Search Results - EGA European Genome-Phenome Archive

TXT_CD138N_15

TPM matrices of counts from RNA sequencing (RNAseq) from longitudinal CD138(–) BM fractions.

Dataset EGAD00001011145

SNF_RNAseq_CD138n_20f

TPM matrices of counts from RNA sequencing (RNAseq) from baseline CD138(–) BM fractions.

Dataset EGAD00001011142

Whole-genome cfDNA TAPS sequencing data from 91 people with various types of cancer and from non-cancer controls

TAPS data in the form of BAM files from 214 samples: plasma (at 80x) and matched germline (at 30x) pairs from 61 cancer and 30 non-cancer subjects, fresh-frozen matched tumour biopsies (at 80x) from 16 subjects, as well as several follow-up plasma samples (at 80x) from 10 subjects with colorectal cancer.

Dataset EGAD50000000996

Metastatic_Breast_Cancer_Whole_Genome

We propose to definitively characterise the somatic genetics of Metastatic breast cancer through generation of comprehensive catalogues of somatic mutations in Metastatic breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

Study EGAS00001000902

Breast_Cancer_FRT_RNA_seq

We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

Study EGAS00001000420

Triple_Negative_Breast_Cancer_RNA_Sequencing

We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

Study EGAS00001000377

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

Chugai_colorectal_organoid_sequencing

Genomic and transcriptomic characterization of drug-resistant colon cancer stem cell lines.

Study EGAS00001000872

Germline genome sequencing samples from the Hereditary Cancer Syndromes (ICCon) Cancer Flagship

A prospective study of individuals with suspicion of a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or was not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing and a comprehensive cancer virtual gene panel analysis were undertaken.

Study EGAS00001007045

Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9125 subjects referred to carrier screening. We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks.

Study phs001482

Genome Wide Association Study of Serum Creatinine during Vancomycin Therapy and Vancomycin Pharmacokinetics

The goal of this study was to identify genetic variants associated with risk for acute kidney injury (AKI) in patients being treated with vancomycin and genetic variants associated with variability in vancomycin pharmacokinetics. AKI is a common adverse drug event and known complication of vancomycin therapy. Known risk factors fail to accurately predict renal toxicity. Our hypothesis, that genetic variants modify the risk of AKI, was tested by performing genome-wide association and linear regression in 429 patients of European descent using the outcome of peak serum creatinine while on vancomycin. We also tested the hypothesis that genetic variants associate with vancomycin pharmacokinetics, using vancomycin trough levels and calculated renal elimination rate constant as outcomes.

Study phs000894

Re-evaluation of human mitochondrial DNA methylation reveals signals consistent with technical artifacts

The existence and functional relevance of mitochondrial DNA (mtDNA) methylation remain controversial. We assessed 5mC and 5hmC in human brain, blood, and related cancers using both enzymatic and native DNA sequencing. While nuclear DNA exhibited expected methylation patterns, mtDNA consistently showed negligible methylation levels, indistinguishable from technical noise. Elevated methylation in nuclear-embedded mitochondrial sequences demonstrates a clear potential to confound mtDNA methylation measurements. Furthermore, technical discrepancies in mtDNA methylation were observed, underscoring the need for careful evaluation when interpreting data generated using earlier sequencing workflows. Our findings provide evidence against the presence of 5mC or 5hmC in mtDNA under the physiological and pathological conditions studied.

Study EGAS50000001186

Identification of putative multiple myeloma (MM) susceptibility genes

We sought to identify novel MM susceptibility genes using a collection of families with multiple cases of MM/MGUS, including 189 affected individuals from 40 families, and index cases from an additional 88 families, along with 170 early-onset (EO) MM cases (≤ 55 years). We analyzed a total of 347 affected individuals using whole exome (N=321) and whole genome (N=26) sequencing. Samples were identified and collected through nation-wide efforts in France, Sweden and Greece. We focused on rare (MAF<0.5%) germline protein truncating and likely deleterious missense variants in genes harboring variants in at least two families showing variant-disease segregation, and in additional index (≥2) and/or early-onset (≥2) cases.

Study EGAS50000001259

Ultra-deep Error-corrected Sequencing of Peripheral Blood for Clonal Hematopoiesis in Patients Undergoing AAA Surgery

Patients undergoing elective abdominal aortic aneurysm (AAA) surgery were enrolled to investigate the prevalence and characteristics of clonal hematopoiesis. Peripheral blood was collected at the time of surgical admission using PAXgene DNA tubes. Genomic DNA was extracted and subjected to ultra-deep error-corrected targeted sequencing using a custom gene panel covering recurrent clonal hematopoiesis-associated genes. Sequencing libraries were prepared following established protocols and sequenced on an Illumina NovaSeq X system. The resulting dataset includes paired-end FASTQ files for each participant, enabling high-sensitivity detection of somatic variants down to low variant allele frequencies. This study provides a comprehensive sequencing resource for evaluating clonal hematopoiesis in AAA patients.

Study JGAS000864

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

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

DNA_repair_in_BLM_deficient_hiPSCs

We are aiming to investigate repair of a double strand break (DSB) within the genome in the presence and absence of the BLOOM protein. Zinc Finger Nucleases introduce DSBs at specified loci within the genome. Using sequencing we will assess the size of the deletion following repair. Protocol1. Transfect normal and BLOOM deficient human iPS cells with ZFNs, using AMXA2. Harvest cells after 5 days3. Perform column extraction of DNA4. PCR-amplify the ZFN region 5. Sequence and analyse repair of the DSBThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Study EGAS00001000740

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

UQCCR/QCMG brain metastasis sequence analysis

The present study, conducted by the UQCCR and QCMG at the University of Queensland, investigated the genomic landscape of brain metastases from 36 patients (with matched normal samples) that originated from a range of primary tumour sites (including breast (11), lung (18), melanoma (6) and oesophageal (1)) utilizing Illumina 2500 HiSeq Exome sequencing. Somatic substitutions were identified using a dual qSNP/GATK calling strategy. The Pindel tool was used to determined short insertions and deletions. Key biological pathways were investigated using pathway analysis tools. It is envisaged that the current work may provide important biological insights into the genomic characterization and evolution of brain metastasis and additionally identify druggable targets of clinical relevance.

Study EGAS00001000722

Whole exome sequencing of a representative cohort of AML

The Genomic DNA Clean & Concentrator kit (ZYMO Research) was used to remove EDTA from the DNA samples. Sample libraries were prepared using 100 ng of input according to the KAPA HyperPlus Kit (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Exomes were captured using the SeqCap EZ MedExome (Roche Nimblegen) according to SeqCap EZ HyperCap Library v1.0 Guide (Roche) with the xGen Universal blockers – TS Mix (Integrated DNA Technologies, Inc.). The amplified captured sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned to the hg19 reference genome using the Burrows-Wheeler Aligner (BWA)3, v0.7.15-r1140.

Dataset EGAD00001007580

The Cancer Dependency Map (DepMap)

The Cancer Dependency Map (DepMap) aims to accelerate precision cancer medicine by creating a comprehensive map of tumor vulnerabilities. The DepMap project genomically profiles a wide range of cancer models and characterizes them for their sensitivity to genetic and compound perturbations. The data is computationally analyzed to create a systematic overview of the genetic dependencies and compound sensitivities of cancer types and the predictive biomarkers that point to patient populations most likely to benefit from targeting of these vulnerabilities. The DepMap public portal has become a comprehensive resource to identify cancer vulnerabilities by providing datasets at scale, cutting-edge computational tools, and sophisticated visualization tools that together have accelerated the discovery of novel targets and biomarkers. Please visit Depmap.org to access the public portal.

Study phs003444

Genetic Alterations in Benign Breast Biopsies of Subsequent Breast Cancer Patients

Fibrocystic changes are associated with an increased risk of breast cancer (approximately 1.5-2 times that of the general population). Although the relative risk seems low, because of the high frequency of such changes, the absolute risk is significant. Genetic alterations have been found in fibrocystic changes with or without epithelial changes, suggesting that critical oncogenic events are occurring at an early stage. We investigated a unique collective of 17 breast cancer patients who, prior to the diagnosis of invasive breast cancer, underwent open surgical biopsy showing fibrocystic changes of the breast. Massive parallel sequencing targeting genes frequently mutated in breast cancer was performed on the fibrocystic breast tissue as well as the ensuing cancer tissue.

Study EGAS00001003563

Count Me In (CMI): The Angiosarcoma (ASC) Project (CMI-ASCproject)

Count Me In - The Angiosarcoma Project: A Patient-Partnered Research Initiative to Accelerate Research in a Rare Sarcoma The Angiosarcoma Project (ASCproject) is a research study that directly engages angiosarcoma patients online and empowers them to accelerate cancer research by sharing medical information and clinical samples. Angiosarcoma is an exceedingly rare soft tissue sarcoma with an incidence of ~300 newly diagnosed cases per year in the United States. This low incidence has impeded large-scale research efforts in this disease that are strongly needed to catalyze research and improve clinical outcomes. The Angiosarcoma Project, launched in March 2017, has demonstrated the feasibility of directly engaging geographically dispersed patients to democratize research and establish a large patient cohort to characterize the genomic and clinical landscape of a rare disease. Angiosarcoma patients living in the US or Canada can access the study and consent online through an online portal (ASCproject.org). Enrolled patients are mailed saliva and blood draw kits, which can be used to extract germline DNA and cell-free DNA (cfDNA), respectively. The study team contacts participants' healthcare institutions to obtain medical records and a portion of archived tumor samples. All received tumor samples are subjected to centralized histological re-review by an expert pathologist to confirm a diagnosis of angiosarcoma. Whole exome sequencing is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing is performed on tumor RNA. De-identified data, including linked genomic, clinical, and patient-reported data, are shared via public databases on a recurring pre-publication basis. Participants are regularly provided updates on the study.

Study phs001931

Uncovering tumor intrinsic and extrinsic factors that regulate hepatocellular carcinoma growth using patient derived xenograft assays

Dac EGAC00001001387

15080 results for "cancer studies using rna-seq"

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