14662 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• A Genome-Wide Association Study in Breast Cancer Patients from the Prospectively Randomized SUCCESS Trial

  The SUCCESS-A Study (http://www.success-studie.de) is a randomized Phase III study of response to treatment of early primary breast cancer with adjuvant therapy after surgical resection. The primary outcome is disease-free survival and secondary outcomes are overall survival and toxicity. The study design includes comparison of two pairs of treatment regimes performed in sequence. The first randomization contrasts treatment with and without Gemcitabine (3 cycles of Epirubicin-Fluorouracil-Cyclophosphamide(FEC)-chemotherapy, followed by 3 cycles of Docetaxel(D)-chemotherapy versus 3 cycles of Epirubicin-Fluorouracil-Cyclophosphamide(FEC), followed by 3 cycles of Gemcitabine-Docetaxel(DG)-chemotherapy). The second randomization contrasts treatment with Zoledronate for two versus five years. Patients were recruited from 2005 to 2007 and a total of 3754 patients were included from 250 study sites across Germany. Genome-wide SNP microarray data and phenotype outcomes for the first phase of the study (treatment with and without Gemcitabine) are included in the GARNET (Genomics and Randomized Trials Network) pharmacogenomic study in this dbGaP submission. (The Zoledronate treatments are still underway). SUCCESS-A is a an open-label, multicenter, 2x2 factorial design, randomized controlled, Phase III study comparing the disease free survival after randomization in patients treated with 3 cycles of Epirubicin-Fluorouracil-Cyclophosphamide(FEC)-chemotherapy, followed by 3 cycles of Docetaxel(D)-chemotherapy versus 3 cycles of Epirubicin-Fluorouracil-Cyclophosphamide(FEC), followed by 3 cycles of Gemcitabine-Docetaxel(DG)-chemotherapy, and to compare the disease free survival after randomization in patients treated with 2 years of Zoledronate versus 5 years of Zoledronate in patients with early primary breast cancer. Patients were required to have histopathological proof of axillary lymph node metastases (pN1-3) or high risk node negative, defined as: pT>2 or histopathological grade 3, or age , ≤ 35 or negative hormone receptor, but were not allowed to have evidence of distant disease. Patients were entered into the study no later than 6 weeks after complete resection of the primary tumor. No antineoplastic treatment other than surgical treatment, the defined cytotoxic and endocrine treatment, and radiotherapy was allowed prior to study entry and during the course of the study. After surgery, leading to complete resection of the invasive and intraductal components of the primary tumor, patients were randomized to one of the following two treatments for the first phase of the project (which is included in this GARNET pharmacogenomics study): AA: 3 cycles of 5-Fluorouracil 500 mg/m² i.v. body surface area and Epirubicin 100 mg/m² i.v. and Cyclophosphamide 500 mg/m² i.v., (FEC100), each administered on day 1, repeated on day 22, subsequently followed by 3 cycles of Docetaxel 75 mg/m² body surface area i.v. (D), and Gemcitabine 1000 mg/m² i.v. (30 min infusion) (G), administered on day 1, followed by Gemcitabine 1000 mg/m² i.v. (30 min infusion) on day 8, repeated on day22 AB: 3 cycles of 5-Fluorouracil 500 mg/m² i.v. body surface area and Epirubicin 100 mg/m² i.v. and Cyclophosphamide 500 mg/m² i.v., (FEC100), each administered on day 1, repeated on day 22, subsequently followed by 3 cycles of Docetaxel 100 mg/m² body surface area i.v. (D), administered on day 1, repeated on day 22 A second randomization was made for assigning patients to one of the following two subsequent treatments for the second phase of the project (NOT included in the pharmacogenetic study in this dbGaP submission): BA: Zoledronic acid 4 mg i.v., every 3 months for the duration of two years, subsequently followed by zoledronic acid 4 mg i.v., every 6 months for the duration of additional three years BB: Zoledronic acid 4 mg i.v., every 3 months for the duration of two years Patients with positive hormone receptor status (≥10% positively stained cells for estrogen and/or progesterone) of the primary tumor were recommended to receive Tamoxifen treatment 20 mg p.o. per day for 2 years, after the end of chemotherapy . Subsequent to chemotherapy, postmenopausal patients with positive hormone receptor status were recommended to be treated with Anastrozole (Arimidex®) 1 mg p.o. for additional 3 years, premenopausal patients will continue Tamoxifen treatment for those additional 3 years. In addition to tamoxifen, all patients with positive hormone receptor status of the primary tumor and under the age of 40 or restart of menstrual bleeding within 6 months after the completion of cytostatic treatment or with premenopausal hormone levels as defined below were recommended to receive Goserelin (Zoladex®) 3.6 mg subcutaneously every 4 weeks over a period of 2 years following chemotherapy. Premenopausal endocrine status will be assumed, if the following serum levels are met: LH < 20 mIE/ml, FSH < 20 mIE/ml and E2 > 20 pg/ml. Endocrine therapy will start after the end of chemotherapy. All patients with breast conserving therapy or more than 3 axillary lymph node metastases or in the following cases after mastectomy will receive adjuvant radiotherapy: T3/T4-carcinoma, T2-carcinoma > 3 cm, multicentric tumor growth, lymphangiosis carcinomatosa or vessel involvement, involvement of the pectoralis fascia or a safety margin < 5 mm. Radiotherapy was usually performed after the chemotherapy and parallel to the beginning of the zoledronic acid therapy. Initially, DNA was extracted for performing SNP microarray assays using blood collected at baseline prior to the first randomization. However, the first set of SNP microarray results indicated a quality problem with approximately 50% of the DNA samples. A majority of the problematic samples were replaced with DNA extracted from redrawn blood. The remaining problematic samples were 'restored' using an Illumina FFPE Restoration procedure. A total of 3322 subjects (1638 from arm AA and 1684 from arm AB) were successfully genotyped. Among those, 1771 were from original blood samples, 1092 from redrawn blood samples and 459 from restored blood samples. The SUCCESS-A study is part of the Genomics and Randomized Trials Network (GARNET, http://www.garnetstudy.org) funded by the National Human Genome Research Institute (NHGRI). The overarching goal is to identify novel genetic factors that contribute to disease-free survival for breast cancer patients using different forms of chemotherapy through large-scale genome-wide association studies of treatment response in randomized clinical trials. The study was conducted at the University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Germany. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data cleaning and harmonization were performed at the GARNET Coordinating Center at the University of Washington.

  Study phs000547

• Data Access Committee for the Nichols Group at LHSC

  Dac EGAC00001002164

• SJCRH pediatric HGG sequencing data

  A DAC to manage access to sequencing data derived from primary patient tumors and associated models, e.g. xenografts and cell lines.

  Dac EGAC50000000101

• DAC_RNA-seq of murine osteosarcoma cell line genetically modified for CYR61

  Data access committee for RNA-seq of murine osteosarcoma cell line genetically modified for CYR61

  Dac EGAC50000000352

• Adrenal scRNA sequencing data access

  Raw sequencing datasets for manuscript "Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution".

  Dac EGAC50000000869

• California Teachers Study (CTS): Whole Genome Sequences From Under-Represented Populations

  The California Teachers Study (CTS) is a prospective observational cohort of N=133,477 adult women who have been followed since 1995. Participants completed up to six surveys and have been linked with cancer, hospitalization, and mortality data. In 2013-2016, over 14,000 CTS participants donated blood samples for future research. For this project, DNA was extracted in 2023 from 1694 buffy coats and 56 blood clots from N=1750 CTS participants whose self-reported race/ethnicity was Asian (398), Asian or Pacific Islander (18), Black or African American (189), Native American (128), Native Hawaiian or Other Pacific Islander (66), White Hispanic (719), or more than one race (232). Whole genome sequencing (WGS) was performed at CIDR in 2023-2024. WGS data and accompanying phenotype data are available through dbGaP. In addition, all CTS data are available to the research community via the CTS Researcher Platform (www.calteachersstudy.org), a secure cloud-based environment that includes data, software, documentation, and collaboration workspaces.

  Study phs002918

• SPECIAL: Dissecting the melanoma ecosystem one cell at the time during immunotherapy

  The aim of this study was to identify potential biomarkers of response to immunotherapy (anti-PD1-based) as well as gain understanding of the biological mechanism of therapy resistance (either intrinsic or acquired) in melanoma patients. Single cell RNA sequencing was performed from pre- and on-treatment (2-3 weeks after immunotherapy) metastatic biopsies from stage III and IV melanoma patients.

  Study EGAS00001006488

• Randomized Evaluation of Sedation Titration for Respiratory Failure (RESTORE-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 The primary aim of the RESTORE clinical trial was to determine whether critically ill children managed with a nurse-implemented, goal-directed sedation protocol would experience fewer days of mechanical ventilation than participants receiving usual care. Background Ensuring the safety and comfort of critically ill infants and children supported by mechanical ventilation is integral to the practice of pediatric critical care. Although sedation therapy benefits young participants who cannot understand the imperative nature of invasive life-sustaining therapies, sedative use is also associated with untoward adverse effects. Specifically, opioids and benzodiazepines commonly used for pediatric sedation may impair bedside neurological assessment, depress spontaneous ventilation, and prolong mechanical ventilation. Over time, drug tolerance develops, which may precipitate iatrogenic withdrawal syndrome when sedation therapy is no longer necessary.Numerous studies in adult critical care support a minimal yet effective approach to sedation management. Sedation goals for mechanically ventilated adults have shifted from an unresponsive state to a calm, easily aroused, readily evaluated participant. Studies in adult participants evaluating targeted sedation, daily interruption and/or titration of sedation, pairing of spontaneous awakening with breathing, and no sedation have reported improved clinical outcomes, including decreased length of mechanical ventilation when compared with usual care. In contrast, few data inform sedation practices in pediatric critical care, and international studies describe significant practice variation. Given unique biobehavioral differences, knowledge generated in adult critical care may not translate to the care of critically ill children. The RESTORE study was conducted to test the effect of a nurse-implemented, goal-directed sedation protocol on clinical outcomes in pediatric participants with acute respiratory failure. Participants There was a total of 2,449 participants (mean age: 4.7 years; range: 2 weeks to 17 years). Design The RESTORE study was a cluster randomized clinical trial conducted in 31 US PICUs. Intervention PICUs (17 sites; 1,225 participants) used a protocol that included targeted sedation, arousal assessments, extubation readiness testing, sedation adjustment every 8 hours, and sedation weaning. Control PICUs (14 sites; 1,224 participants) managed sedation per usual care. The primary outcome variable was duration of mechanical ventilation. Conclusions Among children undergoing mechanical ventilation for acute respiratory failure, the use of a sedation protocol compared with usual care did not reduce the duration of mechanical ventilation. Exploratory analyses of secondary outcomes suggest a complex relationship among wakefulness, pain, and agitation (JAMA 2015; 313(4):379-89).

  Study phs003783

• Genome-Wide Association Studies in Upper Gastrointestinal Cancers (Asian)

  This project aims to conduct genome-wide association studies (GWAS) in two anatomically different upper gastrointestinal (UGI) cancer sites in two populations with distinctly different disease rates and genetic profiles. One population has very high rates for both esophageal squamous cell carcinomas (ESCCs) and gastric cancers (GCs) and is comprised of Asians (the "Asian UGI GWAS"), while the other population has low rates of ESCC and GC and includes non-Asians from the Americas, Europe, and Australia (the "Non-Asian UGI GWAS"). Study participants for the Asian UGI GWAS reported here (Illumina 660W Quad chip) were drawn from 2 studies, the Shanxi Upper Gastrointestinal Cancer Genetics Project (Shanxi) and the Linxian Nutrition Intervention Trial (NIT), a prospective cohort, and included a total of 1898 ESCCs, 1625 GCs, and 2100 controls. For the 2nd phase (8 TaqMan SNPs), additional subjects from Shanxi and NIT as well as subjects from the Shanghai Men's Health Study (SMHS), the Shanghai Women's Health Study (SWHS), and the Singapore Chinese Health Study (SCHS) were also included (217 ESCCs, 615 GCs, 1202 controls). Altogether 2115 ESCCs, 2240 GCs, and 3302 controls were genotyped in this study.

  Study phs000361

• Genetics of gene expression in primary human immune cells Data Access Committee

  Dac EGAC01000000009

• IAMC adult cross sectional

  Data access committee for the manuscript "Alterations in the gut microbiome in inflammatory arthritis implicate key taxa and metabolic pathways across arthritis phenotypes"

  Dac EGAC50000000272

• DAC Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  Data access committee for Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  Dac EGAC50000000527

• Picuris Pueblo Genomic Project (Ancient Data)

  Data Access Committee for the ancient dataset of the project "Picuris Pueblo oral history and genomics reveal continuity in US Southwest".

  Dac EGAC50000000525

• Action to Control Cardiovascular Risk in Diabetes (ACCORD) Clinical Trial

  The Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial was a randomized, multicenter, double 2 x 2 factorial design study involving 10,251 middle-aged and older participants with type-2 diabetes who are at high risk for CVD events because of existing CVD or additional risk factors. The purpose of ACCORD was to determine if intensive glycemic control, intensive lipid management and intensive blood pressure control could prevent major cardiovascular events (myocardial infarction, stroke or cardiovascular death) in adults with type 2 diabetes mellitus. Secondary hypotheses included treatment differences in other cardiovascular outcomes, total mortality, microvascular outcomes, health-related quality of life and cost-effectiveness. The ACCORD trial failed to show a beneficial effect of intensive blood pressure or lipid therapy on the primary outcome, and intensive glycemia management actually increased mortality. The hypothesis underlying this ancillary study is that the failure of ACCORD to achieve its goal of reducing cardiovascular risk in diabetic patients through intensive management of hyperglycemia, dyslipidemia, and hypertension may be the result of variation in drug response due to genetic variation between individual participants. Benefits of intensive therapy may accrue to subsets of subjects with specific genetic variants predisposing to efficacious responses to particular therapeutic regimens, and harms may accrue to those with other variants predisposing to poor efficacy or adverse events. Identifying these variants could lead to a precision medicine approach to treating diabetes where each patient's genetic profile could identify the most efficacious treatment regimen with the lowest likelihood of adverse events. To test this hypothesis, a genome-wide genetic analysis was undertaken, incorporating both common variants distributed across the genome and rare variants targeted to exonic regions. Associations of genetic variants with short term responses to individual medicines as well as long term outcomes were investigated. The dataset is composed of genetic data from the ~6100 participants who agreed to participate in the ACCORD optional genetic studies and who allowed broad investigator access to their samples and the data derived from those samples, and from whom a DNA sample of sufficient quality was obtained. While a total of 8514 participants consented to the optional genetics studies, not all consented to broad investigator access, and those who did not are not included in this dataset, although they were also genotyped. Access to these additional genotypes can only be obtained by direct collaboration with the investigators of this study. Phenotype data used in the association analyses are derived from the ACCORD public release clinical data set, which has been made available through BioLINCC.

  Study phs001411

• WES_dataset1

  Fourteen MEITLs and one EATL previously had been sequenced using the SureSelectXT Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA).

  Dataset EGAD50000001620

• PBMCs of HCC Patients treated with anti-PD1 ICB

  10 samples (one baseline, 9 on-treatment). Fastq files containing 5'GEx data, prepared using 10x Genomics pipeline, sequenced on Illumina HiSeq4000.

  Dataset EGAD00001006645

• Reading about genomic analysis of pan-neuroblastoma

  There are virtually no research fields that do not benefit from the large-scale genomic analysis that are so popular nowadays. For research into diseases with highly diverse clinical behavior like pediatric neuroblastoma, nevertheless, this type of approach has been a game-changer. Samuel W. Brady and colleagues, from St. Jude Children’s Research Hospital in Memphis, have gathered data from 702 neuroblastomas which were profiled by whole genome sequencing (WGS, n = 205), whole exome sequencing (WES, n = 539), and/or RNA-Seq. Less than half of the samples were generated during this study, while the others were obtained from previous work. Part of the WES data was indeed deposited in EGA in 2012 (EGA study EGAS00001000213). A scratchy summary about the huge work from Samuel W. Brady and colleagues, published in Nature Communications this October 2020 “These findings suggest that the sympathetic nervous system, the tissue from which neuroblastoma arises, is susceptible to different oncogenic insults at different times during development, which could be explored in future investigations using animal models.” Conclude the authors, highlighting the importance of their findings. Pediatric neuroblastomas are classified according to clinical and molecular features into low, intermediate, and high risk. Age plays a critical role in the classification, with younger children having an overall better prognosis. The samples included in this study belonged to all ages and risk-groups: the aim of such set up is the identification of age-associated molecular aberrations. The authors defined a mutational landscape of pediatric neuroblastoma including rare driver events, impossible to pick with a smaller data set. Interestingly, most driver mutations' frequency was found to be age-related. Those include alterations on MYCN, TERT, PTPRD, and Ras pathway, in addition to the previously reported ATRX. In addition, the large data set allowed the authors to define co-existence relations between the mutations (mutual exclusion or co-occurrence) which is a crucial puzzle piece to unravel the mechanisms driving the pathogenesis. Enjoy this really interesting article, open source on Pubmed.

  Blog genomic-analysis-of-pan-neuroblastoma

• Picuris Pueblo Genomic Project (Modern Data)

  Data Access Committee for the present-day dataset of the project "Picuris Pueblo oral history and genomics reveal continuity in US Southwest".

  Dac EGAC50000000526

• Chun Lab DAC

  Data Access Committee (DAC) for datasets produced by the Chun Lab @ Sanford Burnham Prebys Medical Discovery Institute in La Jolla, California.

  Dac EGAC50000000011

• This study explored and validated the clinical application of targeted NGS of circulating tumor DNA in identifying tumor-specific mutations and uncovering clinical actionable targets in a variety of solid tumors in large patient cohorts.

  Cancer is a disease of genetic alterations. Comprehensive genetic diagnosis is needed to match each patient to appropriate cancer therapy. However, acquisition of representative tumor samples is invasive and often infeasible. Circulating tumor DNA (ctDNA) is a promising non-invasive biomarker for cancer mutational profiling. Here we implemented targeted next generation sequencing (NGS) with a customized pan-cancer gene panel on 605 clinical ctDNA samples in multiple cancer types. Overall, tumor-specific mutations were identified in 87% of ctDNA samples, with mutation spectra highly concordant with their matched tumor tissues. 71% of patients have at least one clinical actionable mutation with 76% of which have suggested drugs approved or in clinical trials. In particular, our study reveals a unique mutation spectrum in Chinese lung cancer patients, which could be used to guide treatment decision and monitor the appearance of drug-resistant mutations. Taken together, our study demonstrated the clinical utility of target NGS-based ctDNA mutational profiling to guide cancer treatment decision.

  Study EGAS00001002251

• The transcriptomic response of skeletal muscle in life-long high-level trained and untrained men and women after acute exercise

  To investigate the influence of lifelong exercise training on the response of skeletal muscle to a bout of acute exercise we generated global transcriptomic data from long-term endurance (8 men, 8 women) and strength (8 men, 8 women) trained individuals and healthy age-matched untrained controls (8 men, 8 women). Skeletal muscle biopsies were taken from M. vastus lateralis before, directly after, and after 1h and 3hrs following acute exercise. All subjects completed one bout of acute endurance exercise and one bout of acute resistance exercise, separated by 4-8 weeks. All 384 samples were multiplexed in 4 lanes and sequenced (2x250bp paired end) on the Illumina NovaSeq 6000.

  Dataset EGAD00001008663

• Gene-Environment Interactions in COCCaINE Use Disorder: Collaborative Case-Control Initiative in Cocaine Addiction

  Drug addiction is a phenotype that has high heritability estimates. In recent years, association studies of candidate genes and some genome-wide association studies (GWAS) have identified a large number of SNPs associated with substance use, abuse or dependence, particularly in phenotypes related to alcohol and nicotine use. Regarding snorted or smoked cocaine dependency, only one GWAS has been conducted so far. In addition, genetic association studies that specifically evaluated smoked cocaine dependence (e.g. crack) are rare, because of characteristics related to the route of administration and duration of the effect of the drug. Thus, the main aim of this GWAS was to identify genetic variations that modulate the risk for the cocaine dependence.

  Study phs001810

• A Genomics-Driven Artificial Intelligence-Based Model Classifies Breast Invasive Lobular Carcinoma and Discovers CDH1 Inactivating Mechanisms

  We developed an artificial intelligence (AI)-model applied to histological images using CDH1 biallelic mutations, pathognomonic for breast invasive lobular carcinoma (ILC), as ground truth. We evaluated the performance of the AI-model to predict the presence of CDH1 biallelic mutations and to diagnose ILC. Subsequently, we investigated the molecular underpinning cases of predicted by the model to harbor a CDH1 biallelic mutations but lacking these alterations according to targeted sequencing. Among this analyses, we subjected to whole genome sequencing (WGS) one ILC case lacking CDH1 biallelic mutations by targeted sequencing and lacking CDH1 promoter methylation to determine the molecular basis of its lobular phenotype.

  Study EGAS50000000485

• Multi-omic analysis of SDHB-related PCPG

  Hereditary SDHB-mutant pheochromocytomas (PC) and paragangliomas (PG) are rare tumours with a high propensity to metastasize although their clinical behaviour is unpredictable. To characterize the genomic landscape of these tumours and identify metastasis biomarkers, we performed multi-omic analysis on 94 tumours from 79 patients using six molecular methods including: whole-genome sequencing (WGS) of tumour and matched blood (n=94), whole transcriptome sequencing (RNA-seq) (n=91), small-RNA seq (n=90), DNA methylation profiling (n=93). Droplet-based (10x) single nuclei (sn)RNA-seq and snATAC-seq was applied to 9 and 7 cases, respectively. Additionally snATAC-seq was applied to one sample of normal adrenal medulla.

  Study EGAS50000000346

• Impact of cryopreservation on transcriptome analysis of peripheral blood mononuclear cells

  To investigate the effect of cryopreservation on PBMCs, we conducted an experiment using samples from three healthy donors under four conditions: fresh PBMCs, PBMCs subjected to a single freeze–thaw cycle, PBMCs refrozen in freezing mix, and PBMCs refrozen in TRIzol. This resulted in a total of 12 samples (three replicates per condition). RNA was extracted from all PBMC samples using the Qiagen miRNeasy Mini Kit, followed by polyA RNA sequencing on the Illumina NovaSeq 6000 platform. Blood was collected from one male and two female adult donors. Sequencing yielded high-quality data, with an average of 27.8 million reads per sample and over 94% of bases exceeding a Q30 quality score.

  Study EGAS50000001196

• HTAS of CD34+ HSPCs in relation to evaluating gene editing outcomes for CGD-causing variants in CYBA and CYBB

  High-throughput amplicon sequencing were performed on CD34+ hematopoietic stem and progenitor cells (HSPCs) derived from 4 healthy donors and one unaffected heterozygous carrier of a CYBB c.252G>A variant causing X-linked granulomatous disease. Targeted genome editing were performed in the HSPCs of CYBA and CYBB genes using CRISPR-Cas9 and recombinant AAV6. To assess gene editing outcomes in CD34+ HSPCs, the targeted loci were amplified from genomic DNA and sequenced with 150-bp paired-end reads on an Illumina iSeq 100 or MiniSeq. Editing rates were determined with CRISPResso2 in HDR mode using standard parameters. The dataaset here contains paired raw fastq files of each sample.

  Study EGAS50000001155

• ProjectMinE :llumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001003383

• Illumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001002598

• RNA sequencing of undifferentiated sarcomas

  Undifferentiated sarcomas (USARCs) of adults are diverse, rare, and aggressive soft tissue cancers. Recent sequencing efforts have confirmed that USARCs exhibit one of the highest burdens of structural aberrations across human cancer. Here, we sought to unravel the molecular basis of the structural complexity in USARCs by integrating DNA sequencing, ploidy analysis, gene expression, and methylation profiling. We identified whole genome duplication as a prevalent and pernicious force in USARC tumorigenesis. Using mathematical deconvolution strategies to unravel the complex copy-number profiles and mutational timing models we infer distinct evolutionary pathways of these rare cancers. In addition, 15% of tumors exhibited raised mutational burdens that correlated with gene expression signatures of immune infiltration, and good prognosis.

  Study EGAS00001003291

• Immune-Related Adverse Events after Immune Checkpoint Blockade-Based Therapy are Associated with Improved Survival in Advanced Sarcoma

  Immune activation after immune checkpoint blockade (ICB) can lead to a unique group of adverse events (AEs), which have been associated with improved outcome in many carcinomas. The association between immune-related AEs (irAEs) and outcome in patients with sarcoma is not well studied. This study has two components: (1) a retrospective clinical study of irAEs among 131 patients treated with ICB at Memorial Sloan Kettering Cancer Center and (2) an analysis of a subset of these patients who have whole transcriptome sequencing available for analysis. In the clinical study portion, we reviewed a cohort of patients with advanced sarcoma treated on prospective clinical trials utilizing ICB-based therapy between April 2017 and January 2020. The objectives were to pool the safety data from each trial, identify irAEs, and correlate them with best overall response by RECIST 1.1, progression-free survival (PFS) and overall survival (OS). Association of irAEs with response and survival was assessed using a Cox regression model. A total of 131 patients were included. Forty-two (32%) had at least one irAE of any grade and 16 (12%) had at least one Grade ≥ 3 irAE. On Cox analysis adjusting for clinical covariates that were significant in the univariate setting, the hazard ratio (HR) for an irAE (HR 0.662, 95% CI 0.421 - 1.041) approached, but did not reach statistical significance for PFS (P = 0.074), while patients had a significantly lower HR for OS (HR 0.443, 95% CI 0.246 – 0.798; P = 0.007) compared to those without or before an irAE. Tumor samples with available RNA sequencing data were stratified by presence of an irAE to identify patterns of differential gene expression. In total, 71 unique patients had RNA sequencing available for analysis. The transcriptomes of 31 of these patients have been previously uploaded to dbGaP (phs002852), leaving 36 unique transcriptomes that have not been previously publicly shared. Three patients did not agree for their sequencing to be publicly shared. Therefore, 33 unique patient samples will be uploaded to this dbGaP study. Overall, this study found that gene expression profiling on baseline tumor samples from patients who had an irAE had higher numbers of tumor-infiltrating dendritic cells, CD8+ T cells, and regulatory T cells as well as upregulation of immune and inflammatory pathways.

  Study phs003284

• Mind Body Study: A Sub-Study on Psychosocial Factors and Microbiomes of Nurses in the Nurse's Health Study II

  The Mind-Body Study is a sub-study of the Nurses' Health Study II (NHSII) which investigated associations between biomarkers and psychosocial factors. The prevalences of clinically meaningful depressive symptoms, mild-to-severe anxiety symptoms, experiencing major-life discrimination, and food addiction were 19%, 21%, 30%, and 5% respectively. These participants were more likely to have experienced childhood abuse and take psychotropic medications but less likely to have chronic conditions such as diabetes and hypertension than participants in the larger NHSII cohort. Participants (n = 213, mean age = 60.6) provided one or two separate stool samples for microbiome profiling between 2013 and 2014, and completed two online psychosocial assessments 10 months apart. The participants also completed two 30-day FFQs around the two microbiome collections. There was excellent reproducibility of psychosocial factors over 1 year. Moderate-to-strong positive correlations were observed between markers of distress and between positive psychosocial factors such as mindfulness and optimism. Here, the subjects' metadata including phenotypic and diet covariates have been provided. Microbial DNA sequence data from the stool microbiome collections is provided via Sequence Read Archive (SRA).

  Study phs003786

• NGS-based monitoring of the T cell receptor repertoire in living donor kidney transplant patients undergoing combination cell therapy

  PBMCs from six kidney transplant recipients receiving as part of the Trex001 study autologous Tregs and donor bone marrow and six control patients not receiving either of the two treatments were collected pre-transplant and at one, three and six month post-transplant. Donor reactive T-cells were identified by mixed lymphocyte reactions (MLR) and lineage specific T-cell receptor (TCR) repertoires of native T-cells and proliferating and non-proliferating T-cells from MLRs were determined by next generation sequencing based profiling of the TCR.

  Dataset EGAD50000000302

• DAC for Breast Invasive Lobular Carcinoma CDH1 study

  We developed an artificial intelligence (AI)-model applied to histological images trained using CDH1 biallelic mutations, pathognomonic for breast invasive lobular carcinoma (ILC), as ground truth. We evaluated the performance of the AI-model to predict the presence of CDH1 biallelic mutations and to diagnose ILC. Subsequently, we investigated the molecular underpinning of cases predicted by the model to harbor a CDH1 biallelic mutations but lacking these alterations according to targeted sequencing. We then subjected one ILC lacking CDH1 biallelic mutations and lacking CDH1 promoter methylation to whole genome sequencing (WGS) to determine the molecular basis of its lobular phenotype.

  Dac EGAC50000000333

• WGS data subfolder HFG3FCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HFG3FCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008496

• WGS data subfolder HF3FKCCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HF3FKCCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008492

• This committee is composed on individuals who have access to the data corresponding to this project: Gut microbiome modulates response to anti PD-1 immunotherapy in melanoma patients

  Dac EGAC00001000758

• Yale Policy for head and neck cancer and HPV clinical trials

  Yale Policy for human controlled access data associated with head and neck cancer and HPV clinical trials

  Dac EGAC50000000403

• ERDERA Diagnostic Research Workstream DAC

  The ERDERA Diagnostic Research Workstream DAC decides on data access requests according to the principles defined in the ERDERA Data Sharing Framework Agreement.

  Dac EGAC50000000728

• Long-read mRNA sequencing of retinal organoids

  Long-read (PacBio) sequencing of two retinal organoid samples. One sample was treated with cyclohexamide. Files are ccs BAM format files generated by a Sequel IIe machine.

  Dataset EGAD50000000100

• ATAC Dataset for 19 T-ALL patient samples and 1 normal control sample

  19 ATAC-seq from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference

  Dataset EGAD50000000024

• Clinical data and mapping file

  Patient demographic characteristics, treatment, and survival data for IMbrave151 (N = 162), with one patient per line. Mapping file to map anonymized subject IDs to RNAseq IDs

  Dataset EGAD50000000569

• Whole genome sequencing data of relapsed paediatric KMT2A-rearranged acute lymphoblastic leukemia

  Bam-file of the one replased KMT2A-r case. Diagnostic (ALLT-375D) and remission (ALLT-375R) samples can be found from EGA submission EGAD50000001568.

  Dataset EGAD50000001593

• Amplicon sequencing of adenoma to carcinoma paired samples from colon

  Colorectal cancer panel sequencing of 100 adenoma and carcinoma samples . Cancer Hot Spot panel sequencing of 7 samples from one poly.

  Dataset EGAD00001004848

• Expanding the neurodevelopmental phenotypes of individuals with de novo KMT2A variants

  We have sequenced four samples to identify variants in KMT2A gene. Three samples were sequenced with WGS, one was sequenced by WES (Patient2).

  Dataset EGAD00001004838

• Exome and RNA seq data for female patient

  Exome and RNA sequencing data for EGAS00001003776 - one female patient with neurofibroma/schwannoma hybrid nerve sheath tumor (N/S HNST)

  Dataset EGAD00001005249

• Exome reads

  One sample of human genomic DNA. DNA extracted from whole blood. Reads obtained using an exome enrichment kit (Truseq, Illumina) and sequencing of 100bp paired-end reads on a HiSeq 2500 sequencing system (Illumina).

  Dataset EGAD00001003841

• Study of 5'UTR Mutations in Prostate Cancer

  The 5' untranslated region (5' UTR) of mRNA controls the translation of specific transcripts through encoded cis-regulatory elements. Yet exceedingly little is known about the prevalence and function of 5' UTR mutations in cancer. We have uncovered many 5' UTR mutations in our analysis of localized and castration resistant prostate cancer patients, and hypothesize that systematic mutations in critical 5' UTR regulatory regions perturb gene expression to drive prostate cancer progression. To elucidate the functional 5' UTR regulatory landscape of prostate cancer, we have taken a multi-faceted approach including ribosome profiling, in vitro reporter assays and the development of a novel high throughput method to functionally access the impact of recurrent 5' UTR mutations on both transcription and translation.

  Study phs001825

• HiDEF-seq single-molecule sequencing of single-strand mismatches and damage

  Our study sought to resolve, with single-molecule fidelity, the mismatches and damage events that precede DNA mutations. Using a novel single-molecule, long-read sequencing method (HiDEF-seq) we detect base substitutions when present in either one or both DNA strands. We also detect cytosine deamination, a common type of DNA damage, with single-molecule fidelity. This study profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes. These samples revealed single-strand mismatch and damage signatures. Since double-strand DNA mutations are only the endpoint of the mutation process, our approach enables new studies of how mutations arise in a variety of contexts, especially in cancer and aging.

  Dataset EGAD50000000460

• Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  Data access committe for the project: Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  Dac EGAC50000000074

• Data Access Committee of Biobank Lab, Department of Oncobiology and Epigenetics, University of Lodz

  Dac EGAC50000000080