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• National Human Genome Research Institute (NHGRI) Clinical Sequencing Exploratory Research (CSER) The MedSeq Project: Integration of Whole Genome Sequencing into Clinical Medicine (HG006500)

  Whole genome sequencing (WGS) and whole exome sequencing (WES) services are currently available to and being utilized by physicians and their patients in both research and clinical settings, and recently to anyone in the general public via direct-to-consumer companies. But the widespread availability and use of WGS and WES in the practice of clinical medicine is imminent. In the very near future, sequencing of individual genomes will be inexpensive and ubiquitous, and patients will be looking to the medical establishment for interpretations, insight and advice to improve their health. Developing standards and procedures for the use of WGS information in clinical medicine is an urgent need, but there are numerous obstacles related to integrity and storage of WGS data, interpretation and responsible clinical integration. The MedSeq Project is an exploratory trial of WGS in clinical medicine. At the conclusion of this study, we will have helped create innovative protocols and novel outcome measures that can be applied safely in future large-scale multi-site randomized clinical trials with larger numbers of physicians from broad specialties and with more economically and ethnically diverse patients. Together with our colleagues from across the nation through the U01 consortium formed as a result of this funding from the NIH, we will have invented a process of implementation and evaluation whereby the fruits of the Human Genome Project can be applied for the first time to the daily practice of medicine for the betterment of human health. The objectives of the MedSeq Project are to: Recruit, consent and enroll 2 study groups: 10 primary care physicians and 100 of their healthy middle-aged patients 10 cardiologists and 100 of their patients with cardiomyopathy. Randomize each study group to receive standard of care versus standard of care plus WGS. Monitor the entire protocol for subject safety. Only half the enrolled patients were selected for sequencing. Fifty subjects were selected from the primary care cohort and fifty were selected from the cardiomyopathy cohort. Whole genome sequencing was performed at 30x coverage in Illumina's CLIA-certified laboratory on these 100 individuals. Generate and optimize an algorithm for interpreting WGS data covering the spectrum of human genetic variation, in terms of both previously reported and novel variants likely to influence the health of patients. Create patient reports and provide an interface for communicating clinically relevant genomic information to practicing physicians. Describe physicians' and patients' attitudes toward, and preferences for, the disclosure of WGS results at the start of the study. Evaluate physicians' experiences with receiving and interpreting patients' genetic test results and how they communicate these results to their patients. Explore how patients respond to and use WGS results by administering validated scales of psychological impact, personal utility, and behavioral responses, as well as economic and health outcomes. Although we do not have a large enough sample size for statistical comparisons of outcomes, we will conduct exploratory comparisons: Exploratory Hypotheses: Patients who receive WGS results will show equivalent levels of distress compared to patients who receive family history only. Patients with higher genetic literacy and better understanding will report greater satisfaction and less decisional regret. Patients who receive WGS will (a) be more likely to change health behaviors and (b) utilize more health care resources than those who do not receive WGS.

  Study phs000958

• HTAN MCL Pre-Cancer Atlas Pilot Project - Targeted Sequencing Development Study

  The HTAN-MCL Pre-Cancer Atlas Pilot Project (PCAPP) is the result of a collaboration between the seven members of the MCL consortium. Across four organ types, PCAPP's goal is to collect and profile pre-malignant lesions for gene expression, DNA mutations, single-cell gene expression and immune-environment. Most PML are small in size and only available come from formalin fixed paraffin embedded archived tissue. The primary goal of PCAPP is to 1) understand the logistical challenges of PML specimen collection, 2) document technical limitations of the assays that are specific to the PML and 3) overcome them to support the generation of a more comprehensive Pre-Cancer Atlas in the future. The current upload provides RNA and DNA sequencing from participants with DCIS who were studied at the University of San Diego and the University of Vermont. Description of the overall study: A. Background/Significance One of the critical barriers to developing new approaches for cancer detection and prevention is the lack of understanding of the key molecular and cellular changes that cause cancer initiation and progression. Unlike the extensive work that has been done profiling advanced stage tumors, few studies have comprehensively profiled the molecular alterations found in precancerous tissues. Premalignant lesions are currently characterized by histologic changes that precede the development of invasive carcinoma1,2.These lesions can often be identified in regions surrounding an invasive tumor or in biopsies taken from patients undergoing diagnostic evaluation for suspicion of cancer. Currently, limited metrics exist to identify lesions that will likely progress to carcinoma and require intervention from those that will naturally regress or remain stable3,4. Characterization of the molecular alterations in premalignant lesions and the corresponding changes in the microenvironment would hasten the development of biomarkers for early detection and risk stratification as well as suggest preventive interventions to reverse or delay the development of cancer. Our pilot study will establish the feasibility of transcriptomic, genomic and immune profiling of FFPE premalignant lesions from multiple organ sites, collected and profiled with uniform SOPs across multiple institutions within the MCL consortium. We will characterize the molecular alterations in precancerous lesions and the corresponding microenvironment in four major organ sites, in order to uncover the molecular and cellular determinants of premalignancy, and establish standardized sequencing and immunohistochemistry protocols on FFPE precancerous tissue. We will also evaluate the technical feasibility of single nuclei sequencing of small FFPE pre-cancer lesions. Successful completion of the proposed pilot study will set the stage for expansion and development of a comprehensive Pre-Cancer Atlas (PCA) as part of the NCI's moonshot.B. Specific Aims Aim 1: Collect premalignant lesions (PML) and their associated microenvironment via LCM from FFPE tissue across four organ sites (breast, lung, pancreas & prostate). Aim 2: Perform bulk RNA and DNA seq on premalignant FFPE samples (and flash frozen tissue where available) and compare the genomic/transcriptomic alterations within and across organ sites. C. ApproachAim 1: Collect premalignant lesions (PML) and their associated microenvironment via LCM from FFPE tissue across four organ sites (breast, lung, pancreas & prostate). MethodsI. Patient Population/Sample Collection: Overview of the sites collecting PML tissue from the respective organs is provided in Table 1 and a full description of the biospecimens to be obtained is described in detail for each organ type below. Table 1. Breakdown of cohort by tissue type and collection site.Organ siteBreastLungPancreasProstateType of PMLDCISAAH, Squamous Dysplasia/CISIPMNsPINCollection of PatientsUCSF/UCSDUVMBU*/UCLAVanderbilt/MoffittMDACC*JHUStanford*# of Patients201920 (10 of each type)20 (10 of each type)242020Total patients per Organ39402440Note: single nuclei/cell RNA-Seq will be performed on 4-5 FFPE samples from each of the organ types 1. DCIS lesions from breast tissue: DCIS lesions will be collected from 39 patients (20 from UCSF/UCSD & 19 from UVM) with primary low or high-grade DCIS diagnosed from a breast core biopsy. Subsequent resected lumpectomy or mastectomy tissues will be prospectively sampled in the vicinity of the prior biopsy site using multiple approaches: 1) Live cells (heterogeneous mix) will be obtained as a cell scrape slurry from the lesion surface or by fine needle aspirate (FNA); 2) For a subset of specimens where size is sufficient, a block of breast tissue with DCIS will be fresh-frozen; 3) The remainder of the specimen will be taken for routine formalin-fixation and paraffin-embedding (FFPE). The FFPE sample will be annotated to identify the matched FFPE tissue block adjacent to the fresh-frozen sample and will be sectioned for use in bulk and single nuclei sequencing . We will dissect DCIS, adjacent normal and when available, associated carcinoma. In addition, when possible, normal tissue will be collected from a tissue block lacking lesions as well as collection of blood. A subset of patients (n = 5 | FFPE, flash frozen and fresh) will be sent to the Broad Institute for single nuclei/cell sequencing.2. AAH and squamous dysplastic/CIS lesions from airway and lung tissue: For squamous cell lung cancer, we will collect endobronchial biopsies from abnormal airway regions identified on autofluroscence bronchoscopy or identify PMLs in the margins of resected lung tissue. We will study 20 patients (5 each from BU/UCLA/Vanderbilt/Moffitt) with pre-invasive squamous lesions (moderate-severe dysplasia or carcinoma in situ (CIS)) identified on pathologic examination. LCM of the premalignant region and adjacent normal epithelium will be performed as well as the invasive tumor for those collected from the resection margin (n=5 from UCLA). On a subset of lesions collected at bronchoscopy (n=5), we will collect additional biopsies that will be flash frozen and fresh for single nuclei and cell sequencing, respectively, performed at the Broad Institute. In parallel to the work at the Broad, BU will perform single cell RNA-seq on these freshly cell sorted tissues (n = 5). Blood will be collected on all patients for genomic studies. For lung adenocarcinoma, we will collect resected FFPE lung tissues from 20 patients (10 from UCLA and 10 from Vanderbilt/Moffitt) with early stage lung adenocarcinoma that harbor atypical adenomatous (AAH) premalignant lesions in the resection margin. We will LCM multiple AAH regions (3-5 per patient) as well as adjacent regions of normal epithelium and invasive adenocarcinoma. In addition, blood will be collected on all patients for genomic studies. 3. IPMNs from pancreatic tissue: For pancreatic cancer PML, we will collect low and high grade lesions from 24 patients representing macroscopic Intraductal Papillary Mucinous Neoplasms (IPMN) (n=24) from surgically resected specimens along with blood samples. Archival FFPE specimens of microscopic PanIN lesions, occurring multi-focally adjacent to invasive PDAC, and archival IPMN lesions (with or without associated invasive cancer), along with the adjacent normal tissue, will undergo LCM and utilized for bulk DNA and RNA sequencing. If matched frozen tissues are available for a subset of these FFPE samples, we will bank for comparison of profiles. Because IPMNs are macroscopic lesions, they provide an opportunity for obtaining the samples fresh and therefore can be used for single cell sequencing (in contrast to PanINs). Therefore, 5 freshly obtained IPMNs will be used for the single cell RNA sequencing studies performed at both the Broad Institute and MDACC, and the matched FFPE and/or frozen sections from these lesions (obtained from the adjacent PML) will be sent to Broad Institute as a pilot to assess "single nuclei" RNA sequencing.4. PINs from prostate tissue: For prostate cancer PML, there will be 40 samples of Prostatic Intraepithelial Neoplasia (PIN) collected between the Stanford and JHU sites (20 cases per site). At the Stanford site, 20 prostate specimens detected by PSA screening who have/will undergo surgery (radical prostatectomy) for clinically localized disease will make up the final cohort. The age range of the participants would be 40-75, and we anticipate that 18 will be Caucasian, 1 Asian and 1 Latino or African American based on the practice demographics practice at Stanford. Clinical and MRI data will also be collected for these samples. We will collect low grade (e.g. Gleason score of 6/Grade group 1; n=10) and high grade (Gleason score 4+3=7 or higher/Grade group 3 or higher; n=10) PINs from FFPE samples that have prostate carcinoma. In addition to obtaining LCM archival samples of low and high grade PIN, we will also obtain normal prostatic epithelial from the peripheral, central and transition zones as well as multiple samples of prostate carcinoma in order to obtain the spectrum of Gleason grades in the carcinoma as needed. LCM samples will be used for bulk DNA and RNA sequencing. In addition, single cells will be dissected from FFPE samples to prepare single cell RNA seq libraries using techniques developed at Stanford, and FFPE tissue will be sent to the Broad for single nuclei sequencing. When available, flash frozen and fresh samples from these prostates will be archived and prepared for single nuclei and cell sequencing, respectively, at the Broad Institute and at Stanford (single cell only). JHU will also capture 10 cases (5 grade group 1 and 5 grade group 2) of high grade PIN, normal and invasive adenocarcinoma using frozen sections from fresh frozen tissues. When possible these will be from the same patients as the FFPE samples. Since frozen sections can be quite challenging to morphologically determine high grade PIN from normal epithelium, for these samples we will perform a number of additional tissue-based characterizations. These will include a multicolor combined basal cells (p63 and CK903) and PIN/carcinoma markers (AMACR) referred to in the cocktail as "PIN4", c-MYC (referred to as MYC) protein5, by IHC and mRNA by in situ hybridization (AM De Marzo, Q Zheng unpublished observations), telomere length by in situ hybridization6 and the 5'ETS/45S rRNA7. For these slides, the whole slides will be scanned with a Hammamatsu Nanozoomer with a 40x objective and regions of interest will be annotated as a guide for LCM.II. Laser-capture microdissection (LCM): FFPE tissue blocks will be sectioned at 7μm thickness and serial sections will be stained with H&E. LCM will be performed utilizing standard LCM systems, such as Leica LMD7000 and ArcturusXT at each site. Regions of premalignancy will be dissected and RNA/DNA will be extracted from microdissected cells using the Qiagen All Prep DNA/RNA FFPE Kit. Aim 2: Perform bulk RNA and DNA seq on premalignant FFPE samples and compare the genomic/transcriptomic alterations within and across organ sites. Rationale: There have been limited studies characterizing the genomic and transcriptomic landscape of premalignant lesions associated with breast, pancreatic, lung or prostate cancers. Characterizing the molecular determinants of premalignant disease that are unique and shared across multiple organs will enable new candidate biomarkers for early detection and novel therapeutic strategies for early intervention. MethodsBulk RNA-seq of LCM FFPE tissue: All participating sites will perform bulk RNA-seq in accordance with SOPs developed at BU. In brief, total RNA will be isolated from LCM'd lesion and associated microenvironment tissue using the Qiagen All Prep DNA/RNA FFPE Kit and quality will be assessed with the Agilent Bioanalyzer. Libraries will be generated with the Illumina TruSeq Access kit (for FFPE samples). They will be sequenced on the Illumina HiSeq2500 with 75base-pair paired-end reads. Quality of FASTQ files will be assessed with FastQC. Reads will be aligned to the human genome with STAR and gene-level and isoform-level expression will be quantified with RSEM. Splice junction saturation, transcript integrity, and biotype distributions will be calculated for each sample with RSeQC. DESeq2 and EdgeR will be used to identify associations between gene expression profiles and clinical variables while controlling for confounding covariates. BU will serve as an RNA-seq Core to assess reproducibility of FFPE RNA-seq methods across sites. We will perform RNA-seq according to the SOP listed above on a subset of samples for each organ type (total n ~ 20). Bulk seq of DNA from FFPE tissue: All participating sites will perform targeted or whole exome-seq (WES) in accordance with SOPs. In brief, DNA from laser captured material will be isolated using the Qiagen All Prep DNA/RNA FFPE Kit and undergo stringent quality control to ensure high quality input material for genomic profiling. Purified DNA (ideally 100-200 ng) will be used for library preparation and amplification, followed by next generation sequencing using standard protocols distributed by CDMG. Exome-seq methods are considered standardized, thus we will not need a DNA-seq Core to assess reproducibility across sites. We anticipate local centers will use Illumina paired end reads, following the following general approach. 1) DNA library preparation: Paired-end libraries will be prepared following the manufacturer's protocols (Illumina and Agilent), fragmented to 150-200 bp 2) Capture of targeted exome: Whole exome capture will be carried out using the protocol for Agilent's SureSelect Human All Exon kit. Purified capture products will be amplified using the SureSelect GA PCR primers (Agilent) for 12 cycles. 3) Sequencing will be carried out for the captured libraries using at least 100 bp paired-end reads. To achieve high level sensitivity and accuracy for detecting all the mutations in the whole exome, each sample will be sequenced at 200X mean depth. 4) Read mapping and alignment and variant analysis: Sequence short reads will be aligned to a reference genome (NCBI human genome assembly build 38) using BWA-MEM. Local realignment of aligned reads will be performed using Genome Analysis Toolkit (GATK).Data QC: To ensure scientific rigor and consistency among sites in RNA and DNA processing we will include a preliminary analysis of steps in processing and analysis. Protocols for extraction of high quality RNA and DNA from formalin fixed paraffin embedded (FFPE) tissues, which will be used extensively in these studies continue to improve and may have variable implementation among the sites participating in this study. To evaluate consistency of preliminary steps in processing and downstream analyses, we will initially distribute slides from one large FFPE fixed cancer of origin from prostate, breast, lung and pancreatic cancer. Analysis of these samples will allow us to review the DNA and RNA characteristics (yield, purity and strand length) among sites. Downstream analysis of these same samples will also allow us to compare among sites the consistency of variant calls among centers. We will be able to identify if there are some times of calls (such as small insertion deletions) that are more variable among centers versus other types of calls (such as relative gene expression or single base pair substitutions) that we expect to be less variable and to characterize the reliability of findings across sites. We are also including a 5% blind duplicate analysis of RNA sequencing. Samples will be analysed by the participating genomics cores without knowledge of the phenotype. RNA seq and CNA analyses are normalized for batch effects. We will also compare the observed sex to the self-reported sex as based on RNA profiles and exome sequencing of X chromosome genes as another check for processing accuracy and sample management. D. References 1. Wacholder, S. Precursors in Cancer Epidemiology: Aligning Definition and Function. Cancer Epidemiol. Prev. Biomark. 22, 521-527 (2013). PMID: 23549395.2. Berman, J. J. Precancer: The Beginning and the End of Cancer. (Jones & Bartlett Learning, 2011).3. Nasiell, K., Nasiell, M. & Vaćlavinková, V. Behavior of moderate cervical dysplasia during long-term follow-up. Obstet. Gynecol. 61, 609-614 (1983). PMID: 6835614.4. Merrick, D. T. et al. Persistence of Bronchial Dysplasia Is Associated with Development of Invasive Squamous Cell Carcinoma. Cancer Prev. Res. (Phila. Pa.) 9, 96-104 (2016). PMID: 26542061.5. Gurel, B. et al. Nuclear MYC protein overexpression is an early alteration in human prostate carcinogenesis. Mod. Pathol. Off. J. U. S. Can. Acad. Pathol. Inc 21, 1156-1167 (2008). PMID: 18567993.6. Meeker, A. K. et al. Telomere shortening is an early somatic DNA alteration in human prostate tumorigenesis. Cancer Res. 62, 6405-6409 (2002). PMID: 12438224.7. Guner, G. et al. Novel Assay to Detect RNA Polymerase I Activity In Vivo. Mol. Cancer Res. MCR 15, 577-584 (2017). PMID: 28119429.

  Study phs002225

• Center for Common Disease Genomics [CCDG] - Cardiovascular: TexGen

  Cardiovascular disease (CVD), especially coronary heart disease, heart failure and cerebrovascular disease remain the leading causes of death in men and women across all race groups in the United States. Substantial evidence exists for genetic factors underlying CVD risk, and their discovery offers an opportunity to enhance understanding of disease mechanisms, to provide specific diagnostic and prognostic indicators, and to identify novel therapeutic targets. The Centers for Common Disease Genomics (CCDG) are a large-scale genome sequencing effort undertaken as a collaboration to identify rare risk and protective alleles for common chronic diseases, with a current focus on early onset heart disease, hemorrhagic stroke, and autism. In this study, whole genome sequencing (WGS) was performed in 6,146 individuals with any personal or family history of CVD from the TexGen study who were recruited from several institutions in the Texas Medical Center located in Houston, Texas. The participants included patients who were admitted with a variety of diagnoses including acute coronary syndromes, strokes, and transient ischemic attacks, or who underwent percutaneous coronary interventions or coronary artery bypass grafting (CABG) (Virani SS et al. Am J Cardiology 107:1504-1509, 2011). Patients in the TexGen cohort with a confirmed diagnosis of acute coronary syndrome (ACS) or CABG when discharged from the hospital between 2001-2008 were eligible for a follow-up study of recurrent myocardial infarction (Virani SS et al. Circulation J 76:950-956, 2012), while those presenting with ACS beginning in 2007 were recruited for an investigation of the role of depressive symptoms in the risk of major adverse coronary events (Sanner J et al. Biol Res Nurs 20:168-176, 2018). In addition, the initial criterion for enrollment in a third TexGen sub-study undertaken between 2007 and 2013 was the occurrence of premature acute myocardial infarction in men ≤ 50 years and women ≤ 55 years in order to establish a blood sample collection resource with the intention of localizing genes that contribute to disease risk. This definition was later expanded to include individuals with a clinical history of premature coronary heart disease such as CABG or percutaneous coronary interventions.

  Study phs003010

• Effectiveness and Safety of Intermittent Antimicrobial Therapy for the Treatment of New Onset Pseudomonas Aeruginosa Airway Infection in Young Patients With Cystic Fibrosis (EPIC-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. Objectives: To investigate the efficacy and safety of 4 antipseudomonal treatments in children with cystic fibrosis (CF) with recently acquired Pseudomonas aeruginosa (PA) infection.Background: CF is an inherited disease that causes mucus to build up in the lungs and digestive tract, which can cause lung infections and digestive problems. It is the most common type of chronic lung disease in children and young adults and may result in early death. There is no cure for this disease. The primary cause of death in individuals with CF is progressive obstructive pulmonary disease associated with chronic Pseudomonas aeruginosa (PA) infection. PA infection can occur early in life and can become highly resistant to antibiotics. Once an individual has been diagnosed with chronic PA infection, it is almost impossible to manage effectively. The need exists for an effective treatment to control and eliminate PA infection. Past research has shown that if PA infection is treated early, there is a greater likelihood that it may be eliminated completely.Participants: There were 304 participants.Design: Participants were randomized to 1 of 4 antibiotic regimens for 18 months (six 12-week quarters) between December 2004 and June 2009. Participants randomized to cycled therapy received tobramycin inhalation solution (300 mg twice a day) for 28 days, with oral ciprofloxacin (15-20 mg/kg twice a day) or oral placebo for 14 days every quarter, while participants randomized to culture-based therapy received the same treatments only during quarters with positive P aeruginosa cultures. The primary end points were time to pulmonary exacerbation requiring intravenous antibiotics and proportion of PA - positive cultures.Conclusions: No difference in the rate of exacerbation or prevalence of PA positivity was detected between cycled and culture-based therapies. Adding ciprofloxacin produced no benefits (Arch Pediatr Adolesc Med 2011; 165(9):847-856).

  Study phs004067

• Automated machine-learning approach for next generation profiling of sequence alterations, mutation burden, microsatellite instability, and structural variants in human cancers

  Sequence and structural alterations together with tumor mutation burden (TMB) and microsatellite instability (MSI) have been identified as biomarkers for the determination of response to targeted and immune checkpoint inhibitor therapies. However, widespread clinical adoption of these biomarkers has historically been limited due to barriers such as evidence of clinical utility and reimbursement. We have developed 2.2 Mb targeted NGS system and an automated machine-learning analysis approach (PGDx elio™ tissue complete, ETC) that has been FDA cleared for examination of 500+ cancer-related genes and 68 mononucleotide repeats for identification of sequence and structural alterations, TMB, and MSI in solid cancers in a clinical setting. We designed and trained this approach using sequence data from 4,174 cancers and >124,000 in silico alterations and evaluated the methodology in >2,550 tumor or non-cancerous normal samples. Independent analyses of ETC sequence changes in 440 formalin fixed paraffin embedded (FFPE) tumor or cell line samples using MSK-IMPACT™, FoundationOne®, and ddPCR revealed a positive percent agreement (PPA) >97% with high sensitivity as low as 3% mutant allele fraction. We observed high concordance between panel-wide and whole-exome TMB for 307 pan-cancer FFPE tumors (Pearson r=0.95, p < 0.0001) using samples with ≥20% tumor cellularity. Comparison of the mutation context and repeat-based MSI approach in ETC with a multiplex MSI PCR assay in 223 samples revealed a PPA of 99% and negative predictive agreement (NPA) >99%. We confirmed the accuracy and precision of TMB and MSI measurements across three independent laboratories (CV of <5% and average PPA >99%, respectively). Finally, evaluation of amplifications and translocations against DNA and RNA-based approaches exhibited >98% NPA and PPA of 86% and 82% respectively. These results demonstrate high analytical performance for determination of sequence and structural changes, TMB, and MSI using a targeted NGS panel and provide a scalable and facile approach for evaluating these biomarkers in a clinical laboratory.

  Study EGAS00001005556

• Professors Colin Palmer and Ewan Pearson, from University of Dundee, are both members of the Access Group panel for the GoDARTS bioresource, which provided the data for the current study. The current Study used genotypes (EGAD00010000282) generated by the WTCCC2 (EGAS00000000121), on which both Colin and Ewan are also DAC panel members.

  Dac EGAC00001000504

• DAC for "Establishment and characterization of circulating tumor cells-derived organoids from metastatic breast cancer patients."

  This is the DAC for the study "Establishment and characterization of circulating tumor cells-derived organoids from metastatic breast cancer patients." of Andreas Trumpp (a.trumpp@dkfz.de), Roberto Würth (r.wuerth@dkfz.de) and Martin Sprick (Martin.Sprick@hi-stem.de).

  Dac EGAC50000000371

• NGS-based targeted exome sequencing of osteosarcoma

  The present study aimed to identify potential genomic markers for the prediction of chemosensitivity in patients with OS using a genomic approach.

  Study JGAS000282

• Clinical and neuroimaging study on preclinical Alzheimer's disease.

  This clinical study aims to discriminate MCI individuals at risk for development of Alzheimer dementia, as well as preclinical AD without clinical manifestations.

  Study JGAS000272

• Zimbabwe Mendelian Disorders Genomics DAC

  Data Access Committee responsible for reviewing and approving access requests to human genomic data generated from individuals with suspected Mendelian disorders. The DAC ensures ethical use of genomic data in accordance with institutional, national, and international guidelines, protecting participant privacy while enabling responsible data sharing for research purposes.

  Dac EGAC50000000963

• WGS of ecDNA neuroblastoma cell lines

  ecDNA reconstruction for MYCN-amplified neuroblastoma cell lines using shallow long-read whole-genome sequencing (MinION platform, WGS mean-coverage 5-10X).

  Study EGAS50000000349

• scRNA-seq for 4 reactive lymph node and 12 high grade B cell lymphoma samples

  Dataset includes count matrices, barcode tsvs, and features tsv for each sample, generated using Cell Ranger.

  Dataset EGAD50000001386

• miRNA

  miRNA Sequencing of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Dataset EGAD50000001532

• Dataset for "HPV integration induces gene fusions" (pacBio)

  pacBio whole-genome sequencing data for "HPV integration induces gene fusions" We performed long read whole-genome sequencing on four HPV+ head and neck cancer samples using pacBio HiFi. The sequence reads were submitted in fastq format.

  Dataset EGAD50000001304

• WGS dataset for two NUP98-Rearranged Acute Myeloid Leukemia PDX samples

  This dataset includes whole genome sequencing of two patient-derived xenograft (PDX) samples with NUP98-Rearranged Acute Myeloid Leukemia. Bam files are provided for each sample.

  Dataset EGAD50000001563

• Dataset for WGS and RNA melanoma samples

  This dataset contains WGS and RNA sequencing data for 4 melanoma samples. Sequencing was performed on Illumina Novaseq 6000 and Illumina HiSeq X. The sequencing was always paired.

  Dataset EGAD50000000093

• Exome_sequencing_of_Non_syndromic_Congenital_Heart_Defects

  Exome sequencing of ~1,800 patients with non-syndromic Congenical Heart Defects (CHD) to identify genes enriched for damaging rare variants that increase risk of CHD

  Study EGAS00001002522

• WTCCC2 Bacteraemia Susceptibility (BS) samples

  A WTCCC2 project genome-wide association study for bacteraemia susceptibility in 4924 individuals from Kenya, genotyped on the Affymetrix 6.0 array.

  Study EGAS00001001756

• Discordant_Monozygotic_Twins_ALS (Epigenetics)

  We conducted a multi-omics study on a monozygotic twin pair discordant for amyotrophic lateral sclerosis. Here, we submit epigenetic data from EPIC array.

  Study EGAS00001008053

• Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS)

  Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS). The dataset includes 21 samples from 7 families with BAMS; see Gordon et al, Nature Genetics, 2017.

  Dataset EGAD00001003130

• Transcriptomic profiles of neuroblastoma PDXs and primary tumors

  This dataset contains bam files for RNA-seq experiments for 6 neuroblastoma PDXs (Patient Derived Xenograft) and 3 pairs of neuroblastoma tumors at diagnosis and at relapse.

  Dataset EGAD00001003393

• Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Whole Genome Sequencing for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Dataset EGAD00001003435

• Exome and Transcriptome for pan-cancer gene-drug analysis

  Total of 584 tumor specimens and/or patient-derived cells across 14 cancer types were subjected for whole-exome/targeted-exome and/or whole-transcriptome sequencing.

  Dataset EGAD00001003441

• Exome sequencing of patients with acute promyelocytic leukemia

  The dataset consists in 64 fastq files from 23 patients with acute promyelocytic leukemia. Exome sequencing was conducted on several stages (Diagnosis, Remission, Relapse) for each patient. For 5 patients, only Diagnosis and Relapse samples are available.

  Dataset EGAD00001004043

• A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases

  A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases

  Dataset EGAD00001003907

• Oslo University Hospital Data Access Committee no 2 for Celiac Disease datasets submitted to FEGA Norway

  This is the Data Access Committee appointed by Oslo University Hospital for governing access to Celiac Disease datasets submitted to FEGA Norway, under the Regional Ethical Committee approval 6544, with main contact Rasmus Iversen.

  Dac EGAC50000001040

• BLUEPRINT release January 2015, DNase-Hypersensitivity for monocyte

  DNase-Hypersensitivity data for 2 monocyte sample(s). 4 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001185

• Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study

  Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study

  Dataset EGAD00001000806

• Whole Exome Sequencing (WES) for St. Jude High Grade Glioma (HGG) study

  Whole Exome Sequencing (WES) for St. Jude High Grade Glioma (HGG) study

  Dataset EGAD00001000807

• GENCORD2_GENOTYPES

  204 individuals were genotyped with the Illumina 2.5M Omni chip. Filtered genotypes were imputed into the 1000 genomes project European panel SNPs. Beagle R2 is indicated in VCF files for further filtering. See Materials and Methods in publication for details.

  Dataset EGAD00001000428

• BLUEPRINT September 2016, ATAC-seq for bone marrow, on Genome GRCh38

  ATAC-seq data for 4 sample(s) from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002710

• Whole exome sequencing of human and mouse sarcoma samples for personalized therapy

  Whole exome sequencing of human and mouse sarcoma samples for creation of personalized therapy options. Tissues were sequenced directly; no interventions or alterations were made to the tissue samples

  Dataset EGAD00001004885

• Exome sequencing of Non-syndromic Congenital Heart Defects (2019-04-24)

  Exome sequencing of ~1,800 patients with non-syndromic Congenical Heart Defects (CHD) to identify genes enriched for damaging rare variants that increase risk of CHD . This dataset contains all the data available for this study on 2019-04-24.

  Dataset EGAD00001004975

• RNAseq files for Mullighan_GL_reALL RNASEQ2

  RNAseq files for Mullighan_GL_reALL RNASEQ2 paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001005510

• RNASeq files for Mullighan_GL_reALL RNASEQ1

  RNASeq files for Mullighan_GL_reALL RNASEQ1 paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001005511

• Reference exome data for a Northern Brazilian population

  Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from the State of Rio Grande do Nord in Brazil. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil.

  Dataset EGAD00001006407

• Exome and Targeted sequencing of GZL

  Tumor and matching normal exomes for 28 GZL cases (n=56) and targeted capture sequencing for 42 GZL cases with 3 matching normals and 2 pooled normals (n=47)

  Dataset EGAD00001006328

• Single cell karyotype sequencing of 7 samples from colorectal cancer (CRC) patients

  Contains data for all cells sequenced for this study. Data is organized as one bam-file per sample. Individual cells can be identified through the CB tag in the bam-files.

  Dataset EGAD00001006438

• Glioblastoma stem cell lines WGS data

  WGS data for 20 Glioblastoma stem cell (GSC) lines and matched blood samples. Fastq files are available. For 10 GSC samples and the 10 matched blood samples the reads are on 3 fastq files per sample

  Dataset EGAD00001006488

• Cram files for study entitled Compound heterozygous variants in LAMC3 in association with posterior periventricular nodular heterotopia

  This dataset contains three cram files for paired end sequencing of a trio, sequenced with Illumina Hiseq 2500

  Dataset EGAD00001006578

• Data for the genome‐wide association study of cutaneous leishmaniasis in Brazil

  DNAs were genotyped on Illumina Infinium HumanCoreExome Beadchips (Illumina Inc., San Diego, CA, USA) with probes for 551,004 single nucleotide variants (SNVs): 282,373 informative across ancestries; 268,631 exome-focused. Human genome build 37 (hg19) was used.

  Dataset EGAD00001006681

• A95646B

  Whole genome sequencing for single cells for library A95646B 507 cells; filetype=bam

  Dataset EGAD00001007306

• PPIL4 is essential for brain angiogenesis and implicated in intracranial aneurysms in humans

  Patients in IA cohort with PPIL4 mutations (Please see Supplementary Table 3 for clinical characteristics of the patients)

  Dataset EGAD00001008106

• RNA-Seq data for manuscript titled: CBL0137 impairs homologous recombination repair and sensitizes high-grade serous ovarian carcinoma to PARP inhibitors Sequencing

  RNA-Seq data for manuscript titled: CBL0137 impairs homologous recombination repair and sensitizes high-grade serous ovarian carcinoma to PARP inhibitors Sequencing

  Dataset EGAD00001009799

• KiCS WGS data for academic use only

  Data from samples that are marked for academic use only

  Dataset EGAD00001009698

• WGS files for Klco-NUP98 data

  WGS files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015443

• WXS files for Klco-NUP98 data

  WXS files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015444

• RNASeq files for Klco-NUP98 data

  RNASeq files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015445

• Transcriptomic data for Human proximal tubular epithelial cell interleukin-1 receptor signalling triggers cell cycle arrest during hypoxic kidney injury

  Transcriptomic data for manuscript titled: Human proximal tubular epithelial cell interleukin-1 receptor signalling triggers cell cycle arrest during hypoxic kidney injury.

  Dataset EGAD00001015460

• scRNASeq files for Klco-NUP98 data

  scRNASeq files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia" PMID: 39974131, PMCID: PMC11838931, DOI: 10.1101/2025.01.21.25320683

  Dataset EGAD00001015479