14476 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

in 36.54 milliseconds.

• MPB_Bonn

  1000Genomes imputed data set of 581 cases and 417 controls for male-pattern baldness

  Dataset EGAD00001001456

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (28 tumor/control pairs)

  Dataset EGAD00001003207

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (cell_line)

  Dataset EGAD00001003210

• NHLBI GO-ESP: Heart Cohorts Exome Sequencing Project (Ischemic Stroke Genetic Study, ISGS)

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. The Ischemic Stroke Genetics Study (ISGS) is a study of newly onset cases (~600) with ischemic stroke (a stroke due to sudden interruption of blood flow to a part of the brain) compared with sex- and age-matched non-stroke participants. The study was conducted to determine the genes and their variants that contribute to an individual's risk of developing an ischemic stroke. The coordination of the recruitment and flow of the samples occurred at the Mayo Clinic, Jacksonville, FL, under the direction of James F. Meschia, MD. The University of Virginia (Stephen S. Rich, PhD) served as the analytic site for the genetic data. All GWAS data on ISGS participants have been deposited into dbGaP. As part of the NHLBI Exome Sequencing Project, DNA from a subset of ISGS participants will undergo exome sequencing. For the NHLBI ESP, a subset of 92 individuals with lacunar (small vessel) or atherosclerotic (large vessel) TOAST subtypes were selected from among all ISGS participants, excluding those individuals with TOAST subtypes of stroke of other etiology or of stroke with undetermined etiology. All 92 samples pass initial quality control metrics and 89 samples completed exome sequencing. A total of 75 participants with appropriate consent and variant calls had their genetic and phenotypic data deposited into dbGaP.

  Study phs000546

• Whole_exome_sequencing_of_Severe_Insulin_Resistant_patients_

  Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients.

  Study EGAS00001000025

• Identification_and_functional_validation_of_driver_mutations_in_colorectal_cancer

  Targeted exome sequencing of human colorectal cancers for the identification of novel cancer drivers.

  Study EGAS00001000044

• GabonDiv_SNP_genotyping

  Genome-wide SNP genotyping data for 1,235 western Africans by Illumina HumanOmniExpress-12 array, used in the EGAS00001002078 study

  Dataset EGAD00010001209

• Liv_PTB_Genomics

  Liverpool Preterm Birth Biomarker Study Genomics

  Dataset EGAD00010002066

• TOPARP-B patient cell-free DNA targeted sequencing

  Targeted sequencing for TOPARP-B patients as detailed in manuscript

  Study EGAS50000000281

• A Risk Score Incorporating Low Pass Whole Genome Sequencing of Cell Free DNA from Patients Receiving CD19 CAR T-Cell Therapy for Large B-Cell Lymphoma

  Study EGAS00001006308

• LEMA WES files

  This dataset contains WES bam/bai files associated with 133 patients as part of the LEMA Study

  Dataset EGAD50000001311

• ACUITI BAM files

  This dataset contains WES bam/bai files associated with 51 patients as part of the ACUITI Study

  Dataset EGAD50000001401

• germline pathogenic variants found in African patients of prostate cancer

  70 new blood samples added in this project

  Study EGAS50000001132

• BLUEPRINT EpiVar Whole Genome Sequencing

  BLUEPRINT EpiVar Whole Genome Sequencing

  Study EGAS00001000689

• The_mutational_landscape_of_recurrent_Glioblastome_multiforme

  Targeted gene screen of approx 120 patients with primary GBM and recurrent samples.

  Study EGAS00001001764

• ICGC medulloblastoma whole genome sequencing data, ICGC release 16

  ICGC medulloblastoma whole genome sequencing data, ICGC release 16

  Study EGAS00001000744

• Paired WGS data from Wilms Tumors

  Paired whole genome sequencing tumor normal samples of pediatric Wilms tumors

  Study EGAS00001006526

• Whole_genome_sequencing_of_Crohn_s_disease_patients

  Population based sequencing of whole genomes of Crohn's disease patients.

  Study EGAS00001000065

• Disorders_of_growth_and_insulin_action_

  Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients.

  Study EGAS00001000041

• Oulu_Dyslipidemia_families

  These samples include exome sequences of family members with dyslipidemias from northern Finnish origin.

  Study EGAS00001000384

• Aneuploidy_and_human_development

  We will investigate the transcriptomic consequences of copy number changes in human development.

  Study EGAS00001005267

• WES sequencing of TRACERx NSCLC patient-derived xenograft models

  WES sequencing of TRACERx NSCLC patient-derived xenograft models

  Study EGAS00001007364

• Single cell transcriptome profiling of childhood soft tissue sarcomas

  Single cell transcriptome profiling of childhood soft tissue sarcomas

  Study EGAS00001006563

• Reference epigenome ADMSC04_smRNA-Seq data generated from KEP study

  A ADMSC04_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003870

• Reference epigenome ADMSC06 miRNA-Seq data generated from KEP study

  ADMSC06 miRNA-Seq single end data

  Dataset EGAD00001007178

• Reference epigenome ADMSC08 miRNA-Seq data generated from KEP study

  ADMSC08 miRNA-Seq single end data

  Dataset EGAD00001007180

• Reference epigenome KNIH008 WGBS data generated from KEP study

  A KNIH008 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for adipocytes

  Dataset EGAD00001002756

• Reference epigenome CKD27_C_Mesan_WGBS data generated from KEP study

  A CKD27_C_Mesan_WGBS paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003471

• Reference epigenome CKD23_C_Mesan_WGBS data generated from KEP study

  A CKD23_C_Mesan_WGBS paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003468

• Reference epigenome Islet-derived_MSC06 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007897

• Reference epigenome ADMSC05 miRNA-Seq data generated from KEP study

  ADMSC05 miRNA-Seq single end data

  Dataset EGAD00001007177

• Reference epigenome ADMSC07 miRNA-Seq data generated from KEP study

  ADMSC07 miRNA-Seq single end data

  Dataset EGAD00001007179

• Reference epigenome Islet-derived_iPSC04 h3k4me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007892

• Nyamasati study

  Illumina whole genome sequencing to high depth (x50) of four Tanzanian individuals. Genomic DNA derived from peripheral whole blood.

  Dataset EGAD00001004370

• Reference epigenome Islet-derived_MSC08 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007907

• Reference epigenome Islet-derived_MSC08 input ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 input ChIP-Seq paired end data

  Dataset EGAD00001007908

• IPF Core Biopsy Study RNA-Seq Fastqs

  RNA-Seq fastq files for 97 Idiopathic Pulmonary Fibrosis samples.

  Dataset EGAD00001007568

• Reference epigenome Islet-derived_MSC06 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007898

• Reference epigenome Pancreas-Islet06 WGBS data generated from KEP study

  Pancreas-Islet06 WGBS paired end data

  Dataset EGAD00001007884

• Reference epigenome Islet-derived_iPSC04 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007890

• Reference epigenome Islet-derived_MSC06 input ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 input ChIP-Seq paired end data

  Dataset EGAD00001007901

• Reference epigenome Islet-derived_MSC08 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007905

• Reference epigenome Islet-derived_MSC08 h3k4me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007906

• Reference epigenome Islet-derived_iPSC04 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007893

• Reference epigenome Islet-derived_MSC06 h3k27me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007896

• Reference epigenome Islet-derived_MSC08 h3k27me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007903

• Reference epigenome Islet-derived_MSC06 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007895

• Reference epigenome Islet-derived_iPSC04 h3k27me3 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007889

• Reference epigenome Islet-derived_MSC06 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007900

• Reference epigenome ADMSC02 mRNA-Seq data generated from KEP study

  ADMSC02 mRNA-Seq paired end data

  Dataset EGAD00001007151

• Reference epigenome Islet-derived_MSC06 h3k4me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC06 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007899

• Reference epigenome Islet-derived_iPSC04 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007888

• Reference epigenome Islet-derived_iPSC04 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007891

• Reference epigenome Islet-derived_iPSC04 input ChIP-Seq data generated from KEP study

  Islet-derived_iPSC04 input ChIP-Seq paired end data

  Dataset EGAD00001007894

• Reference epigenome Islet-derived_MSC08 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007902

• Reference epigenome Pancreas-Islet08 WGBS data generated from KEP study

  Pancreas-Islet08 WGBS paired end data

  Dataset EGAD00001007887

• Reference epigenome Islet-derived_MSC08 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived_MSC08 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007904

• WGS data for MMML for Study EGAS00001002198

  Whole genome sequencing data for MMML (healthy cell_line)

  Dataset EGAD00001003283

• WGS of CD138+ samples collected from MM patients

  Deep WGS performed on samples collected from MM patients

  Study EGAS00001006731

• The_GENCODE_exome___sequencing_the_complete_human_exome

  We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an addition 5,594 genes and 10.3 Mb compared to current sets which mainly target the CCDS database. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed covers 47.9Mb and performed well in sequence capture experiments with HapMap and clinical samples. Samples within this study are prepared with either the CCDS or GENCODE exome products.

  Study EGAS00001000016

• Primary Cytotoxic T Cell Lymphomas Harbor Recurrent Targetable Alterations in the JAK-STAT Pathway

  Cytotoxic cutaneous T cell lymphomas (CTCLs) are uncommon but highly aggressive cancers of skin-homing cytotoxic T cells. These include the established World Health Organization (WHO) entity primary cutaneous gamma delta T cell lymphomas (PCGDTLs), the provisional WHO entity primary cutaneous CD8+ aggressive epidermotropic T cell lymphoma (PCAETCL), and samples that do not currently fit into a WHO category, referred to as cytotoxic CTCL-NOS (not otherwise specified). In this study, 35 CTCL cases were examined, and 9 PCAETCL cases were confirmed by CD8 expression and full-thickness epidermotropism. Whole genome sequencing (WGS) and bulk RNA sequencing were performed on these samples.  

  Study phs002499

• Effects of tobacco smoking on the tumor immune microenvironment in head and neck squamous cell carcinoma

  This study was designed to measure immune cell differences between HNSCC patients according to smoking history. We measured CD3, CD8, FoxP3, PD-1 and PD-L1 for immune markers and Pancytokeratin to distinguish between tumor and surrounding tissue. We observed that current smokers have significantly lower numbers of immune cells surrounding the tumor than former or never smokers. GSEA analysis of RNAseq data from this cohort suggests that smoking is associated with reduced Interferon (IFN) Alpha and Gamma levels, and also with reduced levels of IFN-response cytokines CXCL9, 10 and 11. These results emphasize the hypothetical benefits of smoking cessation during treatment for HNSCC.

  Study phs001994

• PGRN/PAT: The genomic basis for susceptibility to drug-induced long QT syndrome (diLQTS)

  The goal of this study was to search for genetic variants that could be responsible for modifying the risk of drug-induced long QT syndrome (diLQTS). diLQTS is a relatively common adverse drug event and has been a leading cause for drug relabeling and withdrawal from the market. Our hypothesis, that variants in genes which regulate electrical properties in the heart modify the risk of diLQTS, was tested by sequencing approximately 225 patients of European descent using next-generation targeted captured or whole exome sequencing. Data from cases and controls (1:2) were analyzed to identify both rare and common genetic variation.

  Study phs000808

• Genomic and Transcriptomic Profiling of Patients with Malignant Pleural and Peritoneal Mesothelioma: The NCI Cohort

  Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. Better understanding of mesothelioma genomics and transcriptomics could advance novel therapies. We performed whole-exome sequencing (WXS) of germline and tumors of 122 patients, and RNA-sequencing (RNA-Seq) of tumor samples of 100 patients with pleural, peritoneal, and tunica-vaginalis mesothelioma.The biospecimens used in this study were collected as a part of the Mesothelioma Natural History Protocol (https://clinicaltrials.gov/ct2/show/NCT01950572), wherein, samples were collected from subjects with malignant mesothelioma as listed in the eligibility criteria below and written consent from each participant was obtained before sample acquisition.

  Study phs002207

• Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

  In this study, we describe a systematic analysis of pseudogene 'transcription' from an RNA-Seq resource of 293 samples, from 13 cancer and normal tissue types. We observed a highly prevalent, genome-wide expression of pseudogenes that could be categorized as universally expressed or lineage- and/or cancer-specific. We also explored disease subtype specificity and functions of selected expressed pseudogenes. We provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.

  Study phs000525

• Gene Expression Signatures in CATHGEN

  Case control cohort: The details have been previously published: American Heart Journal. 2010;160:371-379 e372. Briefly, a nested case:control cohort of CATHGEN participants who had experienced death or MI (n = 250) after their index catheterization and age-, sex-, and race-matched controls (n = 250) who were free of death/MI > 2 years after cardiac catheterization was identified as part of the MURDOCK Horizon 1 Cardiovascular Disease Study.21 Sufficient RNA for microarray analysis was available in 447 members of this cohort. Observational cohort: 224 sequential CATHGEN samples were selected for whole blood RNA analysis, of which, 191 had sufficient RNA for microarray analysis.

  Study phs000551

• Genetic Basis of Cryptorchidism

  Non-syndromic cryptorchidism is a common malformation, but the genetic loci that increase susceptibility to cryptorchidism remain unknown. A genome-wide association study (GWAS) was completed to determine whether common allelic variants are associated with susceptibility to cryptorchidism. Two sets of discovery groups were genotyped. Group 1 (559 cases and 1772 controls) was genotyped with HumanHap550v1.0, HumanHap550v3.0 or Human610-quad v1.0. Group 2 (353 cases and 1149 controls) was genotyped with HumanOmniExpress-12v1 or HumanOmniExpress-12v1-1. The sample and marker QCs were performed separately using PLINK (v1.07; http://pngu.mgh.harvard.edu/purcell/plink/) and logistic regression analyses were performed with first and second multidimensional scaling (MDS) components as covariates.

  Study phs000986

• Whole Genome Comparisons of Breast Cancers and their Xenotransplants

  Early passage breast cancer xenografts have been proposed as alternatives to cell lines as model systems for studying the basic biology of tumors and for advancing therapy development. This study explores the relatedness of primary disease genomes to their matched xenotransplants. Using paired-end massively parallel sequencing 17 matched progenitor tumor, xenograft and normal trios were sequenced to at least 30-fold coverage with diploid coverage of at least 95% of the genome as determined by SNP array concordance. RNA sequence was generated from the xenograft tumors. The xenografts were derived from a spectrum of tumor samples from patients with both early and advanced breast cancer.

  Study phs000611

• Genomics of Blastic Plasmacytoid Dendritic Cell Neoplasm

  The goal of this study was to understand the genetic evolution and tumor phylogeny of blastic plasmacytoid dendritic cell neoplasm (BPDCN). BPDCN can present in patients with skin tumors of leukemia cells and no bone marrow or blood involvement, or alternatively, with both skin tumors and blood/bone marrow leukemia cells at the time of diagnosis. Here, we performed longitudinal sampling of tissues from patients with BPDCN, including both skin tumors and bone marrow, and in some cases serially at different time points through the course of diagnosis and treatment. These were studied by whole exome or whole genome DNA sequencing, comparing tumor samples to matched normal samples.

  Study phs003228

• Supraphysiologic MDM2 Expression Impacts P53-Independent Chromatin Networks and Therapeutic Responses in Sarcoma

  We collected multiple liposarcoma samples from different patients, including different subtypes (DD, WD) and normal adipose tissue as control. This study provides the biggest liposarcoma cohort to date, and examined the molecular regulatory circuits associated with MDM2 overexpression. To this end, we obtained not only RNA-seq data, but also ChIP-seq from Jun, RUNX, MDM2, P53 and H3K27ac, as well as hiChIP from tumor samples and cell lines. We found that MDM2 binds to thousands of genes involved in cellular growth and stress response in a P53-independent manner. Furthermore, we described these active genes engaged in multi-way topological interactions that resemble transcriptional hubs.

  Study phs003272

• Integrated Clinical and Transcriptomic Profiling to Characterize Disease Phenotype

  Personalized medicine requires that we first address the challenge of genetic heterogeneity, prominent in rare cancers to common disease. While current clinical DNA sequence data successfully identify novel genetic variants, the genomic data alone are insufficient biomarkers of clinical phenotype. There is an unmet need for systematic integration of specific functional genomic data with patient genetic data, in order to bridge the knowledge gap between genetic variation and clinical phenotype. This specific study is focused on functional genomic data from platelets as disease-specific cells that are also ideal for proof-of-principle transcriptomic investigation (being anucleate), and highly-relevant to multiple disease processes.

  Study phs002121

• Whole Exome Sequencing of Colorectal Cancer Patients from the Nurses' Health Study (NHS) and Health Professionals Follow-up Study (HPFS)

  Colorectal cancer is a molecularly heterogeneous disease. Whole Exome Sequencing from patients diagnosed with colorectal cancer in the NHS and HPFS cohorts will extend our understanding of the genetic changes occurring in specific clinical contexts in the disease. This effort has the potential to discover novel recurrently mutated genes and pathways in colorectal cancer that can be functionally validated and give further insights to colorectal cancer pathogenesis. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000.

  Study phs000722

• Melanoma and Cancer-Associated Fibroblast Short-Term Cultures Derived from Patient Metastases

  The purpose of this study was to obtain tissue specimens derived from patients with melanoma to generate research tools to advance our understanding of the genetics, pathogenesis, and therapeutics of melanoma. Briefly, tissue was obtained from metastatic lesions and used to generate clonal primary cell lines from melanoma cells and fibroblasts from the tumor microenvironment. RNA was extracted from low passage cell lines using Trizol reagent. cDNA libraries were prepared using the TruSeq mRNA sample preparation kit, v2 (Illumina) and sequenced on the HiSeq 2000 platform (Illumina). The submitted files are bam files that contain both unaligned and aligned reads (human genome, build hg19).

  Study phs001115

• Single Cell RNA-Sequencing in Adenoid Cystic Carcinoma

  This study of salivary adenoid cystic carcinoma aimed to profile individual malignant and stromal cells in treatment-naive head and neck adenoid cystic carcinoma, with or without metastatic cervical lymph nodes. Clinical and pathologic information was collected on all patients, in addition to a fresh biopsy sample from the primary tumor and/or metastatic lymph node at the time of initial surgery. A fresh biopsy sample from a matched local recurrence was also collected for a single unique patient. Biopsy specimens were processed for single cell RNA-seq. A total of ~1,700 single cells from seven participants were included in the final dataset.

  Study phs003070

• Somatic Copy Number Analysis of Endometrial Carcinomas

  Endometrial cancer (EC) is the most commonly diagnosed gynecologic malignancy in the United States and is the sixth leading cause of cancer death amongst American women. The purpose of this study was to identify somatic (tumor-specific) copy number alterations in 7 clear cell ECs, 31 serous ECs, 17 endometrioid ECs, and the clear cell components of 2 endometrioid/clear cell ECs. To this end, DNAs from de-identified primary endometrial tumors and matched non-tumor tissues or blood were hybridized to high-density Illumina Infinium HumanHap650Y Beadchips or to high-density Human660W-Quad Beadchips and the data analyzed to annotate somatic copy number alterations throughout the genome.

  Study phs001690

• Genetics of Male Infertility Initiative (GEMINI)

  The Genetics of Male Infertility Initiative (GEMINI) project is a multi-center study designed to discover and characterize genetic variants conferring risk for male infertility. Patients enrolled in GEMINI have been clinically diagnosed with male infertility. Patients are recruited from multiple medical centers and are primarily of European ancestry. DNA from each patient is extracted from peripheral blood or saliva and used for exome sequencing. Genetic data generated by the GEMINI project has contributed to the discovery of over a dozen genes involved in human infertility. A VCF file of genetic data from GEMINI patients that have been appropriately consented will be available through dbGaP.

  Study phs003115

• Integrative Analysis of Lung Adenocarcinoma in EAGLE (Version 2)

  We performed a comprehensive analysis of intratumor heterogeneity of somatic mutations in cancer driver genes, copy number aberrations and DNA methylation in 292 tumor samples from 84 lung adenocarcinoma (LUAD) patients from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. SNVs of 37 established lung cancer driver genes were profiled by deep target sequencing in 180 tumor samples and 55 blood samples and 1 buccal sample from 56 subjects. Somatic copy number alterations were profiled using SNP arrays in 268 tumor samples from 80 subjects. DNA methylation levels were profiled with methylation arrays in 205 tumor samples and 74 normal tissue samples from 68 subjects.

  Study phs001169

• DNA methylation in rhabdomyosarcoma PDX and PDX-derived primary cells

  Conditions to maintain primary tumor cells in culture are largely unknown for most tumor entities including rhabdomyosarcoma. In this collaborative study with Dr. Beat Schäfer's laboratory, we performed DNA methylation profiles of rhabdomyosarcoma patient-derived xenograft (PDX) and their matching PDX-derived primary cells (PPC), where the PPCs were developed and maintained under optimized culture conditions. We further compared DNA methylation profiles between these PDXs and PPCs. Exome sequencing and copy number analysis between these rhabdomyosarcoma PDXs and PPXs were also carried out. These analyses may help us to evaluate a feasibility of in vitro profiling of primary rhabdomyosarcoma cells from a genomic perspective.

  Study phs002051

• Copy Number Variation in Congenital Kidney Malformations

  We report a study of large rare, copy number variants (CNVs) in 192 patients with renal hypodysplasia (RHD). Congenital malformations of the kidney and urinary tract are present in 3 to 7 per 1,000 births, accounting for 16% of birth defects. These malformations account for 40-50% of pediatric and 7% of adult end-stage renal disease worldwide. Among these malformations, RHD represents a severe forms of disease with profound impact on long-term renal survival. We found that a significant fraction of RHD patients have a molecular diagnosis attributable to a genomic disorder, suggesting kidney malformations as a sentinel manifestation of pathogenic genomic imbalances.

  Study phs000565

• Spatiotemporal Transcriptome of the Human Brain

  Comprehensive knowledge about the spatiotemporal dynamics of the brain transcriptome is essential for a better understanding of neurodevelopment, sexual dimorphism, and evolution, as well as our increased susceptibility to certain brain disorders. We generated and analyzed genome-wide exon-level transcriptome data from 16 brain regions of 57 postmortem human brains, spanning from embryonic development to late adulthood and representing males and females of multiple ethnicities. We also performed genome-wide genotyping of 2.5 million SNPs and assessed genome normality for all donors. This study provides a comprehensive, publicly available dataset on the spatiotemporal human brain transcriptome and new insights into the transcriptional foundations of human neurodevelopment.

  Study phs000406

• Ribosomal Depleted Total RNA-Seq of PBMCs and Skin from Controls and Systemic Sclerosis Patients

  This study involved prospective collection of skin biopsies and peripheral blood mononuclear cell (PBMC) samples from controls with no self-reported history of autoimmune or inflammatory disease and cases with Rheumatologist-confirmed systemic sclerosis: limited cutaneous systemic sclerosis (lcSSc), diffuse cutaneous systemic sclerosis (dcSSc), very early diagnosis of systemic sclerosis (VEDOSS), and systemic sclerosis sine scleroderma (SSS). Some SSc cases were sampled at a 6 month routine follow-up visit. PBMCs were collected and lysed immediately. Skin punches were stabilized in RNAlater until extraction. All RNA-Seq libraries were created using Takara/Clontech ribosomal depletion kits, and sequenced on either a HiSeq2500 or HiSeq3000.

  Study phs002902

• NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)

  This is a case pharmacogenetic study of bronchodilator drug response (Albuterol) among racially admixed Latino children with asthma between the ages of 8-40. Lung function testing was performed using the KoKo PFT system and each participant was administered albuterol dependent on age. Participants under 16 years of age, were administered 2 puffs of albuterol from a standard metered dose inhaler and 4 puffs for participants over 16 years old. The overall goal is to identify genetic factors which are predictive of drug response in children with asthma. The principal tools include a questionnaire and biological specimen collection. Participants with asthma have physician-diagnosed asthma, symptoms and medications.

  Study phs001542

• Derivation and Investigation of The First Human Cell-Based Model of Beckwith-Wiedemann Syndrome

  Beckwith-Wiedemann Syndrome (BWS) is the most common human imprinting disorder, and phenotypes include hepatomegaly and hepatoblastoma development. In approximately 20% of patients, this syndrome is caused by uniparental isodisomy of the paternal allele across chromosome 11p15 (pUPD11). From fibroblasts cultured from 2 BWS patients with pUPD11, we derived induced pluripotent stem cells (iPSC) and differentiated to hepatocytes to study a model of the BWS liver transcriptome through RNA-Seq. Compared to 2 similarly derived controls, we observed differential expression in insulin signaling, cell proliferation, and cell cycle pathways, indicating their potential importance in the liver overgrowth and oncogenesis associated with BWS.

  Study phs002365

• Maternal and Developmental Risks from Environmental and Social Stressors (MADRES) Center for Environmental Health Disparities

  MADRES is a prospective pregnancy cohort based in urban Los Angeles, recruiting predominantly low income Hispanic mothers-to-be as part of a children's health study, funded by Environmental Influences on Child Health Outcomes (ECHO). Participants were measured for a number of chemical exposures and biomarkers. Two epigenetic markers will be available through dbGaP: miRNA expression in pregnancy (measured via Nanostring human assay, v3) and DNA methylation from pregnancy and children's cord blood (measured via EPIC array). Principal findings of this research described differences in miRNA expression profiles between early and late pregnancy, as well as miRNA expression affected by psychosocial stress.

  Study phs003194

• BIRC5 Upregulation Enhances DNMT3A-Mutant T-ALL Cell Survival and Pathogenesis

  The goal of this study was to determine how patients with T-ALL who have DNA methyltransferase 3 alpha (DNMT3A) mutations develop resistance to therapy. Since DNMT3A is a methyltransferase, we examined the effect of those mutations on epigenetic regulation using whole genome bisulfite sequencing (WGBS). We also assessed any changes in gene expression using RNA-sequencing. We found that T-ALL patients with DNMT3A mutations are resistant to apoptosis and some chemotherapies. WGBS showed that DNMT3A mutated patients clustered together by their epigenetic profile, which was associated with hypomethylation at TERT and HOX genes. RNA sequencing identified differences in JAK/STAT signaling.

  Study phs003623

• Radiation-Related Genomic Profile of Papillary Thyroid Cancer after the Chernobyl Accident

  The April 26, 1986 accident at the Chernobyl nuclear power plant in northern Ukraine resulted in the release of radioactive contaminants, which were deposited in the surrounding areas in Ukraine, Belarus, and Russia. The main radiation-related health effect resulting from these exposures is the increased occurrence of thyroid cancer among individuals who were children at the time of the accident or born shortly thereafter. The purpose of this study was to conduct a comprehensive genomic landscape analysis of papillary thyroid tumors arising in individuals who were exposed as children to radioactive iodine (I-131) from the Chernobyl nuclear power plant accident.

  Study phs001134

• Systematic immune cell dysregulation and molecular subtypes revealed by single cell RNA-seq of subjects with type 1 diabetes

  Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes and has the potential to guide non-invasive test development and patient stratification.

  Study EGAS50000000231

• Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation

  Background: Glioblastoma (GBM) harbors a highly immunosuppressive tumor microenvironment (TME) which influences glioma growth. Major efforts have been undertaken to describe the TME on a single-cell level. However, human data on regional differences within the TME remain scarce. Goals: we performed single-cell RNA sequencing (scRNAseq) on paired biopsies from the tumor center, peripheral infiltration zone and blood of five patients with primary GBM Details: This EGA study includes raw data sequencing files for the scRNA-seq samples. The processed data (output from Alevin, UMI count matrix and cell metadata) are available from GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197543

  Study EGAS50000000302

• Epigenomic atlas of organoid development

  To investigfate the epigenomic basis of fate decisions in the central nerveous system, we recorded a epigenomic timecourse of human brain organoid development using Cut&Tag with paired scRNA-seq. We further performed perturbation experiment inhibiting EED and profiled the response with scRNA-seq and Cut&Tag. Finally, we profiled a sample of the developing human brain using multiome sequencing and Cut&Tag. In our study, we uncover epigenomic switches during brain region diversification and show that epigenetic activation precedes gene expression during neurogenesis in organoids and in primary tissue. Lastly, we show that transcriptional repression by H3K27me3 is required to stabilize neuroectoderm induction from pluripotency.

  Study EGAS50000000155

• Characterizing the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft model for RNA-based liquid biopsy in a preclinical setting

  This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n=171) derived from a DLBCL PDTX model including 27 humanized (HIS) PDTX, 8 HIS non-PDTX and 21 non-HIS PDTX NOD-scid IL2Rgnull mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either R-CHOP, huCD20-Fc-AFN-CHOP, or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform using the SMARTer Stranded Total RNA-seq pico v3 kit.

  Study EGAS50000000566

• Genetic Analysis of Epidermal Inclusion Cysts

  The goal of this study was to identify a potential driver of epidermal inclusion cysts, or epidermoid cysts, (EICs) in human skin. Individuals were recruited at EIC excision appointments made a priori, with no exclusion criteria. Fresh biopsies and saliva were taken from consented patients, and DNA harvested immediately. Whole exome sequencing was performed (150-bp paired end reads) to 200X in tissue and 80X in saliva via Illumina NovaSeq 6000 sequencer. Identification of somatic mutations was performed using GATK best practices. Somatic variants in the NEK9 gene were found in 12/14 cases sequenced, with clustering of variants within the RCC1 and kinase domains of the protein.

  Study phs003776

• Whole Exome Sequencing and RNA Sequencing of High Grade Serous Ovarian Cancer in Black and White Patients

  In this study, we generated new RNA and whole exome sequencing data from high-grade serous ovarian cancer tumor samples of self-identified Black and White individuals. Our RNA-Seq analysis revealed that, while the prevalence of subtypes varied across racial groups, the cluster-specific gene expression patterns were consistent. Despite these differences in subtype prevalence, the subtype-specific survival rates were similar across racial groups. Additionally, we used the WES-Seq data to characterize mutational signatures and their underlying causes in Black high-grade serous ovarian cancer (HGSC) cases, and compared the prevalence and distribution of these signatures with those in White TCGA cases.

  Study phs003632

• Single-Cell Genomic Analysis of Gastrointestinal Cancer

  Our study aimed to define the heterogeneity of gastrointestinal cancers at a single-cell resolution. We subjected single-cell suspensions derived from surgical resections of gastrointestinal cancer tissue, paired normal tissue, peripheral blood mononuclear cells (PBMCs) or their ex vivo cultures to high-throughput microfluidics based single-cell RNA and DNA sequencing. We analyzed the features of the tumor microenvironment including fibroblasts, endothelial cells, macrophages and lymphocytes to determine their contribution to tumor growth and progression. We also characterized the mechanisms of immunosuppression in these tumors. This analysis led to novel insights into the biology of the microenvironment and also enabled the identification of new treatment targets.

  Study phs001818

• Clinical evaluation of long read sequencing-based episignature detection in developmental disorders

  Some developmental disorders (DD) are marked by specific genome-wide methylation changes, known as episignatures, which can support diagnosis and reveal underlying mechanisms. Current methods rely on indirect methylation profiling. Here, we assessed whether long-read whole genome sequencing with nanopore technology could directly detect both episignatures and genetic variants. We sequenced forty controls and twenty DD patients, using clustering and dimensional reduction to compare methylome patterns with microarray-based signatures. Our classifiers accurately identified episignatures in 17 of 19 patients with pathogenic variants, matching microarray results. This study shows nanopore sequencing enables comprehensive, haplotype-aware genomic and epigenomic analysis for DD diagnostics.

  Study EGAS50000000719

• Understanding Rare Variant Contributions to autism: Lessons from Dystrofin-Deficient Model

  This project generated a whole-exome sequencing (WES) dataset of 83 boys with a pathogenic variant in the DMD gene, along with WES data from the parents of 38 of them, totaling 159 samples. Pathogenic DMD variants, besides causing dystrophinopathies, are also known risk factors for neurodevelopmental disorders (NDDs). However, the low penetrance of NDDs in individuals with dystrophinopathies suggests that additional factors contribute to their manifestation. This study aimed to: (1) characterize ASD in males with dystrophinopathies; (2) determine the relevance of additional de novo and inherited rare risk variants for their neurodevelopmental phenotype; and (3) clinically and functionally characterize the identified risk variants.

  Study EGAS50000000754

• Mayo Clinic Adult Diffuse Glioma Illumina OncoArray SNP Data

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

  Study phs003041

• Investigating immunopathological signatures associated with COVID-19 severity post Omicron

  The aim of this study was to investigate the type and duration of protective immunity alongside immunopathological signatures associated with COVID-19 severity. RNA sequencing was performed using the Illumina Stranded mRNA Prep Ligation kit to investigate the protein coding transcriptome of PBMC cells. T cell receptor (TCR) repertoire profiling was performed with the TakaraBio SMART-Seq Human TCR (with UMIs) on PBMC cells to investigate the depth and persistence of SARS-CoV-2 targeting TCRs. The cohort (n=20) consisted of 10 non-hospitalised and 10 Hospitalised individuals with samples analysed 3 months post positive SARS-CoV-2 PCR.

  Study EGAS50000000926

• NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)

  The CHIRAH project was a community-based study of the factors associated with asthma morbidity in the African American population. CHIRAH evaluated the role of various variables (biologic/environmental, psychologic/behavioral, and socioeconomic) on asthma morbidity and the function of changes in these variables on asthma morbidity in a longitudinal fashion. This involved collection of a cohort-based on school screening which was sampled to include similar numbers of underprivileged and non-underprivileged subjects which roughly equally represented self-reported African Americans and self-reported non-African Americans. Subjects were followed up every 3 months of this cohort over the course of 2 years.

  Study phs001605

• Targeting EGFR in NF1 Mutant Melanoma

  Our study focused on melanoma patients with driver mutations in the neurofibromin 1 (NF1) tumor suppressor gene, a subset of melanoma patients that have not benefitted from recent treatment advances. We have leveraged patient-derived short-term cultures (STCs) and multiomics approaches to identify molecular features that could be developed into therapies for NF1 mutant melanoma patients. Our studies revealed that the epidermal growth factor receptor (EGFR) is highly expressed and active in NF1 mutant melanoma cells, and that genetic or pharmacological EGFR inhibition impaired tumor cell proliferation, survival, and cell growth in patient-derived NF1 mutant but not NF1 wild-type melanoma models.

  Study phs003906

• Targeted DNA sequencing and mRNA sequencing data from patients with peritoneal metastasis from colorectal cancer

  Patients with peritoneal metastasis from colorectal cancer (PM-CRC) have inferior prognosis and respond particularly poorly to chemotherapy. This study aims to identify the molecular explanation for the observed clinical behavior and suggest novel treatment strategies in PM-CRC. Tumor samples (230) from a Norwegian national cohort undergoing surgery and hyperthermic intraperitoneal chemotherapy (HIPEC) with mitomycin C (MMC) for PM-CRC were subjected to targeted DNA sequencing, and associations with clinical data were analyzed. mRNA sequencing was conducted on a subset of 30 samples to compare gene expression in tumors harboring BRAF or KRAS mutations and wild-type tumors.

  Study EGAS50000000404