit and on a PRN basis. The primary study objectives are as follows: To study the natural history of Fabry renal disease and measure renal function and renal structure in male and female Fabry's patients. These patients would encompass the broad age range from childhood to adulthood and from normal renal function to moderate renal insufficiency [serum creatinine (SCr) ≤ 2.5mg/dl (chronic kidney disease or CKD3)]. To utilize the resultant cross-sectional information to determine the renal structural parameters or composite of parameters that most closely relates to the onset and progression of clinical renal disease in Fabry patients.

  Study phs001333

• T2D-GENES Project 2: San Antonio Mexican American Family Studies

  The Type 2 Diabetes (T2D) Genetic Exploration by Next-generation sequencing in Ethnic Samples (T2D-GENES) Consortium is a collaborative international effort to identify genes influencing susceptibility to T2D in multiple ethnic groups using next generation sequencing. T2D-GENES Project 2 is a complex pedigree-based study designed to identify low frequency or rare variants influencing susceptibility to T2D, using whole genome sequence (WGS) information from 1,043 individuals in 20 Mexican American T2D-enriched pedigrees from San Antonio, Texas. The major objectives of this study are to identify low frequency or rare variants in and around known common variant signals for T2D, as well as to find novel low frequency or rare variants influencing susceptibility to T2D. The sampled individuals are obtained from two studies: the San Antonio Family Heart Study (SAFHS) and the San Antonio Family Diabetes/Gallbladder Study (SAFDGS), collectively referred to as the San Antonio Mexican American Family Studies (SAMAFS). The strategy is to sequence approximately 600 individuals at an average of 50x coverage across the entire genome, then impute genome wide genotypes for about 440 additional family members. The 600 sequenced individuals are specifically chosen for their value in imputing sequence information into other family members. By studying large pedigrees, we expect to find multiple individuals carrying each genetic variant, even if this variant is very rare in the population at large. Thus, a pedigree-based approach provides an excellent opportunity for identifying rare novel variants influencing risk of T2D and quantitative variation in T2D-related phenotypes. The whole genome sequencing has been done commercially by Complete Genomics, Inc. (CGI). The final data set includes whole genome sequence data for 607 individuals. After quality control, 585 sequenced individuals provide data for family based imputation, using Merlin linkage analysis software, into approximately 440 additional family members for whom chip based genotypes are available to indicate which parental haplotype is transmitted. Extensive phenotype data is provided for 1048 individuals. These include 5 sequenced individuals who do not belong to any of the 20 large pedigrees. Phenotype information was collected between 1991 and 2011 in the two contributing longitudinal studies. SAFHS participants may have information from up to 5 visits, and SAFDGS participants may have up to 4 visits. The clinical variables reported are coordinated with T2D-GENES Project 1 (multi-ethnic exome sequencing) and include T2D status and age at diagnosis, glycemic traits (fasting and 2 hour glucose and insulin), blood pressure, blood lipids (total cholesterol, HDL cholesterol, calculated LDL cholesterol and triglycerides), clinical chemistry (cystatin c, glutamic acid decarboxylase antibody titer (GadAb), creatinine, adiponectin and leptin). Glycated hemoglobin (HbA1c) was not measured for these individuals and insulin C-peptide is not included in this data set. Additional phenotype data include the medication status at each visit, classified in four categories as any current use of diabetes, hypertension or lipid-lowering medications, and, for females, current use of female hormones. Anthropometric measurements include age, sex, height, weight, hip circumference, waist circumference and derived ratios. Each phenotype variable has an initial summary column containing the most recent non-missing measurement for each individual, followed by the five potential time points for each individual, the number of non-missing measurements, and the age and year for the most recent non-missing measurement. For historical reasons, the order in which variables are presented on the dbGaP web site differs from their order in the data download file. When reading the comment fields for each variable, please note that commas are omitted to support data exchange in .csv format.

  Study phs000462