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• Admixture Mapping of Staphylococcus aureus Bacteremia

  In this study, we used admixture mapping to test the hypothesis that genomic variations with different frequencies in European and African ancestral genomes influence susceptibility to Staphylococcus aureus bacteremia (SAB) in a sample of African Americans. A total of 565 adult African Americans were genotyped for admixture mapping. Cases were unique African American adult inpatients with monomicrobial SAB (N=390) and controls are age-matched adult African American inpatients with no current or past S. aureus infection (N=175). After empirical multiplicity adjustment, one region on chromosome 6 (52 SNPs, P = 4.56e-05) in the HLA class II region was found to exhibit a genome-wide statistically significant increase in European ancestry. This region encodes genes involved in HLA-mediated immune response and these results provide additional evidence for genetic variation influencing HLA-mediated immunity, modulating susceptibility to SAB.

  Study phs001441

• A Multimodal Atlas of Human Brain Cell Types

  "A multimodal atlas of human brain cell types" includes sample data targeting two cell types that show species differences between mouse and human. First, it includes a detailed transcriptomic, morphological, and electrophysiological characterization of cell types in layer 1 of human middle temporal gyrus, focusing primarily on different inhibitory cell types. This project also includes gene expression data collected from nuclei in layer 5 of human fronto-insula, with a goal of identifying transcriptomic signatures of Von Economo neurons. Control samples collected as part of the same experiment are also included in the data set. This study was conducted as part of a collaboration between the Allen Institute for Brain Science, the University of Szeged, and the J. Craig Venter Institute. Collaborators request that publications resulting from these data cite their original publication: Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type (PMID: 30150662).

  Study phs001791

• Childhood Cancer Data Initiative (CCDI): Identification and Targeting of Treatment Resistant Progenitor Populations in T-cell Acute Lymphoblastic Leukemia

  Our goal with this study was to identify the mechanisms of treatment resistance in T-cell acute lymphoblastic leukemia (ALL) using single-cell genomics. We profiled 40 T-ALL cases from the Children's Oncology Group AALL0434 clinical trial using CITE-seq/snATAC-seq, capturing a breadth of immunophenotypes, including early T-cell precursor (ETP) and near-ETP/non-ETP subtypes. By integrating analyses of T-ALL cells with the normal T-cell developmental trajectory, the study identified a specific subgroup of leukemia cells resembling bone marrow progenitors (BMP-like cells). These BMP-like cells were associated with treatment failure and poor overall survival in T-ALL patients. Overall, this study reveals comprehensive multiomic signatures for rapidly assessing risk and tailoring targeted treatment for high-risk T-ALL patients.

  Study phs003432

• Gene Variants in Pheochromocytoma and Paraganglioma

  Pheochromocytoma and paraganglioma (PPGL) are rare neuroendocrine tumors that arise from chromaffin cells in the adrenal medulla and in extra-adrenal locations, respectively. PPGL has the strongest hereditary risk of all endocrine neoplasms with about 40% of cases harboring germline mutations and another 25-30% of cases arising from somatic mutations. To date, over 20 susceptibility genes have been suggested to play a role in PPGL pathogenesis, with more genes still being researched. This project will seek to identify new candidate genes in apparently sporadic PPGLs to reveal a possible genetic background in cases without variants in known susceptibility genes. Knowledge of the genetic background and the genes involved in the pathogenesis of PPGL allows for clustering and/or development of targeted therapies for the tumors that cannot be surgically resected or tumors that have metastasized.

  Study phs002405

• Recurrent CLTC::SYK fusions and CSF1R mutations in juvenile xanthogranuloma of soft tissue

  In this study, the genomic landscape of extracutaneous juvenile xanthogranuloma (JXG) was analyzed. By leveraging the Dutch Nationwide Pathology Databank (Palga), tumor samples were obtained from different academic medical centers in the Netherlands. The study was approved by the Palga Scientific Council and Privacy Committee (LZV-2016-183) and the Institutional Review Board of Leiden University Medical Center (B19.074). In addition, the study was approved by the Biobank and Data Access Committee of the Princess Máxima Center for Pediatric Oncology (PMCLAB2024.0512). Provided are whole transcriptome sequencing (WTS) data of 3 histiocytic tumors with CLTC::SYK fusions. WTS was performed in the routine workflow of the Princess Máxima Center for Pediatric Oncology (as described in Hehir-Kwa, et al. JCO Precis Oncol 2022). RNA was derived from formalin-fixed paraffin-embedded tumor tissue (n=1) or from frozen tumor tissue (n=2).

  Study EGAS50000000584

• Whole-genome sequencing of BRCA-mutant breast cancer patient samples from tumour, germline tissue and plasma

  The use of circulating tumor DNA (ctDNA) to profile mutational signatures presents a non-invasive opportunity for understanding cancer mutational processes. In this study we developed MisMatchFinder, a liquid biopsy approach for mutational signature detection using low- coverage whole-genome sequencing of ctDNA. Through analysis of plasma samples across multiple different cancers, we demonstrated that MisMatchFinder accurately infers single-base and doublet-base substitutions as well as indels to enhance detection of ctDNA and clinically relevant mutational signatures. This study contains fastq files from whole-genome sequencing of temporally matched tumour (fresh frozen biopsies), blood germline and plasma samples collected from a BRCA1-mutant breast cancer patient to directly compare mutation signature analysis using gold-standard tumour-germline paired variant calling with our novel ctDNA-based method (MisMatchFinder).

  Study EGAS50000000569

• Methylation-Based Immune Deconvolution in Prostate Cancer Patients Before and After Radical Prostatectomy

  To explore whether surgical treatment for prostate cancer leads to long-term immune changes, we conducted a pilot study of n=11 prostate cancer patients treated with radical prostatectomy. We also included n=8 patients managed with active surveillance as a comparison group. We examined intra-individual changes in circulating immune cell subsets using serial blood samples collected pre- and approximately 6-months post-prostatectomy, and from matched time points for the patients managed on active surveillance. Immune cell subsets were deconvoluted using genome-wide methylation data. We observed no meaningful changes in circulating immune cell subsets in either patient group, suggesting that any surgery-induced immune changes to the circulating immune profile may not be long-lasting. The genome-wide methylation data from the two time points will be made available through dbGaP.

  Study phs003660

• Immune Determinants of Resistance to PD-1 Blockade in Renal Cell Carcinoma

  We performed an integrated bulk and single-cell transcriptomic analysis of tumors from 102 advanced renal cell carcinoma patients enrolled in a phase II clinical trial of frontline nivolumab (NCT03117309) to investigate determinants of response to anti-PD1 monotherapy. The present study includes 112 archival or pre-treatment tumors of clear cell and non-clear cell histologies from 90 patients that underwent bulk RNA sequencing (RNA-seq). For 76 patients, 74 of whom had matched RNA-seq, whole exome sequencing (WES) was also performed on tumor samples as well as matched peripheral blood. Additionally, 19 fresh tumor samples from 17 patients, including pre and post-treatment samples and mixed histologies, were locally cryopreserved and centrally processed for single cell RNA (scRNA-seq) and TCR (scTCR-seq) sequencing. 7 patients had matched scRNA/scTCRseq, RNAseq, and WES.

  Study phs003618

• Next Generation Sequencing to Predict Risk of Events from Coronary Artery Disease

  Coronary artery disease (CAD) and myocardial infarction (MI) remain the leading cause of death worldwide and in the US. In recent years, clinical studies that considered intermediate phenotypes (phenotypic or genomic data isolated between DNA and the main disease phenotype) have greatly enhanced our understanding of complex traits like CAD by enabling inference of biological networks from the combination of genetic and genomic datasets isolated from disease-relevant tissue(s). The NGS-PREDICT study used whole transcriptome sequence data generated from primary macrophages derived in vitro from venous blood that was obtained from CAD cases and non-CAD controls. This study provided a valuable resource for the validation of biomarkers identified in STARNET NGS data from macrophages obtained from patients with and without CAD. It also can be used as a reference dataset for the study of metabolic syndrome as well as other systemic inflammatory diseases.

  Study phs003883

• Prospective Investigation of Pulmonary Embolism Diagnosis (PIOPED-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 determine the sensitivities and specificities of ventillation/perfusion (V/Q) lung scans for acute pulmonary embolism (PE).Participants: A total of 1487 participants were enrolled.Conclusions: Almost all participants with pulmonary embolism had abnormal scans of high, intermediate, or low probability, but so did most without pulmonary embolism. Only in a minority of participants did the clinical assessment combined with the V/Q scan interpretation improve the overall chance of reaching a correct diagnosis of acute PE. Although a high probability scan usually indicated the presence of PE, only a small number of participants with PE had a high probability scan. Reference: PIOPED Investigators, 1990, PMID: 2332918.

  Study phs004020

• Human papillomavirus integration induces oncogenic host gene fusions in oropharyngeal cancers

  HPV integration disrupts host genomic structure and expression, but whether these alterations promote cancer development remains unclear. Multiple genomic analyses of oropharyngeal cancers identified several host gene fusions, including recurrent FGFR3-TACC3 fusions, expressed from rearranged genomic loci adjacent to HPV integration sites. Evolutionary modeling implicated integration of virus concatemers into the host genome as a common initiating event in fusion formation. Co-expression of HPV16 E6/E7 and FGFR3-TACC3, but neither alone, was sufficient for tumor development in both xenograft and syngeneic mouse models and led to unique transcriptional programs implicated in carcinogenesis. FGFR3-TACC3 expression decreased the ubiquitination and degradation of E6 and E7, thereby increasing oncoprotein abundance. We conclude that expression of HPV16 oncoproteins and host gene fusions generated from HPV integration sites can be sufficient for cancer development.

  Study EGAS50000000892

• Epigenomics of Neurocognitive Function in Breast Cancer

  This study harnessed the data and biospecimens from the Exercise Program in Cancer and Cognition (EPICC) study (parent study) that collected data on cognitive function, demographics, other symptoms and biospecimens at two time points (T1: enrollment, T2: six months later) within the context of a six-month randomized controlled trial of a moderate intensity aerobic exercise intervention. This study collected genome wide DNA methylation data from T1 and T2 and conducted epigenome-wide association-based analyses to find genes and biological pathways explaining variability in cognitive function and explaining how exercise mitigates cognitive decline. Our initial findings identified cg10331779 near CTNND2 (p-value=9.65×10-9) associated with processing speed and cg25906741 in MLIP (p-value=2.01×10-8) associated with subjectively measured cognitive function. Additionally, differentially methylated regions were identified near SLC6A11, PRKG1/CSTF2T, and FAM3B for processing speed and near PI4KB and SGCE/PEG10 for mental flexibility.

  Study phs003959

• Estimating the Efficacy of Pharmacogenomics Over a Lifetime

  The goal was to evaluate the potential impact of pharmacogenomic testing on drug prescribing over a lifetime. To address this goal, 300 random patients enrolled in Marshfield Clinic's PMRP biobank with life-long medical records were whole genome sequenced and evaluated for known clinically actionable pharmacogenomic variants as defined by CPIC and FDA. This genomic data was evaluated in the context of extensive longitudinal prescription record data from patient EHR. Results show nearly all (93%) carry a clinically actionable pharmacogenomic variant and 80% with a variant were prescribed approximately three medications on average that may have been impacted because of their variants, the optimal age for pharmacogenomic testing was prior to age 50, but most patients well past their 50s can still benefit from pharmacogenomic testing. Results available include genotype and drug prescribing data.

  Study phs003454

• Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis

  The role of non-coding variants in polygenic skin disease and their connection to homeostatic transcription factors (TFs) in epidermis was investigated. Homeostatic TFs were identified by perturb-seq in differentiating keratinocytes, using either 10x or split-pool approaches to sequencing, with follow-up validation by siRNA and RNA-seq. TF binding events were profiled by population sampling Cleavage Under Targets & Release Using Nuclease (CUT&RUN), in which a random population of neonatal foreskin keratinocytes were assayed by CUT&RUN for homeostatic TFs under progenitor growth and differentiation conditions. Heterozygous alleles were identified from the TF binding data and examined for allele specific binding events (ASBs). ASBs were then compared with non-coding variants linked to skin disease. Variants with potentially pathogenic effects were identified. Promoters and high TF occupancy genomic regions were found to be "buffered" against variants causing ASBs.

  Study phs003977

• Detection of brain cancer using genome-wide cell-free DNA fragmentomes

  Diagnostic delays in patients with brain cancer are common and can impact patient outcome. Development of a blood-based assay for detection of brain cancers could accelerate brain cancer detection. In this study, we analyzed genome-wide cell-free (cfDNA) fragmentomes, including fragmentation profiles and repeat landscapes, from the plasma of individuals with (n=148) and without (n=357) brain cancer. Machine learning analyses of cfDNA fragmentome features detected brain cancer across all grade gliomas (AUC=0.90, 95% CI: 0.87-0.93) and these results were validated in an independent prospectively collected cohort. cfDNA fragmentome changes in patients with gliomas represented a combination of fragmentation profiles from glioma cells and altered white blood cell populations in the circulation. These analyses reveal the properties of cfDNA in patients with brain cancer and open new avenues for noninvasive detection of these individuals.

  Study EGAS50000000986

• ProstOmics: spatial and bulk multi-omics of prostate cancer

  In this ERC-funded ProstOmics project we have used spatial and bulk multi-omics on fresh frozen prostate cancer samples to investigate cancer biology and find for biomarkers to improve patient treatment. All tissue material were collected from prostate cancer patients undergoing radical prostatectomy who had not received any prior cancer-specific treatment.Of the 498 prostate tissue samples (114 patients) included in our project, 176 samples (N=37 patients) have been analyzed with bulk transcriptomics (RNA-seq). Some of these 176 samples were also analyzed with spatial transcriptomics (n=32, N=8, Visium 10x RNA-seq) and DNA methylomics (n=96, N=24, array). All datasets include metadata for histopathological evaluation. Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Study EGAS50000000413

• Dynamic Evolution of Fibroblasts Revealed by Single Cell RNA Sequencing of Human Pancreatic Cancer

  Understanding the constituents of the pancreatic ductal adenocarcinoma (PDAC) microenvironment may illuminate more efficacious targets for treating this aggressive malignancy. However, the compositional changes occurring in untreated and treated PDAC relative to both normal and inflamed pancreas have not been well characterized. To provide a more comprehensive understanding of the PDAC tumor microenvironment relative to the non-cancerous pancreas, we performed single-cell expression profiling (10X Genomics Chromium) on samples of upfront resectable PDAC, FOLFIRINOX-based treated PDAC, chronic pancreatitis, and normal pancreas specimens from 19 patients. Spatial gene expression profiling (10X Genomics Visium) was performed to gain additional insight into cell populations. Our analysis revealed that fibroblasts are central mediators of cell-cell communication in both inflamed and malignant settings and defined unique roles for these cell populations in different disease contexts.

  Study phs003751

• Highly prevalent NF-kappa B signaling pathway-activating somatic mutations in intracranial aneurysms

  Intracranial aneurysms (IAs) are a high-risk factor for life-threatening subarachnoid hemorrhage. Their etiology, however, remains mostly unknown. We conducted screening for somatic mutations in 65 IA tissues and identified 16 genes that were mutated with a high prevalence (92%). In particular, six genes, including PDGFRB, were mutated commonly in fusiform and saccular IAs and are linked to the NF-kappa B signaling pathway. Mutant PDGFRBs constitutively activate NF-kappa B signaling and induce inflammation-related gene expression in vitro. Spatial transcriptomics also detected similar changes in IA tissues. Virus-mediated expression of a mutant PDGFRB induces a fusiform-like dilatation of the basilar artery in mice. This study reveals a high prevalence of somatic mutations in NF-kappa B signaling genes in IAs and opens a new avenue of research toward development of its pharmacological interventions.

  Study JGAS000591

• Mutational anysis of breast cancer stem cells

  Exome sequences of breast cancer have been investigated for many patients. Recently it has been shown that there are intra-heterogeneity in tumor tissues. When the tumor cells were sequenced in bulk condition, only the major populations��� (clones���) mutations will be detected. Based on cancer stem theory, each populations��� cells are derived from each cancer stem cells, which their numbers are not so different among different clones. Here, we separated cancer cells into cancer stem cells and non-cancer stem cells exploiting cancer stem cell specific surface markers. By comping two groups��� mutation, we identified mutations, which were only detected in stem cell population. These mutations could be the mutations in cells of small size populations, and maybe the important mutations to understand the heterogeneity of tumor tissues, progression, and/or prediction for the outcome to therapies.

  Study JGAS000304

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Study EGAS50000001328

• BLUEPRINT Hematopoietic Stem/Progenitor Cell Methylomes

  An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. HSCs and MPPs were also sorted from fetal liver (HSCs only), cord blood, and bone marrow. Single-cell methylomes using the scWGBS protocol (Farlik et al. 2015 Cell Reports) were established for six cell types (HSC, MPP, CMP, GMP, CLP, MLP0). Gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done for nine stem/progenitor cell types (HSC, MPP, CMP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).

  Study EGAS00001002070

• Reconstructing the dispersals and adaptive history of Bantu-speaking populations in Africa and North America

  Bantu languages are spoken by ~310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1,318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with autochthonous populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans.

  Study EGAS00001002078

• CD49f single-cell methylomes

  Single-cell DNA methylation has emerged as a powerful tool to study molecular heterogeneity within cellular populations. We report the development of a bisulfite based whole genome protocol suitable for use on single index sorted primary mammalian cells. Application of this protocol to human hematopoietic stem cells provided quantitative DNA methylation measurements of up to 5.7 million CpGs in a single cell. Analysis of cis CpG methylation states in single cells revealed a loss of concordance beyond 2kb, which supported the development of a new analytical framework (PDclust) for single-cell DNA methylation datasets that considers heterogeneity of methylation states at single CpG resolution. PDclust identified epigenetically distinct subpopulations within highly purified and functionally defined human stem cell populations. In silico merging of the methylation states from the single cells allowed us to ascribe function to these epigenetically distinct subpopulations on the basis of their epigenetic states.

  Study EGAS00001002789

• Genotyping_of_additional_Inflammatory_Bowel_Disease_cases___2014

  Both internal and external funding has enabled 5000 inflammatory bowel disease cases to be whole genome sequenced (CD @4X, UC @2X). The Anderson and Barrett groups are currently generating genotypes across these samples for comparison to 4000 population controls sequenced as part of UK10K. The UK10K project has shown that imputing sequenced genetic variation into previously GWASed samples greatly increases power to detect association. Given that our study has been designed to detect association to low frequency variation (0.5% and above) these gains in power are especially important. Overall, the UKIBDGC has GWAS data for around 1800 CD samples (Affy 500K) and 3000 UC samples (Affy6), though some of these samples have also been whole genome sequenced. Here, we apply to get all remaining non-GWAS and non-WGS IBD cases in the UKIBDGC (N=X) genotyped genotyped on the Illumina Core Exome Array

  Study EGAS00001000924

• Pharmacogenomic landscape of patient-derived cells informs precision oncology therapy

  Outcomes of anticancer therapy vary dramatically among patients, which may be caused by the specific molecular alterations in each patient’s tumor. Precision oncology aims to apply optimal therapies for each tumor based on its molecular characteristics. We have established a resource reporting the genomic and transcriptomic profiles of 462 patient tumor-derived cells (PDCs) across 14 cancer types, together with responses to 60 targeted agents. Compared with long-term cultured cancer cell lines, PDCs better recapitulate the molecular profiles of the original tumors. Among other unreported associations, we identify molecular factors inducing resistance to EGFR inhibitors in glioblastoma, and we suggest repurposing ibrutinib (currently used in hematological malignancies) for EGFR-specific therapy in gliomas. Lastly, using a retrospective clinical study, we find that PDC-derived sensitivities can be used to predict patient responses.

  Study EGAS00001002515