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• WGS and RNA-Seq data from a GBM patient PT-GC1519

  WGS and RNA-Seq data from a GBM patient PT-GC1519

  Dataset EGAD00001004239

• WGS and RNA-Seq data from a GBM patient PT-VO7089

  WGS and RNA-Seq data from a GBM patient PT-VO7089

  Dataset EGAD00001004263

• WGS and RNA-Seq data from a GBM patient PT-MD9088

  WGS and RNA-Seq data from a GBM patient PT-MD9088

  Dataset EGAD00001004254

• WGS and RNA-Seq data from a GBM patient PT-JE6375

  WGS and RNA-Seq data from a GBM patient PT-JE6375

  Dataset EGAD00001004246

• WGS and RNA-Seq data from a GBM patient PT-RD1291

  WGS and RNA-Seq data from a GBM patient PT-RD1291

  Dataset EGAD00001004256

• WGS and RNA-Seq data from a GBM patient PT-WT4796

  WGS and RNA-Seq data from a GBM patient PT-WT4796

  Dataset EGAD00001008532

• Genome and transcriptome sequence data from a GBM (H3 K27M mutant) tumor patient

  Genome and transcriptome sequence data from a GBM (H3 K27M mutant) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015328

• Genome and transcriptome sequence data from a high-grade glioma, glioblastoma tumor patient

  Genome and transcriptome sequence data from a high-grade glioma, glioblastoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015336

• Genome and transcriptome sequence data from a neurofibromatosis type 1 (NF1) tumor patient

  Genome and transcriptome sequence data from a neurofibromatosis type 1 (NF1) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015266

• Genome and transcriptome sequence data from a NHL large B cell tumor patient

  Genome and transcriptome sequence data from a NHL large B Cell patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015274

• Genome and transcriptome sequence data from a malignant granular cell tumor tumor patient

  Genome and transcriptome sequence data from a malignant granular cell tumor patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015275

• Genome and transcriptome sequence data from a progressive facial plexiform neurofibroma tumor patient

  Genome and transcriptome sequence data from a progressive facial plexiform neurofibroma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015282

• Knoll et al Identification of drug candidates targeting monocyte reprogramming in people living with HIV

  Introduction People living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics layers. Methods Bulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation was performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study. Results Single-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Moreover, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV. Discussion These scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.

  Study EGAS00001007460

• Genetic Components of Knee Osteoarthritis (GeCKO) Study: The Osteoarthritis Initiative

  The Osteoarthritis Initiative (OAI) is a publicly and privately funded prospective longitudinal cohort with a primary objective of identifying risk factors for incidence and progression of tibiofemoral knee OA. The OAI utilized a focused population-based recruitment to enroll 4,674 men and women between the ages of 45-79 years who either had radiographic symptomatic knee OA or who were without radiographic symptomatic OA in both knees but were considered high risk for OA because they had two or more known risk factors for knee OA. Subjects were recruited into the baseline phase of the OAI at multiple sites throughout the US between 2004 and 2006. All subjects were invited back for follow-up examinations to assess incidence or progression of OA annually, for up to 5 years. Phenotype data from the baseline and follow-up examinations are available for public access from the Osteoarthritis Initiative (OAI) database at http://www.oai.ucsf.edu/. The Genetic Components of Knee Osteoarthritis (GeCKO) Study was initiated in 2009 as a genetic ancillary study to perform a genome-wide association study to identify genetic variants associated with radiographic osteoarthritis. This study included 4,482 individuals participating in the parent OAI study. Following sample cleaning (e.g., removal of duplicates, sex mismatches, poor sample quality, etc.), the final sample set included 4,129 individuals.

  Study phs000955

• Ischemic Stroke Genetics Study (ISGS)

  The third leading cause of death in the United States, stroke is an acute neurological event leading to death of neural tissues. Although the majority of strokes are ischemic strokes, meaning there is oxygen deprivation to the brain, almost 20% of strokes are hemorrhagic, resulting from bleeding into the brain. Stroke is a complex disorder and likely multigenic in nature, resulting from a combination of genetic and environmental factors. These well characterized risk factors that contribute to the incidence of stroke include hypertension, cardiac disease, sickle cell disease, hyperhomocysteinemia, family history of stroke and smoking. ISGS aim is to perform a prospective genetic association study of ischemic stroke focusing on the hemostatic system. ISGS is a 5-center case-control study of first-ever ischemic stroke cases and concurrent controls individually matched for age, sex and recruitment site. This data includes that from subjects both banked in the NINDS repository with biologicals publicly available, and those whose samples are not banked/not available. Important links to apply for individual-level data Data Use Certification Requirements (DUC) Apply here for controlled access to individual level data Participant Protection Policy FAQ --> This study utilized the NINDS Repository Cerebrovascular/Stroke Study, and neurologically normal controls from the sample population which are banked in the National Institute of Neurological Disorders and Stroke (NINDS Repository) collection for a first stage whole genome analysis.

  Study phs000102

• Natural History, Pathogenesis and Outcome of Melorheostosis

  Melorheostosis is a rare osteosclerotic disease resulting in exuberant excessive bone growth with a characteristic radiographic appearance often described as "dripping candle wax". As a result of these bony formations, patients report mild to moderate pain that interferes with their routine activities. It is usually diagnosed on radiographs but bone biopsy may be performed to exclude other osteosclerotic diseases and/or osteosarcoma. Deformities, limb-length discrepancy, muscle atrophy, neurological deficit have been reported as complications. A subset of patients have somatic mutations in MAP2K1. The cause of this disease is not known in all patients, the natural history poorly described and there is no clearly-defined systemic therapy. We propose a prospective observational study to investigate the natural history and pathogenesis of the disease. Subjects will undergo standardized initial evaluation and medically indicated testing. Skin biopsies may be performed to test for known mutations related to melorheostosis, and if negative affected bone and/or skin may be sent for genetic testing for acquired somatic mutations in genes that control bone homeostasis. Enrolled subjects will be followed every two to three years for assessment of disease progression and receive clinically indicated testing and treatment. The study of this rare bone disease offers the potential to generate new insights, provide answers as well as generate new questions into the biology of the skeletal and mineral metabolism.

  Study phs001976

• Whole exome sequencing to discover genetic variation associated with aortopathy in Turner Syndrome

  Turner syndrome is a disorder affecting only girls and women, which is caused by a complete or partial loss of the second sex chromosome. Girls and women with Turner syndrome have a variety of phenotypes. Of interest to this study is aortopathy, including bicuspid aortic valve (BAV) and thoracic aortic dilation (TAD) in which we know that 25 - 50% of girls with Turner syndrome are born with. The aorta is the main artery that conducts the blood out of the heart. The aortic valve guards the entrance to the aorta. When the aortic valve has two leaflets instead of the usual three it is called a BAV. BAV is more common than all other congenital heart defects combined. BAV commonly causes obstructions to blood flow out of the heart or become leaky over time. BAV often occurs in combination with TAD. In Turner syndrome, TADs are increased 50-100 fold compared to the general population. Currently, there are no effective approaches or pre-surgical treatments for aortic disease. Therefore, progression of aortic disease in individuals with BAV/TAD can result in catastrophic aortic dissection, rupture, and death. Our goal is to leverage DNA sequencing and carefully curated patient samples to gain a better understanding of the molecular mechanisms that cause these inter-related aortic diseases.

  Study phs001531

• Children's Hospital of Philadelphia (CHOP) Control Copy Number Variation (CNV) Study

  We present a database of copy number variations (CNVs) detected in 2,026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. This large cohort analyzed for CNVs in a single study using a uniform array platform and computational tools, comprises mainly of Caucasians (65.2%) and African-Americans (34.2%), We have catalogued and characterized 54,462 individual CNVs, 77.8% of which were identified in multiple unrelated individuals. These non-unique CNVs mapped to 3,272 distinct regions of genomic variation spanning 5.9% of the genome; 51.5% of these were previously unreported, and >85% are rare. Our annotation and analysis confirmed and extended previously reported correlations between CNVs and several genomic features such as repetitive DNA elements, segmental duplications and genes. We demonstrate the utility of this data set in distinguishing CNVs with pathologic significance from normal variants. Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics. The CNV resource is available at: http://cnv.chop.edu. Reprinted from Shaikh T., et al., High-Resolution Mapping and Analysis of Copy Number Variations in the Human Genome: A Data Resource for Clinical and Research Applications Genome Research. 2009, with permission from Genome Research. CHOP CNVs from 2,026 disease-free individuals are available through dbVar at http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd21.

  Study phs000199

• Identification and characterisation of pathogenic and non-pathogenic FGF14 repeat expansions

  Repeat expansions in FGF14 cause autosomal dominant late-onset cerebellar ataxia (SCA27B) with estimated pathogenic thresholds of 250 (incomplete penetrance) and 300 AAG repeats (full penetrance), but the sequence of pathogenic and non-pathogenic expansions remains unexplored. Here, we demonstrate that STRling and ExpansionHunter accurately detect FGF14 expansions from short-read genomic data using outlier approaches. By combining long-range PCR and nanopore sequencing in 169 patients with cerebellar ataxia and 802 controls, we compare FGF14 expansion alleles, including interruptions and flanking regions. Uninterrupted AAG expansions are significantly enriched in patients with ataxia from a lower threshold (180-200 repeats) than previously reported based on expansion size alone. Conversely, AAGGAG hexameric expansions are equally frequent in patients and controls. Distinct 5' flanking regions, interruptions and pre-repeat sequences correlate with repeat size. Furthermore, pure AAG (pathogenic) and AAGGAG (non-pathogenic) repeats form different secondary structures. Regardless of expansion size, SCA27B is a recognizable clinical entity characterized by frequent episodic ataxia and downbeat nystagmus, similar to the presentation observed in a family with a previously unreported nonsense variant (SCA27A). Overall, this study suggests that SCA27B is a major overlooked cause of adult-onset ataxia, accounting for 23-31% of unsolved patients. We strongly recommend re-evaluating pathogenic thresholds and integrating expansion sequencing into the molecular diagnostic process.

  Study EGAS50000000481

• Collection: Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

  The Hispanic Community Health Study / Study of Latinos (HCHS/SOL) is a multi-center epidemiologic study in Hispanic/Latino populations to determine the role of acculturation in the prevalence and development of disease, and to identify risk factors playing a protective or harmful role in Hispanics/Latinos. The study is sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and six other institutes, centers, and offices of the National Institutes of Health (NIH). The goals of the HCHS/SOL include studying the prevalence and development of disease in Hispanics/Latinos, including the role of acculturation, and identifying disease risk factors that play protective or harmful roles in Hispanics/Latinos. A total of 16,415 persons of Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American backgrounds were recruited through four Field Centers affiliated with San Diego State University, Northwestern University in Chicago, Albert Einstein College of Medicine in the Bronx area of New York, and the University of Miami. Seven additional academic centers serve as scientific and logistical support centers. Study participants aged 18-74 years took part in an extensive clinic exam and assessments to ascertain socio-demographic, cultural, environmental and biomedical characteristics. Annual follow-up interviews are conducted to determine a range of health outcomes.To request access to this collection, select phs003650 in the dbGaP when submitting a data access request.

  Study phs003650

• In vitro reconstitution of epigenetic reprogramming in the human germ line

  Epigenetic reprogramming resets parental epigenetic memories and differentiates primordial germ cells (PGCs) into mitotic pro-spermatogonia or oogonia, ensuring sexually dimorphic germ-cell development for totipotency. In vitro reconstitution of epigenetic reprogramming in humans remains a fundamental challenge. Here, we establish a robust strategy for inducing epigenetic reprogramming and differentiation of pluripotent stem cell (PSC)-derived human PGC-like cells (hPGCLCs) into mitotic pro-spermatogonia or oogonia, coupled with their extensive amplification (~>1010-fold). Strikingly, bone morphogenetic protein (BMP) signalling is a key driver of these processes: BMP-driven hPGCLC differentiation involves an attenuation of the mitogen-activated protein kinase/extracellular-regulated kinase (MAPK/ERK) pathway and both de novo and maintenance DNA methyltransferase (DNMT) activities, likely promoting replication-coupled, passive DNA demethylation. On the other hand, hPGCLCs deficient in tens-eleven translocation (TET) 1, an active DNA demethylase abundant in human germ cells, differentiate into extraembryonic cells, including amnion, with de-repression of key genes bearing bivalent promoters; these cells fail to fully activate genes vital for spermatogenesis and oogenesis, with their promoters remaining methylated. Our study elucidates the framework of epigenetic reprogramming in humans, making a fundamental advance in human biology, and through the generation of abundant mitotic pro-spermatogonia and oogonia-like cells, represents a milestone for human in vitro gametogenesis (IVG) research and its potential translation into reproductive medicine.

  Study JGAS000690

• Organoid BulkRNAseq

  Here, we aim to understand early determinants of brain organoid quality and generated a set of brain organoids from 12 different hPSC lines using an adaptation of the unguided Lancaster protocol (Lancaster & Knoblich, 2014). All cell lines were obtained from healthy donors. 12 donor hPSC lines were differentiated into brain organoids and a set of 72 individual organoids (6 per line) were randomly selected morphologically diverse organoids and subjected to bulk RNA sequencing for gene expression analysis. RNA was extracted using the RNeasy kit (Qiagen, Germany) according to the manufacturer’s instructions. A total of 1000 ng per sample was sent for RNA sequencing to Azenta Life Sciences (Genewiz Leipzig, Germany) for sequencing. Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). mRNAs were first enriched with Oligo(dT) beads. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5 at a depth of >20 million reads in each sample. Raw sequence data (.bcl files) generated from Illumina NovaSeq6000 was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. The raw sequence reads were aligned to the human reference genome GRCh38 using the STAR aligner (Dobin et al., 2013). Gene expression levels were quantified using the FeatureCounts tool (Liao et al., 2014).

  Study EGAS50000000659

• Identification of RNA biomarkers in Parkinson's disease iPSC-derived neuronal cells

  Parkinson?s disease (PD) is an age-related, chronic and progressive neurodegenerative disorder characterized by a loss of multifocal neurons and subsequent motor symptoms. These overt motor symptoms are often preceded by prodromal non-motor symptoms. Though a number of genetic and environmental factors have been identified to play a role in PD, more exact methods for both diagnosing and assessing prognosis are yet to be discovered. Probing the transcriptomes of control and PD cells can give some interesting insight into changes caused by the disease (in both coding and non-coding gene expression), highlighting potential RNA biomarkers that may be used for PD diagnosis and as new drug targets. The study consists of two main sources of data: matched neural stem cell (NSC) and fully differentiated dopaminergic neurons derived from iPS cells. Both sets of data are made up of three samples from a control cell line, and five samples carrying a mutation in one of several genes known to be linked to heritable PD: PARK2, PARK22 or PARK9. All transcriptome libraries were synthesized and sequenced using no-amplification non-tagging cap analysis of gene expression (nAnT-iCAGE) on the Illumina HiSeq 2500 platform. Resulting data was mapped to the human genome annotation (hg38) and processed CAGE tags were clustered ready for differential expression analyses. The 16 samples here described were sequenced across two lanes.

  Study JGAS000142

• Identification of RNA biomarkers in Parkinson's disease iPSC-derived neuronal cells

  Parkinson���s disease (PD) is an age-related, chronic and progressive neurodegenerative disorder characterized by a loss of multifocal neurons and subsequent motor symptoms. These overt motor symptoms are often preceded by prodromal non-motor symptoms. Though a number of genetic and environmental factors have been identified to play a role in PD, more exact methods for both diagnosing and assessing prognosis are yet to be discovered. Probing the transcriptomes of control and PD cells can give some interesting insight into changes caused by the disease (in both coding and non-coding gene expression), highlighting potential RNA biomarkers that may be used for PD diagnosis and as new drug targets. The study consists of two main sources of data: matched neural stem cell (NSC) and fully differentiated dopaminergic neurons derived from iPS cells. Both sets of data are made up of three samples from a control cell line, and five samples carrying a mutation in one of several genes known to be linked to heritable PD: PARK2, PARK22 or PARK9. All transcriptome libraries were synthesized and sequenced using no-amplification non-tagging cap analysis of gene expression (nAnT-iCAGE) on the Illumina HiSeq 2500 platform. Resulting data was mapped to the human genome annotation (hg38) and processed CAGE tags were clustered ready for differential expression analyses. The 16 samples here described were sequenced across two lanes.

  Study JGAS000318

• Immune heterogeneity in small cell lung cancer and vulnerability to immune checkpoint blockade

  Following the pivotal Phase III IMpower133 study, atezolizumab (anti–PD-L1), combined with carboplatin and etoposide (CE), was the first immune checkpoint inhibitor approved for first-line treatment of extensive-stage small cell lung cancer (ES-SCLC) and is now a standard of care. A clearer understanding of therapeutically relevant SCLC subsets is needed to improve outcomes and to identify rational combination strategies. Transcriptomic analyses and nonnegative matrix factorization were conducted on 271 pre-treatment patient tumor samples from IMpower133 and four subsets with general concordance to previously reported SCLC subtypes were identified. Deeper investigation into the immune heterogeneity relevant to clinical outcomes uncover two subsets with differing neuroendocrine (NE) versus non-neuroendocrine (non-NE) phenotypes that demonstrated hallmarks of immune cell infiltration. The balance of tumor-associated macrophage (TAM) to T-effector signals distinguished these inflamed subsets. Tumors with low TAM but high T-effector signals had a NE phenotype and demonstrated longer overall survival with PD-L1 blockade and CE versus CE alone than did tumors with high TAM and high T-effector signal, which had a non-NE phenotype. The delineation of SCLC immune heterogeneity offers a clinically relevant approach to discriminate SCLC patients likely to benefit most from immunotherapeutic approaches and highlights the complex mechanisms underlying response and resistance to immune checkpoint blockade. 

  Study EGAS50000000138