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• Nala TAS-LRS PGx Study

  Pharmacogenomics (PGx) testing improves medication safety and efficacy by identifying genetic variants that affect drug response. However, current technologies often fail to resolve complex loci, detect structural variants, or phase alleles accurately. Here, we present an end-to-end PGx workflow based on Targeted Adaptive Sampling-Long Read Sequencing (TAS-LRS), integrating a streamlined laboratory protocol with a bioinformatics pipeline that includes a novel CYP2D6 caller. Using 1,000 ng of DNA and three-sample multiplexing on a single PromethION flow cell, the assay achieves consistent on-target (25x) and off-target (3x) coverage, enabling accurate, haplotype-resolved testing of 35 pharmacogenes alongside genome-wide genotyping from off-target reads. We further developed the workflow into a clinically ready service and validated its performance across 17 reference and clinical samples. The assay demonstrated high concordance for small variants (99.9%) and structural variants (>95%), with phased diplotypes and metabolizer phenotypes reaching 97.7% and 98.0% concordance, respectively. Improved calls were observed in 12 genes due to enhanced genotyping, phasing, or novel allele detection. In addition, off-target reads supported accurate genome-wide imputation, comparable to short-read sequencing and superior to microarrays. These results establish the feasibility of long-read sequencing for clinical PGx testing and position TAS-LRS as a scalable solution combining both targeted and genome-wide utility.

  Study EGAS50000001116

• Liquid biopsy for molecular characterization of diffuse large B-cell lymphoma and early assessment of minimal residual disease

  Circulating tumor DNA (ctDNA) allows genotyping and minimal residual disease (MRD) detection in lymphomas. Using a NGS approach (Euroclonality-NDC), we evaluated clinical and prognostic value of ctDNA in a series of R-CHOP-treated DLBCL patients at baseline (n=68) and after 2-cycles (n=59), monitored by metabolic imaging (PET/CT). A molecular marker was identified in 61/68 (90%) ctDNA samples at diagnosis. Pre-treatment high ctDNA levels significantly correlated with elevated LDH, advanced stage, high risk IPI and a trend to shorter 2-year PFS. Valuable NGS data after 2-cycles of treatment were obtained in 44 cases, and 38 achieved major molecular response (MMR; 2.5-log drop in ctDNA). PFS curves displayed statistically significant differences among those achieving MMR vs. those not achieving MMR (2yr PFS of 76% vs. 0%, p<0.001). Similarly, more than 66% reduction in SUVmax by PET/CT identified two subgroups with different prognosis (2yr PFS of 83% vs. 38%; p<0.001). Combining both approaches MMR and SUVmax reduction, a better stratification was observed (2yr PFS of 84% vs. 17% vs. 0%, p<0.001). Euroclonality-NDC panel allows the detection of a molecular marker in the ctDNA in 90% of DLBCL. ctDNA reduction at 2 cycles and its combination with interim PET results improves patient prognosis stratification.

  Study EGAS50000000215

• Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_cytoscan)

  Cancer progression is driven in part by genomic alterations located in oncogenes or tumor suppressor genes. The genomic characterization of cancers has shown a large interpatient heterogeneity regarding the driver alterations, leading to the concept that generating a genomic profiling by multigene sequencing in patients with cancer could allow selecting effective targeted therapies. While this concept has been broadly implemented in daily practice, there is no evidence that such approach improves patient outcome, and how to optimally select the therapy to administer. A genomic profiling using next generation sequencing and copy number analyses was performed 1462 patients with Her2-non overexpressing metastatic breast cancer included in SAFIR02 Breast trial. 238 of these patients were randomized in two trials between a targeted therapy matched to genomic alteration and a maintenance chemotherapy. The trial shows that targeted therapies matched to genomics improves progression free survival (PFS) when genomic alterations are classified level I/II according to ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT) (adjusted HR: 0.41, 90% CI: 0.27-0.61, p&lt;0.001), but not when alterations are classified beyond level II (unadjusted HR: 1.15, 95% CI: 0.76-1.75). This trial provides evidence that the treatment decision led by genomics should be driven by a framework of target actionability in patients with mBC.

  Study EGAS00001005584

• Coding and non-coding drivers of mantle cell lymphoma identified through exome and genome sequencing

  Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we re-sequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent non-coding mutations surrounding a single exon of the HNRNPH1 gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent non-coding mutations in disrupting an auto-regulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly implicate a role for aberrant regulation of mRNA processing in MCL pathobiology.

  Study EGAS00001004289

• Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_oncoscan)

  Cancer progression is driven in part by genomic alterations located in oncogenes or tumor suppressor genes. The genomic characterization of cancers has shown a large interpatient heterogeneity regarding the driver alterations, leading to the concept that generating a genomic profiling by multigene sequencing in patients with cancer could allow selecting effective targeted therapies. While this concept has been broadly implemented in daily practice, there is no evidence that such approach improves patient outcome, and how to optimally select the therapy to administer. A genomic profiling using next generation sequencing and copy number analyses was performed 1462 patients with Her2-non overexpressing metastatic breast cancer included in SAFIR02 Breast trial. 238 of these patients were randomized in two trials between a targeted therapy matched to genomic alteration and a maintenance chemotherapy. The trial shows that targeted therapies matched to genomics improves progression free survival (PFS) when genomic alterations are classified level I/II according to ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT) (adjusted HR: 0.41, 90% CI: 0.27-0.61, p&lt;0.001), but not when alterations are classified beyond level II (unadjusted HR: 1.15, 95% CI: 0.76-1.75). This trial provides evidence that the treatment decision led by genomics should be driven by a framework of target actionability in patients with mBC.

  Study EGAS00001005586

• Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_agilent)

  Cancer progression is driven in part by genomic alterations located in oncogenes or tumor suppressor genes. The genomic characterization of cancers has shown a large interpatient heterogeneity regarding the driver alterations, leading to the concept that generating a genomic profiling by multigene sequencing in patients with cancer could allow selecting effective targeted therapies. While this concept has been broadly implemented in daily practice, there is no evidence that such approach improves patient outcome, and how to optimally select the therapy to administer. A genomic profiling using next generation sequencing and copy number analyses was performed 1462 patients with Her2-non overexpressing metastatic breast cancer included in SAFIR02 Breast trial. 238 of these patients were randomized in two trials between a targeted therapy matched to genomic alteration and a maintenance chemotherapy. The trial shows that targeted therapies matched to genomics improves progression free survival (PFS) when genomic alterations are classified level I/II according to ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT) (adjusted HR: 0.41, 90% CI: 0.27-0.61, p&lt;0.001), but not when alterations are classified beyond level II (unadjusted HR: 1.15, 95% CI: 0.76-1.75). This trial provides evidence that the treatment decision led by genomics should be driven by a framework of target actionability in patients with mBC.

  Study EGAS00001005587

• Intratumoural heterogeneity and immune modulation in lung adenocarcinoma of female smokers and never smokers

  Lung cancer is still the leading cause of cancer death worldwide despite declining smoking prevalence in industrialised countries. Although lung cancer is highly associated with smoking status, a significant proportion of lung cancer cases develop in patients who never smoked, with an observable bias towards female never smokers. A better understanding of lung cancer heterogeneity and immune system involvement during tumour evolution and progression in never smokers is therefore highly warranted. We employed single nucleus transcriptomics of surgical lung adenocarcinoma (LADC) and normal lung tissue samples from patients with or without smoking history. Immune cells as well as fibroblasts and endothelial cells respond to tobacco smoke exposure by inducing a highly inflammatory state in normal lung tissue. In the presence of LADC, we identified differentially expressed transcriptional programmes in macrophages and cancer-associated fibroblasts, providing insight into how the niche favours tumour progression. Within tumours, we distinguished eight subpopulations of neoplastic cells in female smokers and never smokers. Through pseudotemporal ordering, we inferred a trajectory towards two differentiated tumour cell states implicated in cancer progression and invasiveness. A proliferating cell population sustaining tumour growth exhibits differential immune modulating signatures in both patient groups. Our results resolve cellular heterogeneity and immune interactions in LADC, with a special emphasis on female never smokers and implications for the design of therapeutic approaches.

  Study EGAS00001006331

• Treatment of Preserved Cardiac Function Heart Failure with an Aldosterone Antagonist (TOPCAT-BioLINCC)

  Data Access NOTEPlease refer to the "Authorized Access" section below for information about how access to the data from this accession. Access differs from many other dbGaP accessions. BiospecimensAccess to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from TOPCAT include Buffy Coat, DNA, Plasma, Serum, Urine, and Whole Blood. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives The TOPCAT trial evaluated the effectiveness of aldosterone antagonist therapy in reducing cardiovascular mortality, aborted cardiac arrest, and heart failure hospitalization in patients who have heart failure with preserved systolic function. Background Many patients with heart failure have a normal, or near-normal, left ventricular ejection fraction (LVEF). Such patients share similar signs and symptoms as patients who have heart failure and a reduced LVEF, as well as an impaired quality of life and a poor prognosis. However, at the time of TOPCAT, the benefit of medical therapies for heart failure were limited to those with a reduced LVEF. Due to a lack of favorable evidence from clinical trials, clinical guidelines offered no specific recommendations for the management of heart failure in patients with preserved LVEF, except for attention to coexisting conditions. Among patients with heart failure and a reduced LVEF and those with myocardial infarction complicated by heart failure and left ventricular dysfunction, mineralocorticoid receptor antagonists have been shown to be effective in reducing overall mortality and hospitalizations for heart failure. In small mechanistic studies involving patients with heart failure and preserved left ventricular function, mineralocorticoid receptor antagonists improved measures of diastolic function. However, rigorous testing was needed regarding their effect on clinical outcomes in patients with preserved LVEF. Therefore, the TOPCAT trial was initiated to determine whether treatment with spironolactone, an aldosterone antagonist, would improve clinical outcomes in patients with symptomatic heart failure and a relatively preserved LVEF. Participants A total of 3445 participants were enrolled, with 1722 assigned to the spironolactone group and 1723 assigned to the placebo group. Among these, 2464 participants were enrolled via the hospitalization stratum and 981 were enrolled via the BNP stratum. Design TOPCAT was a phase 3, multicenter, international, randomized, double-blind, and placebo controlled trial. Eligible participants were randomly assigned to receive either spironolactone or placebo in a 1:1 ratio. Randomization was stratified according to whether the patient met the criterion for previous hospitalization or BNP elevation. The baseline visit included assessment of socio-demographics, physical characteristics, medical history, lifestyle factors, laboratory measures, electrocardiography variables and health-related quality of life and functional status. Study drugs were initially administered at a dose of 15 mg once daily, which was increased as tolerated to a maximum of 45 mg daily during the first four months after randomization. Subsequent dose adjustments were made as required and subjects continued to receive other treatments for heart failure and co-existing illnesses. Measurement of potassium and creatinine levels was required within 1 week after a change in the study-drug dose and at each scheduled study visit. Follow-up visits to monitor symptoms, medications, and events and to dispense study drug were scheduled every four months during the subject's first year on the study, and every six months thereafter. The mean follow-up interval was 3.3 years in each study group. Repository blood and urine samples were collected at the baseline and 1 year visits from consenting subjects. The primary endpoint was a composite of cardiovascular mortality, aborted cardiac arrest or hospitalization for the management of heart failure. Secondary endpoints included all-cause mortality, hospitalization for heart failure management, new onset of diabetes mellitus or atrial fibrillation, and quality of life. A subset of subjects also participated in the Echocardiography or Echocardiography and Vascular Stiffness ancillary studies. Echocardiography, and additionally tonometry in the Echocardiography and Vascular Stiffness study, were performed at baseline and at either 12 or 18 months following randomization. If the subject was already enrolled in the TOPCAT trial at the time the ancillary study was initiated, but had not yet reached the 18 month visit, baseline was determined via a retrospective analysis performed on any echocardiographic images completed within 60 days prior to TOPCAT enrollment and no tonometry was performed if applicable. Conclusions In patients with heart failure and a preserved ejection fraction, treatment with spironolactone did not significantly reduce the incidence of the primary composite outcome of death from cardiovascular causes, aborted cardiac arrest, or hospitalization for the management of heart failure. However, the drug reduced the secondary endpoint of heart failure hospitalization incidence.

  Study phs003665

• FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

  We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts such as misalignments or random pairing of transcript fragments and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including 8 cancers with and without known rearrangements.

  Study phs000311

• Modelling Multi-Dimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research

  The Center for Cancer Research (CCR), of the intramural NCI undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers who were enrolled on other therapeutic trials to determine the feasibility of a genome guided precision therapy protocol in these patients.Note: NCIPM001blood - This sample was previously submitted with study phs002207, with sample ID NCIPM001blood_E and SRR ID SRR18544311.

  Study phs001052

• Cookies

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  Documentation cookies

• An IL-1β driven neutrophil-stromal cell axis fosters a BAFF-rich microenvironment in multiple myeloma

  This depository contains data from two bulk RNA sequencing experiments: 1) Bulk RNA sequencing data of peripheral blood neutrophils from healthy donors cultured with a) human adipose-derived stromal cells (ADSC) as a model for mesenchymal stromal cells (MSC), and b) IL-1β stimulated ADSC as a model for inflammatory MSC as found in multiple myeloma (MM). 2) Bulk RNA sequencing data from ADSCs cultured a) without stimuli, b) with recombinant human IL-1β, c) with supernatant from iMSC-like cells, d) with neutrophils previously cultured with MSC, e) with neutrophils previously cultured with iMSC, f) with neutrophils previously cultured with iMSC in the presence of anti-human IL-1β or g) with neutrophils previously cultured with iMSC in the presence of an isotype control.

  Dataset EGAD00001010080

• DLBCLR

  Evaluating gene expression in DLBCL using a quantitative nuclease protection assay

  Study EGAS00001007479

• Neoantigen Landscape in a Hypermutated Glioblastoma Arising in a Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy

  Whole genome and exome-based DNA sequencing of germline and tumor specimens from serial samples of patients with glioblastoma. The data set includes several metastases and recurrences from a patient with germline POLE-deficiency. The data reveal extensive tumor heterogeneity, clonal evolution, and genomic responses to immunotherapy.

  Study phs001663

• Germline WES-data of pediatric cancer patients with variants in HBOC-related genes

  This study focused on the identification of (likely) pathogenic germline variants (LP/PV) in 25 adult-onset HBOC-related genes in a cohort of 372 pediatric cancer patients. The cohort was sequenced on Illumina platforms. The files uploaded here belong to the 27 individuals with such a LP/PV.

  Study EGAS50000001073

• Genome sequencing of biliary tract cancers

  Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous with poor response to treatments. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed genome sequencing analyses for a large scale samples of BTCs to investigate their somatic and germline driver events and characterize their genomic landscape.

  Study JGAS000109

• Genome sequencing of biliary tract cancers

  Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous with poor response to treatments. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed genome sequencing analyses for a large scale samples of BTCs to investigate their somatic and germline driver events and characterize their genomic landscape.

  Study JGAS000389

• Understanding_population_genetics_and_patterns_of_genome_wide_heterozygosity_in_a_sample_of_the_Croatian_isolated_populations__ESGIDalmatians_

  Using high-throughput sequencing technologies and analytical tools, we conduct an exome sequencing study that will help understand the populationgenetics of a Croatian island isolate, in a sample of 200 subjects from the Adriatic island of Vis who wereselected to reflect islanders with at least four known ancestors in grandparental line who are original islanders.

  Study EGAS00001000336

• Analysis_of_resistance_to_PLX4032

  We have collected material from a patient who had BrafV600E mutant melanoma that wastreated with PLX4032. We have germline DNA from the patient and DNA and RNA fromdistinct lesions before and after treatment with PLX4032. We would like to exome sequencethese samples to gain a snap shot of the mechanisms of resistance that are operative.

  Study EGAS00001000415

• _WGS__Somatic_mutation_in_skin_epidermis__SMS_

  Previously we have sequenced 2mm2 biospies of human epithelia at high depth using a custom bait set. This has identified a range of mutations. Some of the biospies are predicted to be clonal and we would like to perform WGS to give an insight into mutational burden, and CNV which may be associated with these mutations.

  Study EGAS00001004464

• Lung cancer Early Molecular Assessment

  This study aimed to validate the potential utility of a clinically accessible, highly sensitive tumor-informed circulating tumor DNA (ctDNA) assay. The study considers a ‘landmark’ time period (between two weeks and four months after definitive treatment), as well as longitudinal sampling (>2 weeks) and compares two independent, retrospectively collected real-world cohorts.

  Study EGAS50000000896

• The_Transcriptome_of_PLX4032_resistance

  We have collected material from a patient who had BrafV600E mutant melanoma that wastreated with PLX4032. We have germline DNA from the patient and DNA and RNA fromdistinct lesions before and after treatment with PLX4032. We have transcriptome sequenced these samples to obtain a snap shot of the mechanisms of resistance that are operative.

  Study EGAS00001000413

• The_life_history_of_colorectal_cancer_metastases_study_WGS_X10

  Whole genome sequencing of a series of metastasis collected from 2 patients at autopsy will be used to construct a life history of the cancer, including phylogenetic relationship between the different metastases an also whether there is evidence of convergence towards common biological processes that underpin the metastatic process but though different mutational events

  Study EGAS00001000864

• MPN_Tissue_WGS_NanoSeq

  An exploration of the somatic mutational landscape of a patient with myeloproliferative neoplasm (MPN) and squamous cell carcinoma (SCC). In particular this study aims to identify mutational signatures present in SCC lesion compared to a region of healthy skin, especially searching for the presence of signatures specific to hydroxycarbamide from previous chemotherapy treatment.

  Study EGAS00001007761

• Partially methylated domains across multiple cell types

  Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them.

  Study EGAS00001003157