14312 results for ""Pennsylvania+German"+ACS+study+'Socius'+open+access"

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• Melanoma-Til Study RNAseq

  In this study, mutations present in a series of human melanomas (stage IV disease) will be determined, using autologous blood cells to obtain a reference genome. From each of the samples that are analyzed, tumour-infiltrating T lymphocytes have also been isolated. This offers a unique opportunity to determine which (fraction of) mutations in human cancer leads to epitopes that are recognized by T cells. The resulting information is likely to be of value to understand how T cell activating drugs exert their action.

  Dataset EGAD00001000325

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015718

• Whole Genome-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015709

• Whole-genome sequencing of rhabdomyosarcoma tumouroids (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumoroids data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015707

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015714

• Single-cell RNA-sequencing of rhabdomyosarcoma tumouroids (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumouroids data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015708

• Whole Genome-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015716

• SNP Genotype Data: Subpopulations of Filipino, Malaysian, and Papua New Guinea

  In the context of the study 'Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G,' this repository contains 11 VCF files. Each file includes genetic data from 22 autosomes, representing distinct subpopulations. The subpopulations are as follows: Malaysian: Aeta (15 samples) Agta (11 samples) Batak (10 samples) Mamanwa (6 samples) Filipino: Jehai (13 samples) Kintaq (6 samples) Temiar (5 samples) Papua New Guinea: Highlands (2 samples) Koinambe (10 samples) Kosipe (10 samples) Sepik (2 samples) The numbers in parentheses indicate the sample size for each respective subpopulation.

  Study EGAS50000000044

• Avelumab or M7824 for People with Recurrent Respiratory Papillomatosis

  This submission includes genomic data derived from the study of clinical samples from two different phase II trials. These trials evaluated the clinical efficacy and safety of avelumab or M7824 in the treatment of adults with recurrent respiratory papillomatosis (RRP). Subjects with aggressive RRP were treated with three to six doses of avelumab or M7824. Pre-treatment or post-treatment snap frozen papilloma and normal mucosa samples were subjected to whole exome sequencing and bulk RNA-seq. A total of twenty subjects were enrolled and treated. 

  Study phs002373

• Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes

  We performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium, corresponding to the luteal phase of the ovarian cycle. Biopsies were collected from 58 women with two or more early pregnancy losses and 53 of these samples passed all quality control. RNA was extracted from endometrial biopsies and DNA was extracted for sequencing from blood. Gene expression data can be found at NCBI GEO Series GSE77688.

  Study phs001146

• A Somatic Reference Standard for Cancer Genome Sequencing

  In this study, we separately performed PCR-free whole genome sequencing on the paired tumor/normal melanoma COLO-829 and lymphoblastoid COLO-829BL cell lines across three separate institutions (TGen, Illumina, Genome Sciences Centre at the British Columbia Cancer Agency). We performed a meta-analysis of all data, in combination with the originally reported analysis of these cell lines by Pleasance et al., and report a somatic reference standard based on consensus events. This standard can be used as a reference for tumor/normal whole genome analyses.

  Study phs000932

• Leveraging Extended Families for Cardiovascular Disease Genomic Discovery

  This study characterizes a large early onset atrial fibrillation family and identifies a rare causative mutation (R231H) in the KCNQ1 gene. The age of this mutation is ~5000 years, as estimated using IBD-coalescent methods. The geographic distribution and demographic history of the mutation is described. Induced pluripotent stem cell derived cardiomyocytes carrying the mutation have abbreviated action potential duration, indicating a gain-of-function. This data resource provides exome or whole genome sequencing data for six patients and RNA-seq data from the cardiomyocyte experiments. 

  Study phs002464

• Genomic Sequencing of Lung Adenocarcinoma

  Lung carcinoma is the leading cause of cancer death in the United States and world-wide; lung adenocarcinoma is the most common cause of lung cancer. Pilot studies of lung adenocarcinoma with hybrid-capture based whole exome sequencing will enable us to identify new targets for therapy and improve diagnosis. We will analyze a blend of whole exome and whole genome sequencing data as well as copy number and somatic mutation calls for 200 tumor and matched normal controls. When completed this study will represent the most comprehensive lung adenocarcinoma genome dataset to date.

  Study phs000488

• Characterization of CNS Metastases

  Metastatic disease to the central nervous system (CNS) is devastating, with a poor prognosis. There are limited treatment options for patients with CNS metastases, and in particular with leptomeningeal carcinomatosis (LMD). In this study, we evaluated the molecular and cellular features of parenchymal brain metastases and LMD. We used single-cell RNA and cell-free DNA profiling of CSF from patients with LMD receiving immunotherapy to demonstrate shifts in the liquid LMD tumor microenvironment. We also characterize the tumor microenvironment of parenchymal brain metastases using single cell sequencing, before and after treatment with immunotherapy.

  Study phs002416

• Differential Mutations in Matched Primary and Metastatic Colorectal Cancers

  This study compares DNA mutations detected in matched primary and metastatic colorectal cancer samples from 18 individuals across 1,321 genes. We found many more mutations were shared between tumor pairs (avg. 33.3 mutations/tumor) than were discordant (avg. 2.3 mutations / tumor). Nearly all tumors showed at least one discordance, and these were observed in genes known to be involved in colorectal cancer progression. Therefore, although primary and metastatic colorectal tumors are highly genetically concordant, evidence exists for discordance, which has clinical implications especially in situations of chemotherapy resistance or insensitivity.

  Study phs001084

• Breakpoint detection using long insert whole genome sequencing

  In this study, we hypothesize that shallow long insert whole genome sequencing (LI-WGS) increases our power for detecting breakpoints compared to shallow short insert WGS. We performed a priori analyses to demonstrate the benefits of LI-WGS, developed a long insert library preparation protocol based off Illumina's protocol, and compared LI-WGS against short insert WGS on test samples. We then used long insert WGS to identify translocations and copy number changes in tumor and germline samples collected from cancer patients with different malignancies.

  Study phs000646

• Pharmacogenomic Analysis of Microtubule Targeting Agent Response and Toxicity

  Microtubule targeting agents are commonly prescribed for early and metastatic breast cancer and other solid tumors. However, interindividual variability in microtubule targeting drug response and toxicity can cause limited therapeutic benefit and impact quality of life. In the present study, genome-wide analyses were performed to investigate how genetic factors can be used to increase prediction of treatment response and toxicity, identify genes or gene pathways associated with chemotherapy-induced neurotoxicity, and inform further in vitro studies that may help isolate differences in response and toxicity of microtubule targeting agents.

  Study phs002060

• Metagenomic Deep Sequencing in Meningitis and Encephalitis

  This is a prospective observational study seeking to identify pathogens in cases of unexplained neurological disease, particularly those in which there is a presumed infectious cause. This next generation analytical approach will hopefully allow for rapid identification of foreign genomic material, and through a sophisticated bioinformatics pipeline developed in the DeRisi lab, these foreign genomic sequences can be aligned to all known sequences in publicly available databases (i.e. GenBank) which may allow for identification of novel pathogens or known pathogens that are not frequently tested for as part of standard diagnostic work-ups.

  Study phs001067

• The Vaginal Microbiome in Reproductive Age Women

  The focus of this cross-sectional study was to characterize the vaginal microbiota of asymptomatic, sexually-active, and reproductive-age women representing four self-reported ethnic groups (White, Black, Asian, and Hispanic). Each woman self-collected two mid-vaginal swabs. The first swab was used to prepare a vaginal smear for Nugent gram stain analysis. The second swab was used for DNA extraction, 16S rRNA gene amplicon sequencing, and detection of Candida albicans. In addition, participants measured vaginal pH and completed a detailed questionnaire on sexual health and behaviors.

  Study phs001909

• Identification of Putative Neoantigens in Stage III Melanoma

  This study of three metastatic melanoma patients utilized exome sequencing and RNA sequencing to help identify putative neoantigen peptides that could be further validated by standard immunological assays before design of a personalized vaccine. For each set of neoantigens identified and verified by standard assays, we designed GMP peptides that correspond to the top neoantigens, then used these to condition dendritic cell isolates from each patient. The conditioned dendritic cells were used as the vaccine in three rounds of vaccination, followed by monitoring for T cell memory response to each of the neoantigens.

  Study phs001005

• Genomic and Transcriptomic Markers Associated with Response to Immune Checkpoint Blockade

  The neoantigen presentation score (NEOPS) study was designed to better understand molecular determinants of response to immunotherapies, including pembrolizumab and nivolumab in stage III or IV melanoma patients. From this work, we developed a composite approach to predicting neoantigens (NEOPS), which takes into account additional escape mechanisms, including HLA LOH (human leukocyte antigen loss of heterozygosity) and the impact of deleterious mutations to the antigen presentation machinery (APM), yielding an improved prediction of response to immunotherapy compared to TMB (tumor mutational burden) or neoantigen burden alone.

  Study phs002388

• Whole exome sequencing of 184 unrelated subjects with 22q11.2 deletion syndrome (DiGeorge syndrome/velo-cardio-facial syndrome)

  Our goal is to find genetic modifiers of major phenotypes in patients with 22q11.2 deletion syndrome, also known as DiGeorge syndrome or velo-cardio-facial syndrome. Whole exome sequencing was performed as part of a contract to the NHLBI, Resequencing and Genotyping Service. We have obtained cardiac phenotype information from the de-identified subjects enrolled in the study, either by echocardiography report or medical doctor report. All of the subjects have a 3 million base pair 22q11.2 deletion flanked by low copy repeats, LCR22, A-D.

  Study phs000987

• Next Generation Mendelian Genetics: Atypical Werner Syndrome

  Werner syndrome (WS) is an adult-onset progeroid syndrome characterized by accelerated aging. The International Registry of Werner Syndrome in the Department of Pathology, University of Washington, collects WS cases from all over the world. Classical WS is caused by WRN mutations. Those who do not carry WRN are categorized as "atypical Werner syndrome." A small subset of atypical WS is caused by LMNA mutations. There also are many cases whose causes are still unknown. The purpose of this study is to identify other causative gene(s) of atypical WS.

  Study phs000434

• Inherited Defect in ST6GalNAc1 Reveals Roles of Sialylation in Intestinal Homeostasis

  We have conducted a study of patients with unique mutations in the gene ST6GALNAC1 that encodes the protein ST6GALNAC1 (ST6). Exome sequencing was used to screen worldwide inflammatory bowel disease cohorts, which identified human loss of function mutations of ST6 in individual patients. The affected patients had very early onset (< 6 years old) inflammatory bowel disease. A comprehensive investigation of these gene mutations through in vivo and in vitro experiments revealed that decreased sialylation caused defective mucus proteins and congenital inflammatory bowel disease.

  Study phs002598

• Genomic Translation for ALS Care (GTAC) - WGS

  To look for genetic correlates of disease progression, the GTAC study recruited patients with motor neuron disease from 13 academic medical center clinics and followed them longitudinally for up to 5 years. Participants were regularly assessed for changes in respiratory function, the ALS Functional Rating Scale, and the ALS Cognitive Behavioral Scale. Participants underwent PCR-free whole genome sequencing on the Illumina NovaSeq, as well as repeat-prime PCR assessment of the C9ORF72 repeat expansion. Participants had PBMCs and whole blood RNA banked for future correlative studies.

  Study phs002973

• Genomic and transcriptomic characterization of chordoma

  In this study, we performed paired tumor/normal whole exome and shallow long insert whole genome sequencing, as well as tumor RNAseq, from archival chordoma specimens collected from four patients at the Barrow Neurological Institute in Phoenix, AZ. The purpose of this analysis was to identify potential therapeutic targets. In three patients, we observed that although different DNA and RNA changes were present in each tumor, alterations fell on converging pathways. In the fourth patient, constitutional DNA demonstrated potentially pathogenic alterations that may have predisposed the patient to chordoma.

  Study phs001643

• Genomic Analysis of Bevacizumab-induced Hypertension

  Bevacizumab use in the treatment of cancer can lead to the development of hypertension in some patients, and high-grade toxicity can limit therapy or lead to cardiovascular complications. The factors that contribute to interindividual variability in blood pressure rise during bevacizumab treatment are not well understood. In the present study, whole exomes and flanking regulatory regions of candidate genes associated with vasodilation and blood pressure were sequenced in bevacizumab-treated subjects with the objective of identifying genes harboring multiple variants associated with severe, early-onset bevacizumab-induced hypertension.

  Study phs001597

• Genetic Variants Influence on the Placenta Regulatory Landscape

  This study of the regulatory landscape of the placenta relies on the identification of associations between genetic variant and gene expression changes (eQTLs); genetic variant and DNA methylation changes (mQTLs); and, gene expression change and DNA methylation change (eQTMs). It involves the analysis of DNA sequence variation (n=303), DNA methylation (n=303) and mRNA expression data (n=80) from placentas from healthy women. Such studies are crucial to fully apprehend the complexity of the regulatory landscape and to support further analysis focusing and disease driven phenotype.

  Study phs001717

• Caregiving as a Natural Stressor in Studies of the Role of Genes That Affect Serotonin Function in Regulating Risk Factors for Coronary Heart Disease (CAREGIVER)

  The burden of caregiving for an ill relative has been shown to interact with existing comorbidities to increase risk of several health outcomes including metabolic syndrome and blood pressure reactivity. The CAREGIVER study was developed to compare cardiometabolic risk factors in caregivers and controls. These risk factors include physiologic measures, psychologic measures, neighborhood characteristics, and genetic and genomic factors. DNA and plasma were collected and used for examination of cardiometabolic and stress biomarkers, genotyping and methylation analysis.

  Study phs001747

• Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

  This observational study was designed to determine the cellular tropism of Influenza A and B Viruses (IAV, IBV) from samples taken from the upper respiratory tract collected during routine nasal washes during the 2017-2018 season. Using single-cell RNA sequencing (scRNA-seq) we sought to determine which cell types could be infected, what the cellular response was to infection in both infected and bystander cells, and to compare the intra/inter-host variability of IAV and IBV during a single season at a single healthcare provider location.

  Study phs002039

• Gastrointestinal Cancer Treatment Responders

  Comprehensive genomic profiling of colon adenocarcinomas has revealed multiple recurrent alterations that may inform new treatment strategies. Clinical trials of these agents are ongoing, although the mechanisms of response and resistance to these agents are not well characterized. The goal of this study is to perform comprehensive profiling of pre-treatment and post-resistance tumor and germline samples obtained from patients with colon cancer who receive these agents by carrying out whole exome sequencing and RNA sequencing, and to use these data to identify mechanisms of response and resistance.

  Study phs000803

• Prediction of DNA Repair Inhibitor Response in Short Term Patient-Derived Ovarian Cancer Organoids

  In this study, 34 ovarian tumor organoids generated from 23 patients underwent paired DNA damage repair defect functional analyses and whole exome sequencing analysis to compare genetic mutational status to DNA repair functional capacity. 22 of the patients had high grade serous cancer and 1 of the patients had low grade serous cancer. A normal control, fresh parent tumor, and cells from the organoid culture generated from the parent tumor underwent whole exome sequencing analysis and the data from the sequencing analysis is provided here.

  Study phs001685

• In Vivo Cytokine eQTL Interactions from a Lupus Clinical Trial

  The purpose of this study is to discover in vivo cytokine expression quantitative trait locus (eQTL) interactions from a cohort of patients with systemic lupus erythematosus. 157 lupus patients were enrolled in a clinical trial to test the efficacy and safety of an anti-IL-6 monoclonal antibody. At three time points, we measured interferon (IFN) status, anti-IL-6 drug exposure and genome-wide gen expression. We identified 4,818 cis-eQTLs and then observed a statistically significant enrichment of in vivo eQTL interactions with IFN status and anti-IL-6 exposure.

  Study phs001702

• Patient Microbiome and Surgical Site Infection in Spine Surgery

  Single center, prospective cohort study on the contribution of the preoperative patient microbiome and resistome to surgical site infection (SSI) and resistance to surgical antibiotic prophylaxis in spine surgery. The samples in this entry comprise a subset of patients for whom paired preoperative microbiome samples and postoperative wound culture isolates were obtained. These samples were analyzed by Illumina-based sequencing of metagenomic libraries enriched for the SSI pathogen of interest using the GenCap-Seq methodology (PMID: 36121157) to identify instances of endogenous infection with strains present in the preoperative microbiome.

  Study phs003358

• Phenotypic Signatures of Circulating Neoantigen-Reactive CD8+ T Cells in Patients with Metastatic Cancers

  Following enrichment of neoantigen-reactive T cells using pHLA tetramers or cell-surface markers, we performed single-cell sequencing (RNA-seq and TCR-seq) of circulating CD8+ T cells from metastatic cancer patient samples (Melanoma, Colorectal, and Breast cancer). In samples from previously studied patients, we identified cells bearing neoantigen-reactive T cell receptors and were able to study their phenotypic program. By studying the circulating neoantigen-reactive T cell program, a gene-signature was derived to identify neoantigen-reactive T cells from blood samples prospectively.

  Study phs003064

• Germline Genome Sequencing from Patients with Early-Onset Merkel Cell Carcinoma

  Merkel cell carcinoma (MCC) is a rare neuroendocrine skin cancer associated with advanced age. Approximately 5% of cases are early-onset MCC, occurring in individuals younger than 50 years. This study used genome sequencing to identify germline risk factors among patients with early-onset MCC. The available data in the database of Genotypes and Phenotypes (dbGaP) includes genome sequencing of peripheral blood mononuclear cell (PBMC) DNA from 37 patients with early-onset MCC (age ATM = 2, BRCA1 = 2, BRCA2 = 1, TP53 = 1, and MAGT1 = 1).

  Study phs003485

• Protracted Neuronal Recruitment in the Temporal Lobe of Young Children

  This study describes a stream of migrating neurons directed to the human entorhinal cortex. This migration is among the most protracted in the developing human brain, with young neurons still arriving at 2-3 years of age. We did not observe a similar migratory process in the early postnatal macaque brain, which suggests that this migration may be uniquely delayed or extended into early postnatal human life. Using immunohistochemistry and single‐cell RNA sequencing (scRNA‐seq), we identified these late-arriving neurons as being mainly CGE-derived LAMP5+/RELN+ interneurons.

  Study phs003509

• NHLBI TOPMed - NHGRI CCDG: AF Biobank LMU in the context of the MED Biobank LMU

  The Atrial Fibrillation Biobank Ludwig Maximilian University (AFLMU) Study contributes to the spectrum of disease by adding carefully characterized patients with atrial fibrillation. Atrial fibrillation, one of the most common human arrhythmias confers major morbidity, mortality and health care cost, and has been demonstrated to be caused and influenced by genetic and -omics factors. Particularly, AFLMU enrolled patients with an early onset of atrial fibrillation to increase the genetic burden on disease pathophysiology. All patients were recruited applying standardized protocols to maintain homogeneity in data and DNA quality.

  Study phs001543

• Multivalent State Transitions Shape the Intratumoral Composition of Small Cell Lung Carcinoma

  Small cell lung carcinoma (SCLC) is an aggressive, tobacco-associated tumor characterized by rapid growth, early metastases, and initial response followed by almost invariable resistance to chemotherapy. Studies to date have not resolved the extent that diverse transcriptional programs drive SCLC and contribute to its lethality. We combined patient-derived xenograft (PDX) (n = 64) resources with multi-omic profiling, single-cell fluorescence tracking of ex vivo tumor cells, and mathematical and statistical models to study the topology of the SCLC transcriptional state space and its plasticity.

  Study phs003102

• Single-Cell Analysis of the Multiple Myeloma Microenvironment after Gamma-Secretase Inhibition and CAR T-Cell Therapy

  We examined the effects of gamma-secretase inhibition (GSI) on the bone marrow microenvironment in multiple myeloma patients before anti-B-cell maturation antigen (BCMA) CAR T-cell therapy. Single-nuclei RNA and ATAC sequencing revealed significant changes in gene expression and chromatin accessibility, especially in monocytes and tumor cells, following exposure to GSI. The findings suggest that GSI influences not only BCMA signaling but also broader cellular interactions within the tumor microenvironment. De-identified sequencing data from the study is available through dbGaP.

  Study phs003741

• Arcagen - Extra-pulmonary neuroendocrine tumour or cancer grade 3 (NET / NEC G3) domain

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here were are submitting the dataset that contains NGS files from patients with extra-pulmonary neuroendocrine tumour or cancer grade 3 (NET / NEC G3) (n=85).

  Study EGAS50000000644

• Gene Expression Signature in Normal Mammary Gland from 83 Breast Cancer Patients Indicates Pre-tumorous Changes and Adverse Outcomes

  This study assessed the transcriptomic profiles of 242 samples from 83 breast cancer patients with unfavorable outcomes, including paired uninvolved mammary gland samples collected at varying distances from primary lesions. As a reference, control samples from 53 mammoplasty individuals without cancer history were studied. A custom panel of 634 genes linked to breast cancer progression and metastasis was employed for expression profiling (targeted RNA sequencing), followed by whole-transcriptome (RNA sequencing) verification experiments and statistical analyses to discern molecular signatures and their clinical relevance.

  Study EGAS50000000011

• Aerobiology, Immunology, and Mycobacterium Tuberculosis Transmission

  We submit data from the TB Aerobiology, Immunology and Transmission (TBAIT) study examining clinical and transcriptomic characteristics associated with Tuberculosis cough aerosolization. From a prospective longitudinal cohort of 142 participants with previously untreated pulmonary Mycobacterium tuberculosis (Mtb) infection, we assessed presence of culturable Mtb aerosols using a cough aerosol sampling system (CASS), as well as other clinical, microbiologic, and immunologic characteristics. We performed whole blood transcriptional profiling (submitted here) on a convenience subset of 29 cough aerosol culture (CAC) positive participants and 29 CAC negative participants, using Illumina NextSeq RNA Sequencing (RNA-Seq).

  Study phs003727

• Deciphering the complex clonal heterogeneity of polycythemia vera and the response to interferon alpha

  We integrated colony formation and differentiation assays with single-cell RNA sequencing and single-cell genotyping in PV patient-derived cells vs. healthy controls to dissect how IFNa targets diseased clones during erythroid differentiation. Our findings indicate that PV-derived clones either undergo apoptosis or pass through their typical differentiation cycle, contributing to the long-term exhaustion of mutant cells in the bone marrow. The pivotal roles of ribosomal genes and clonal prerequisites in the therapeutic mechanism of IFNa are underscored by our study.

  Study EGAS50000000904

• Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

  Gastric cancer (GC) is a major cause of global cancer mortality with high levels of heterogeneity, and intratumoral heterogeneity (ITH) represents a significant barrier to GC patient outcomes. In this study, we applied GeoMx DSP technology to identify ITH in GC. We found spatially colocalized RNA-based intratumor subgroups within samples, each correlated with distinct spatially oriented TME and immune profiles. The findings broadening our understanding of the spatial and molecular complexity of GC ITH and offering a valuable data resource for future exploration and discovery.

  Study EGAS50000000345

• Splicing signature analysis of RNU4-2, RNU5A-1 and RNU5B-1

  Pathogenic variants in the snRNA RNU4-2 were recently described as a frequent cause of neurodevelopmental disorders. In our study we further delineate the phenotype associated with RNU4-2 and we also identify pathogenic variants in RNU5A-A and RNU5B-1. Capture-based RNA-Seq were performed to compare splicing pattern between affected and control individuals. A strong signature based on alternative 5' splice site usage was found for RNU4-2 patients, and we suggest an either 5' or 3' signature depending on the variant's localiztion in U5 genes.

  Study EGAS50000000889

• Pyoderma Gangrenosum Caused by Molecular Uncoupling of OTULIN Catalytic Activity and LUBAC Binding

  This is a single-cell RNA sequencing (scRNA-seq) study using peripheral blood mononuclear cells (PBMC) from 3 healthy donors and 2 patients with OTULIN-related Pyoderma Gangrenosum (ORP). Samples were not hashed or multiplexed. The 10X Genomics Platform was used for sequencing. Principal findings include transcriptome changes due to a mutation in OTULIN that causes OTULIN-Related Pyoderma gangrenosum (ORP), without affecting OTULIN function but abrogating its binding ability to the linear ubiquitin assembly complex (LUBAC). FASTA files will be available through dbGaP.

  Study phs004114

• An investigation into the effects of progestin on follicular development and oocyte maturation during controlled ovarian stimulation using the Progestin-Primed Ovarian Stimulation (PPOS).

  In recent years, the Progestin-Primed Ovarian Stimulation (PPOS) method, utilizing progestin as ovulation suppressants, has gained traction as a controlled ovarian stimulation (COS) strategy in assisted reproductive technology (ART). However, the impact of progestin agents on follicular fluid, granulosa cells, and cumulus cells at the levels of gene and protein expression has not been fully assessed. This study aims to evaluate the effects of progestin agents, used in the PPOS method, on follicular development and oocyte maturation.

  Study JGAS000770

• Amplicon sequencing of long non-coding RNA associated with gastritis and gastric carcinogenesis

  This study aimed to identify dysregulations of long non-coding RNA (lncRNA) in gastric cancer, and to reveal molecular functions of lncRNAs associated with gastritis and gastric carcinogenesis. We also aimed to reveal the correlation between clinicopathological characteristics and lncRNA alterations. To this end, we will try to develop predictive markers of gastric cancer risk, which enables prevention and early detection of gastric cancer. We will also try to develop molecular markers which enable us to select treatment strategies for gastric cancer.

  Study JGAS000353

• Acute lymphoblastic leukemia in children produces endogenous T-cells targeting tumor associated antigens and neoantigens in peripheral blood

  In this study we investigated the presence of endogenous T-cells recognizing private tumor-associated antigens and predicted neoantigens. To this end, HLA-I and HLA-II restricted tumor associated antigens (TAAs) and neoantigens were respectively identified and predicted from matched tumor and germline (PBMCs) in three acute lymphoblastic leukemia patients. Circulating T-cells targeting both Mass spectrometry (MS)-identified TAAs and predicted neoantigens were identified in virtually all pediatric BCP-ALL patients, extending up to two years on remission.

  Study EGAS50000000925