16452 results for "sec+and+unspecified+malignant+neoplasm"

in 51.74 milliseconds.

• Southern African Prostate Cancer Study (SAPCS) Ethnic Disparity

  The cohort (n=130) consists of prostate cancer patients from South Africa (n=123) and Brazil (n=7). For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B” as suffix and tumour BAMs are named with “-T” as suffix.

  Dataset EGAD00001009067

• Somatic pathogenic variants in the normal mammary gland of sporadic breast cancer patients

  This dataset contains .fastq files generated by targeted DNA sequencing of 542 cancer-associated and cadidate genes (52 individuals), and targeted duplex sequencing of PIK3CA and TP53 genes (4 individuals).

  Dataset EGAD00001008327

• Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

  Single-cell RNA-Sequencing of three primary breast cancers, two primary prostate cancers, and a metastatic melanoma sample from Wu et al. (2021) Genome Medicine study. Each tumour was sequenced across different cryopreservation conditions including Fresh Tissue (FT), cryopreserved single-cell suspensions (CCS), cryopreserved solid tissue fragments (CT) and a cryopreserved after overnight cold storage (CO). Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq platform.

  Dataset EGAD00001007030

• Somatic mutant selection is altered by prior NOTCH1 mutation in ageing esophageal epithelium

  Authors: Charlotte King1, Emilie Abbie1, Joanna C. Fowler1, Irina Abnizova1, Roshan K. Sood1, Swee Hoe Ong1, Michael W. J. Hall1,2, Faye Lynch-Williams3, Benjamin A. Hall4, Philip H. Jones1,2,5 Abstract: In cancer evolution, genome alterations often occur in a specific order, implying selection depends on the prior clonal genotype 1-3. It is unknown if similar constraints operate in normal epithelia. Here, we mapped mutations in normal mid-esophagus of aged UK subjects. Mutant NOTCH1 clones colonized most of the epithelium by age 60 and above 70 tissue was saturated with mutants under strong competitive selection. Mutant TP53 was more strongly selected in donors over 60 years of age. Samples predominantly mutant for NOTCH1 showed increased selection of NOTCH2 mutants and weaker selection of mutant TP53 compared with samples that were mostly NOTCH1 wild type. In mouse esophagus lacking Notch1 we observed strong selection of mutant Notch2 and other genes not selected in wild type esophagus. In normal ageing esophagus, the first driver mutation may change the trajectory of subsequent somatic evolution by altering mutant selection.

  Dataset EGAD00001015256

• Somatic mutant selection is altered by prior NOTCH1 mutation in ageing esophageal epithelium

  Authors: Charlotte King1, Emilie Abbie1, Joanna C. Fowler1, Irina Abnizova1, Roshan K. Sood1, Swee Hoe Ong1, Michael W. J. Hall1,2, Faye Lynch-Williams3, Benjamin A. Hall4, Philip H. Jones1,2,5 Abstract: In cancer evolution, genome alterations often occur in a specific order, implying selection depends on the prior clonal genotype 1-3. It is unknown if similar constraints operate in normal epithelia. Here, we mapped mutations in normal mid-esophagus of aged UK subjects. Mutant NOTCH1 clones colonized most of the epithelium by age 60 and above 70 tissue was saturated with mutants under strong competitive selection. Mutant TP53 was more strongly selected in donors over 60 years of age. Samples predominantly mutant for NOTCH1 showed increased selection of NOTCH2 mutants and weaker selection of mutant TP53 compared with samples that were mostly NOTCH1 wild type. In mouse esophagus lacking Notch1 we observed strong selection of mutant Notch2 and other genes not selected in wild type esophagus. In normal ageing esophagus, the first driver mutation may change the trajectory of subsequent somatic evolution by altering mutant selection.

  Dataset EGAD00001015258

• Whole genome sequencing in 1038 index cases reveals novel causative genes in pulmonary arterial hypertension

  Pulmonary arterial hypertension (PAH) is a rare disorder with a poor prognosis. Deleterious variation within genes encoding components of the transforming growth factor-ß pathway underlie the majority of heritable forms of PAH. Identifying the missing genetic contribution is challenging, even with genes of large effect size, since it likely involves mutations in genes confined to small numbers of PAH cases. In this study, we performed whole genome sequencing, comparing 1038 PAH index cases to 6385 subjects with other rare diseases. Rare variant analysis identified mutations in novel causal genes, namely ATP13A3, AQP1 and SOX17, and provided independent validation of a critical role for GDF2 in PAH. We detected mutations predicted to be disruptive of function in most, but not all, previously reported PAH genes. Taken together these findings provide new insights into the molecular basis of PAH, and support a central role for endothelial dysregulation in disease pathogenesis.

  Dataset EGAD00001003423

• Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

  CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene independent manner. In contrast, amplifications caused by whole chromosomal duplications have little to no impact on fitness. This effect is cell line specific and dependent on the ploidy status. We devise a copy-number ratio metric that substantially improves the detection of gene-independent cell fitness effects in CRISPR-Cas9 screens. Furthermore, we develop a computational tool, called Crispy, to account for these effects on a single sample basis and provide corrected gene fitness effects. Our analysis demonstrates the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage, with implications for the use of CRISPR-Cas9 gene-editing in cancer cells.

  Dataset EGAD00001004124

• Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

  Dataset EGAD00001000856

• cqmuGWAS1

  DNA for 1546 individuals from Chongqing was extract from peripheral blood and genotyped by Illumina Omni Zhonghua-8 version 1 gene chips.

  Dataset EGAD00010001527

• PMBCL IL4R DASL

  Expression data for 42 PMBCL patient samples (32 IL4R WT cases and 10 cases with mutations in IL4R)

  Dataset EGAD00010001542

• oacoch-M-1

  Methylation changes in OA patients with chronic exposure to cobalt and chromium

  Dataset EGAD00010001040

• OSC HumanCoreExome Genotypes

  DNA was extracted from saliva samples and genotyping was performed on Illumina Infinium HumanCoreExome beadchips.

  Dataset EGAD00010002375

• PDAC organoid genomic heterogeneity

  Two primary tumor-derived PDAC organoids were subjected to SNP array, RNA-seq, and single-cell WGS

  Dataset EGAD00010002408

• SNParray_PGT_samples_scGBS

  PGT samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002169

• SNParray_HapMap_samples_scGBS

  HapMap samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002168

• scRaCH-seq data targeting BTK and SF3B1

  Data set for scRaCH-seq manuscript. We base call the fast5 using guppy.

  Dataset EGAD50000000235

• HMO-microbiome study dataset, 16S sequencing

  This dataset contains 16S sequencing of fecal and milk samples for HMO-microbiome Lifelines NEXT study

  Dataset EGAD50000000532

• Cancer Genomics, ICR, summary data

  DAC for summary level data from the Cancer Genomics group, Division of Genetics and Epidemiology at the Institute of Cancer Research, Sutton, UK.

  Dac EGAC50000000050

• PDiamond Korean Lung Cancer Data

  WES and RNA-seq data of PDiamond Korean lung cancer data

  Dataset EGAD50000000844

• 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

• Neurodevelopment_Nantes_hospital

  The neurodevelopmental team in the genetics unit of Nantes hospital focus on the identification on new genes causing neurodevelopmental disorders through whole-genome and transcriptomics sequencing.

  Dac EGAC50000000542

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  Dataset EGAD00001010049

• U12 Spliceosome Defect Data Access Committee

  This Data Access Committee controls access to data pertaining to the study of the minor spliceosome and it's role in monogenic diabetes.

  Dac EGAC50000000892

• RNAseq of fibroblasts

  RNA sequencing data of fibroblasts from 3 controls and 3 patients with RBMX variants.

  Dataset EGAD50000002371

• KUI6280

  RNA seq data normal and hypomethylation

  Dataset EGAD00001009887

• Long-term organoid culture of a small intestinal neuroendocrine tumor

  tissue, organoid and normal bam files for whole exome samples

  Dataset EGAD00001010162

• COVID-19 Postmortem Medulla and Olfactory Mucosa snRNA-seq

  Time-dependent characterization of CNS response in COVID-19

  Dataset EGAD00001009075

• H3Africa TrypanoGEN+ Fastq

  TrypanoGEN+ data containing fastq files of 183 samples from DRC, Malawi and Uganda using NextSeq500.

  Dataset EGAD00001011666

• Sardinia Population SNPs frequencies

  List of SNPs, and their frequencies, extracted from a low pass whole genome sequencing of 3,514 individuals.

  Dataset EGAD00001003141

• Somatic cancer gene mutation screening

  Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2

  Dataset EGAD00001001010

• WGBS files for PCGP NBL_MYCN_ATRX

  WGBS files for PCGP NBL_MYCN_ATRX paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"

  Dataset EGAD00001004559

• MPB_Bonn

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

  Dataset EGAD00001001456

• The UCSF Low Grade Glioma Genome Project #2"

  Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor

  Dataset EGAD00001001305

• Chugai colorectal organoid sequencing

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

  Dataset EGAD00001001446

• AML exome sequencing

  Raw data (fastq files) from whole exome sequencing of AML patients (paired diagnosis and complete remission samples)

  Dataset EGAD00001002116

• Bulk RNA-Seq Digital Gene Expression Matrix

  Raw read counts and normalized read counts for each gene

  Dataset EGAD50000002489

• DNA methylomes of monozygotic twins clinically discordant for multiple sclerosis

  Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system. Although genetic susceptibility is important, a modest concordance rate for MS in monozygotic (MZ) twins suggests that interaction with other risk factors is required to develop clinical symptoms. In this study, we examined whether DNA methylation differences contribute to the discordant clinical manifestation of MS in MZ twins, and studied the impact of MS treatments on the DNA methylome. Genome-wide DNA methylation profiles of peripheral blood mononuclear cells (PBMCs) of 45 MZ twins clinically discordant for MS were generated using the Illumina HumanMethylationEPIC array. Repetitive element methylation and selected differentially methylated positions (DMPs) were validated using targeted deep bisulfite sequencing (TDBS). In addition, we performed whole genome bisulfite sequencing (WGBS) to profile CD4+ memory T-cells of a subset of four MS discordant MZ twins. Our results show that interferon treatment causes robust DNA methylation changes and several epigenetic biomarkers for interferon treatment response were identified. However, overall the PBMC-based methylomes of the MS discordant MZ twins were highly similar, since large systematic methylation differences (>5%) were absent in the data. This suggests that previously reported large methylation changes are probably caused by genetic rather than epigenetic differences. In addition, our data does not support the hypothesis that the observed maternal parent-of-origin effect in MS is due to genomic imprinting errors, and no evidence was found that copy number variations explain the discordant phenotype in these MZ twins. Although not genome-wide significant, a couple of DMPs associated with the MS phenotype were identified and successfully technically replicated using TDBS, including a differentially methylated region (DMR) in the promoter of the transmembrane protein encoding gene TMEM232. Another MS-associated DMP, located in an enhancer in the gene body of the transcription factor ZBTB16, was also associated with medium-term glucocorticoid treatment history. WGBS analysis confirmed this DMP as a promising epigenetic biomarker for glucocorticoid treatment. In conclusion, this epigenome-wide association study (EWAS) in genetically identical twins identified a DMR in the TMEM232 promoter as a candidate loci associated with the clinical manifestation of MS. In addition, epigenetic biomarkers for MS treatments were identified, revealing that not only short-term, but also medium-term treatment effects are detectable in immune cells, which should be taken into account in future EWAS designs.

  Study EGAS00001003147

• EGAD00000000114

  Whole transcriptome sequence data from 18 ovarian clear-cell carcinoma samples and one TOV21G ovarian clear-cell carcinoma cell line

  Dataset EGAD00000000114

• EGAD00010000288

  All cases and Finnish, Dutch, Italian control samples (Hap550)

  Dataset EGAD00010000288

• EGAD00010000292

  All cases and Finnish, Dutch, Italian control samples (Hap300)

  Dataset EGAD00010000292

• Carcinoma of the oral tongue (OTSCC) genomic landscape characterisation

  18 Exomes for discovery set and 60 Targeted panel for prevalence set

  Dataset EGAD00001001465

• cqmuGWAS2

  DNA for 2482 individuals from Chongqing was extract from peripheral blood and genotyped by Illumina Omni Zhonghua-8 version 2 gene chips.

  Dataset EGAD00010001526

• RNAseq_Landscape

  RNAseq reads were aligned with STAR 2.5.3a and gene expression was quantified with RSEM 1.3.0

  Dataset EGAD00010001703

• Multi-omics RNA profiling of glioblastoma patient tissues

  Multi-omics profiling of paired primary and recurrent glioblastoma patient tissues

  Dataset EGAD00010001895

• Mapping the breast cancer metastatic cascade onto circulating tumour DNA using genetic and epigenetic clonal tracking

  Dataset EGAD00001005507

• Whole-genome sequencing of a thyroid carcinoma harboring a ETV6-NTRK3 fusion and a NTRK3 G623R mutation (HIPO-021)

  Dataset EGAD00001006243

• Genetic and transcriptomic landscape of DLBCL

  Affymetrix SNP6.0 data for 341 DLBCL patients

  Dataset EGAD00010001980

• RealSeqS ovarian amplicon counts

  Dataset contains text files that describe the chromosome, position, and read count for an amplicon using the RealSeqS assay.

  Dataset EGAD50000000013

• Transcriptomics dataset from human prefrontal cortex tissue - ALS vs CTR

  Fastq files and BAM files

  Dataset EGAD50000000467

• Single-cell transcriptomics of neuroblastoma tumors

  Single-cell, single-nucleus and CITE-sequencing of neuroblastoma tumors with 10X Genomics

  Dataset EGAD50000000328

• WGS Sequencing of Urothelial Carcinoma from Taiwan

  Normal and Tumor paired WGS sequencing of UC Tissues

  Dataset EGAD50000001547

• Papua New Guinea Pangenome Project Data Access Policy

  This data policy applies to data access to the PNG15 and PNG16 sequencing data as well as derived genomic variant calls.

  Dac EGAC50000000674

• PacBio long-read scRNA-seq

  Full-length single-cell cDNA PacBio Kinnex whole-transcriptome sequencing data for adrenal sampleA and sampleB.

  Dataset EGAD50000002211

• Intellectual disability exome sequencing

  Exome sequencing of ID trios and sibpairs

  Dataset EGAD00001005442

• RNASeq files for GenomePaint paper

  RNASeq files for GenomePaint paper titled "Exploration of coding and non-coding variants in cancer using GenomePaint."

  Dataset EGAD00001006680

• dataset1

  Contains control and PXR KD human small intestinal organoids

  Dataset EGAD00001009785

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  spatial transcriptomics

  Dataset EGAD00001015262

• Neuroblastoma sequencing data

  This dataset contains tumor and normal whole exome DNA sequence data for a patient with neuroblastoma

  Dataset EGAD00001008120

• WGS fastq for EGAS00001004572

  Bulk WGS fastq files for germline and tumours in EGAS00001004572.

  Dataset EGAD00001006902

• WXS files for Zhang PanNBL

  WXS files for Zhang PanNBL paper titled "Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations"

  Dataset EGAD00001005484

• RNAseq

  This dataset contains RNAseq performed on 35 human acute erythroid leukemia patient samples and Xenografts.

  Dataset EGAD00001006076

• RNA-Seq dataset

  10 RNA-Seq bam files including 4 cases with fusion and 6 controls without fusion.

  Dataset EGAD00001004360

• THE MEDICAL RESEARCH COUNCIL – BRAIN BANK (MRC-BB) CONSORTIUM EXOME DATASET

  1461 Neuropathological and clinically characterised cases from the MRC Brain Bank

  Dataset EGAD00001001925

• Patient 16CH

  One file of patient 16 with WGS done on Illumina HiSeq X-Ten. For research purpose and authorised user only.

  Dataset EGAD00001003440

• Whole Exome and Targeted Sequencing in Tourette Syndrome Multiplex Families

  This study consists of 771 individuals from 15 extended, multi-generational Tourette Syndrome (TS) pedigrees collected by the Tourette Syndrome Association International Consortium for Genetics (TSAICG), 213 of whom are affected either with TS or its broader, genetically related phenotype, chronic tic disorder (CT). Prior microsatellite linkage analysis, including 624 individuals from these families, has identified a genome-wide significant TS/CT susceptibility locus on chromosome 2p21-24 with two additional loci meeting criteria for suggestive linkage on chromosomes 6p12-21 and 17p11-q11. Subsequent joint linkage and association analysis, incorporating genome-wide SNP genotyping on the Illumina Hap610 platform from 221 individuals, has strengthened the evidence for a major TS/CT locus on chromosome 2p but did not refine the locus further. In addition, haplotype analyses suggest that multiple TS/CT loci may exist on the short arm of chromosome 2. The goal of the current sequencing study is to use exon-focused sequencing, supplemented with targeted sequencing of additional known functional elements on chromosome 2p, to identify susceptibility variants contributing to the highly penetrant TS/CT phenotype in these families.

  Study phs000415

• Final results and ctDNA analyses from the randomized phase 3 IMpassion031 trial evaluating peri-operative atezolizumab for early-stage triple-negative breast cancer

  In IMpassion031, adding atezolizumab to neoadjuvant chemotherapy significantly improved pathologic complete response (pCR) rate (primary endpoint) for stage II/III triple-negative breast cancer (TNBC). Patients with stage II/III TNBC were randomized 1:1 to neoadjuvant chemotherapy plus peri-operative atezolizumab or pre-operative placebo. Descriptive secondary endpoints included event-free, disease-free, and overall survival. Long-term outcomes favored the atezolizumab group (event-free survival HR 0.76, 95% CI: 0.47–1.21). Among patients without pCR, 14/70 (20%) atezolizumab-treated and 33/99 (33%) placebo-treated patients received additional adjuvant therapy, frequently capecitabine. In exploratory analyses, pCR was prognostic for long-term outcome. Patients with baseline ctDNA-negative status (6%) had excellent long-term outcomes. Most patients (87%) had cleared ctDNA at surgery. ctDNA-positive status at surgery identified a subset of non-pCR patients with poorest prognosis. Long-term safety was consistent with primary results. Adding atezolizumab to chemotherapy for stage II/III TNBC is associated with more favorable long-term outcomes. ctDNA dynamics provide prognostic value beyond pCR. ClinicalTrials.gov identifier: NCT03197935

  Study EGAS50000000974

• Rucaparib in patients presenting a metastatic breast cancer with Homologous Recombination Deficiency, without germline BRCA1/2 mutation, pronostic value of high LOH genomic score and predictive value of HRDetect (microarray)

  Breast cancer may present genomic alterations leading to homologous recombination deficiency. PARP inhibitors have proved their efficacy in patients with HER2-negative metastatic breast cancer (mBC) harboring germline (g) BRCA1/2 mutations. We conducted the phase 2 RUBY trial to assess the efficacy of rucaparib in HER2-negative mBC with high genomic loss of heterozygosity (LOH) score or somatic, without gBRCA1/2 mutation. 220 of 711 patients with mBC screened for LOH presented high LOH score which was associated with a higher likelihood of death (HR = 1.39, 95% CI: 1.11-1.75, p = 0.005). The primary objective was not reached with a clinical benefit rate (objective response or SD>16 weeks) of 13.5%. Two LOH-high patients, without somatic BRCA1/2 mutation, presented a complete and durable response (14 and 32 months). HRDetect tended to be associated with response to rucaparib, whithout reaching statistical significance (median HRDetect responders versus non responders: 0.465 versus, 0.040, p = 0.2135). Our data suggests that a small subset of patients with high LOH score could derive benefit from PARP inhibitors.

  Study EGAS00001004755

• Immunoreactive_p53_areas_in_human_skin_2

  Previous work has suggested that in mice there may be a difference in mutational burden between areas expressing stabilised p53 protein and others. We wish to see if this observation holds true in human sun-exposed epidermis. We will take 0.25mm punch biopsies from peeled human skin epidermis which will be submitted to the low input pipeline prior to sequencing.

  Study EGAS00001004463

• Evaluating potential drug candidates for the treament of Henamgiopericytoma on patient derived cell line models

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1. Potential drug candidates that could be repurposed for the treatment of SFT/HPC were screened.

  Study EGAS50000000027

• Single-cell RNA-seq of immune cells from human tumor fragments after 48 hour culture ex vivo (Kaptein et al., 2024)

  Single-cell RNA-seq profiling of immune cells from human ovarian carcinoma, renal carcinoma and melanoma samples after 48h of ex vivo culture using the patient-derived tumor fragment platform (5 samples total). Samples were cultured in various conditions, including: untreated, CD8-IL2v-treated, CD8-IL2v + LCKi -treated, aPD1-treated, CD8-IL2v + aPD1 -treated, Untargeted IL2-treated, aCD3-treated and aCD3 + CD8-IL2-treated . FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on immune cells from all conditions combined per patient.

  Dataset EGAD50000000377

• NHLBI TOPMed: The Vanderbilt Atrial Fibrillation Registry (VU_AF)

  The Vanderbilt Atrial Fibrillation (AF) Registry was founded in 2001. Patients with AF and family members are prospectively enrolled. At enrollment a detailed past medical history is obtained along with an AF symptom severity assessment. Blood samples are obtained for DNA extraction. Patients are followed longitudinally along with serial collection of AF symptom severity assessments.

  Study phs001032

• Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer

  This study evaluates integrated genomic models of response to immune checkpoint blockade for lung cancer patients. A computationally adjusted tumor mutation burden was combined with HLA class I genetic variation, mutational smoking signature and activating mutations in receptor tyrosine kinase genes to generate a prognostic classifier that outperforms tumor mutation burden.

  Study phs001940

• Genome Wide Association Studies in ECOG 2997 Trial

  The ECOG 2997 trial was a randomized controlled trial for patients with previously untreated CLL comparing fludarabine monotherapy to the combination of fludarabine and cyclophosphamide. The initial clinical findings of this study were published in the Journal of Clinical Oncology in 2007 (JCO 25:793-8). Additional laboratory studies have also published (JCO 25:799-804).

  Study phs000621

• Drop-BS: High-Throughput Single-Cell Bisulfite Sequencing on a Microfluidic Droplet Platform

  We present a high-throughput droplet-based bisulfite sequencing library preparation platform. Our protocol allows the production of a BS library of 2,000-10,000 single cells within 2 days. In addition to validation using mixed cell lines, we also used the technology to profile various cell types in mouse and human brain samples.

  Study phs002123

• Washington University Coronary Artery Disease Study

  The genetic basis of coronary artery disease in individuals of non-European ancestry is largely unknown. The Washington University Coronary Artery Disease Study (WUCADS) recruited participants of non-European ancestry with and without coronary artery disease to address this question. Whole genome sequencing in WUCADS was performed at the McDonnell Genome Institute at Washington University.

  Study phs001227

• The Genetic Landscape of Mutations in Burkitt Lymphoma

  Burkitt lymphoma (BL) is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. We sequenced exomes of 59 BL tumors, 14 of which had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a novel tumor suppressor gene.

  Study phs000562

• CALGB 80303:Genome-Wide Association Study of Advanced Pancreatic Cancer Patients - A Randomized Phase III trial of Gemcitabine Plus Bevacizumab versus Gemcitabine Plus Placebo in Patients with Advanced Pancreatic Cancer

  CALGB 80303 was a randomized, phase III study in advanced pancreatic cancer patients treated with Gemcitabine plus either Bevacizumab or placebo. No difference in overall survival (OS) was observed between the two arms. We prospectively collected germline DNA and conducted a genome-wide association study (GWAS).

  Study phs000250

• Determinants of Asthma Following RSV Bronchiolitis in Early Life

  The goal of the RSV Bronchiolitis in Early Life (RBEL) study is to determine how specific genetic, biologic, and immunologic characteristics interact to predispose individuals to develop asthma. Participants were carefully recruited by selecting a prospective cohort of 206 infants with severe respiratory syncytial virus (RSV) bronchiolitis who were at substantial risk of developing asthma.

  Study phs001009

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778

• Whole Exome Sequencing of Six Signet Ring/Plasmacytoid Variant Bladder Tumors

  In this study, six plasmacytoid bladder cancers were analyzed by whole exome sequencing. The results show loss of the CDH1 gene in every sample and correlate with E-cadherin loss of expression by immunohistochemistry. A separate validation cohort of plasmacytoid samples showed loss of E-cadherin expression by CDH1 mutation or promoter hypermethylation.

  Study phs001064

• Single cell transcriptomic profiles of advanced melanoma patients treated with checkpoint inhibitor immunotherapy

  Little is known about the resistant clones within the tumour ecosystem treated with immunotherapy. This work provides a comprehensive and integrative analysis of each individual non-responding melanoma patients, including clinical features integrated with single cell analysis, which is critical to understand features of resistance in order to improve cancer patients’ outcomes.

  Study EGAS50000000339

• DCLRE1B/Apollo germline mutations associated with renal cell carcinoma

  Highlights of Bories et al. article submitted to BBA - Molecular Basis of Disease: We identified 2 germline mutations in the DCLRE1B gene encoding the Apollo protein by Whole Exome Sequencing (WES) in two families with inherited clear-cell Renal Cell Carcinoma. Our study suggests a putative link between DNA repair, telomere protection and renal oncogenesis.

  Study EGAS50000000216

• Single nuclei ATAC-Seq data from the human ganglionic eminences

  We performed the single nuclei Assay for Transposase-Accessible Chromatin with Sequencing (snATAC-Seq) to map potential regulatory genomic regions operating in individual cell populations of the human GE, using these to test for enrichment of schizophrenia common genetic variant liability and to functionally annotate non-coding variants associated with the disorder.

  Study EGAS50000000411

• HCC cfMeDIP-seq

  This dataset comprises 406 raw fastq files derived from 203 plasma cfDNA samples from 90 patients diagnosed with hepatocellular carcinoma (HCC). The samples include 90 baseline HCC (b-HCC) samples, collected during liver transplant or resection surgeries, and 113 postoperative follow-up (f-HCC) samples. For each sample, 10ng of cfDNA was used for library preparation utilizing cfMeDIP-seq technology based on the 5mC antibody-immunoprecipitation strategy. Libraries were validated via Bioanalyzer trace analysis and sequenced on Illumina NovaSeq 6000 or HiSeq 2500 platform with paired-end 150-bp (NovaSeq) or 125-bp (HiSeq) model for ~100 million reads per sample.

  Dataset EGAD50000000651

• Tumor Normal Pair for SV mosaic

  Simulated (based on real world data) tumor normal pair designed for benchmarking and optimisation of structural variation callers. The calls are derived from 12 patients in the hartwig database requested by the EUCANCan project. Paired-end sequencing data was imputed into the normal reference data to simulate real world variation like purity as well as technical impact of sequencing technologies. The dataset contains a tumor sequenced to ±90x depth and a normal control sequenced to ±30 x depth of these imputed events. The break junctions of all detected SVs in the original cases are imputed in this data from diagnostic WGS sequencing data.

  Dataset EGAD50000000668

• Diagnostic yield and clinical utility of whole-exome sequencing in pediatric patients with rare and undiagnosed diseases in the Czech Republic

  In our single-center study, we have launched a pilot program for pediatric patients with undiagnosed diseases in the second-largest university hospital in the Czech Republic. WES was implemented as a first-line test after inclusion in the study as part of the diagnostic workflow.

  Study EGAS50000000442

• Immune Landscape of Cervical Lymph Nodes in Multiple Sclerosis

  This study aimed to investigate the cellular compartment of deep cervical lymph nodes (dcLNs) during early MS before the influence of immunosuppressive treatments. We used ultrasound-guided FNAs followed by scRNA-seq,CITE-seq, TCR and BCR seq to characterize the immune landscape in MS patients compared to controls within the dcLNs.

  Study EGAS50000000843

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

  PPM1D, a central regulator of the DNA damage response, is commonly mutated in therapy-related clonal hematopoiesis (CH), acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). PPM1D mutations have been shown to expand under selective pressure of DNA-damaging chemotherapy. However, whether PPM1D mutations promote the development of hematologic malignancies remains unclear.

  Study EGAS50000000840

• Alpha synucleinopathy spectrum - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA seq dataset from prefrontal cortex for a total of N=44 samples. Tissue samples correspond to patients with different alpha synucleinopathies. Specifically, idiopathic Parkinson's disease (PD, N=20) monogenic PD caused by LRRK2 mutations (LRRK2-PD, N=7), multiple system atrophy (MSA, N=6) and neurologically healthy controls (N=11). RNA seq was carried out using ribosomal depletion. The totality of these samples were also sequenced using single nucleus RNA seq, and available within the same study as a separate dataset.

  Dataset EGAD50000000430

• RNA-seq datatset of primary human thymocyte subsets

  FASTQ-files of RNA-seq experiments of 8 primary human thymocyte subsets, isolated by flow-cytometry (FACS) from neonatal thymus biopsies. All samples were sorted to be negative for the expression of the lineage surface markers CD11c, CD19, CD56, CD141 and CD303 and additionally had the following surface phenotypes: DN1 (CD4-CD8-CD7+CD1a-CD161-CD38-); DN2 (CD4-CD8-CD7+CD1a-CD161-CD38+CD3-TCRab-); DN3 (CD4-CD8-CD7+CD1a+); ISP (CD4+CD8-CD3-TCRab-CD1a+); DPE (CD4+CD8+TCRab-CD69-); DPL (CD4+CD8+TCRab+CD69+); SP4 (CD4+CD8-); SP8 (CD4-CD8+). Samples were sorted from 2-4 pediatric patients undergoing heart surgery.

  Dataset EGAD50000001599

• PD1-targeted delivery of an IL-2 variant induces a multifaceted anti-tumoral T cell response in human lung cancer

  To explore PD1-IL2v-specific effects on CD8 and CD4 T cells at a transcriptomic level, we performed single-cell RNA sequencing of patient-derived tumor fragments (PDTFs) which were treated with either Isotype (DP47), Isotype-IL2v (DP47-IL2v), anti-PD1 (PembroPGLALA) or PD1-IL2v (PembroPGLALA-IL2v) for 48 hours.

  Study EGAS50000000396

• Prevalence of rare pathogenic variants in cancer-predisposing genes among Japanese advanced prostate cancer patients.

  The prevalence of rare pathogenic variants in cancer-predisposing genes including those associated with DNA repair remains unknown among Japanese patients with advanced prostate cancer. This study was designed to elucidate the prevalence of pathogenic variants in 27 known cancer-predisposing genes and to explore the prognostic significance of the variants identified.

  Study JGAS000509

• RNA sequencing of Notch inhibitor treated HCC PDX models across timepoints

  To study the effect of Notch inhibition on the transcriptional profiles our PDX models, we generated bulk RNA-seq data for two Notch inhibition sensitive and three Notch inhibition insensitive models across multiple timepoints (8h, 24h, 48h, 7d, 17d) using anti-JAG1, anti-Notch2, anti-Notch1 or anti-gD antibodies. 3-5 samples were collected for each treatment condition, resulting in a total of 96 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000737

• Whole genome sequence: cardiomyopathy, 1 myotonic dystrophy patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000706

• Amplicon based re-sequencing of multi-region PDAC samples

  Multi-region tumor samples were cut from frozen sections or FFPEs and reviewed from microdissection and H&E staining in order to select ones with high cellularity. DNA extraction was done using DNeasy Blood & Tissue Kits for frozen samples following the manufacturer’s guideline. Extracted DNAs were processed on an Illumina HiSeq 2500 in a paired end mode (100x100) using a custom targeted panel based on the list of all unique somatic mutations from the original WES data by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (New York, NY).

  Dataset EGAD50000000354

• Paraganglioma Smart-Seq2 Single Nuclei Sequencing Data

  Paraganglioma is a rare neuroendocrine tumor that originates from chromaffin cells of the adrenal medulla or extra-adrenal paraganglia. This study aims to investigate the heterogeneity of this tumor and to identify potential biomarkers associated with its malignancy. To achieve this, we performed single-nucleus RNA sequencing of human paraganglioma samples using the SMART-Seq2 protocol.

  Study EGAS50000001184

• Single-cell RNA-seq profiling of patient derived organoids

  The aim of this study was to profile developement of resistance to cancer treatments using organoids. Two patient derived colorectal cancer organoids were profiled using single cell RNAseq after treatment with a combination of different anticancer drugs. The organoids were profiled both after 4 weeks of treatment and after a drug holiday of 2 weeks.

  Study EGAS50000001025

• A single-cell atlas of the early COPD lung - Nanopore long-read

  Single cell atlas of the human airways from 10 patients suffering of early stage Chronic Obstructive Pulmonary Disease and 12 healthy age matched volunteers. This dataset was sequenced by 10X Genomics 3’ RNA-seq profiling. It is composed of more than 400 000 cells coming from 119 samples total. Sampling was performed by brushings and biopsies from the nose to the 6 th division of the airways. 14 samples were also sequenced using Nanopore long-read sequencing.

  Dataset EGAD50000001002

• Chordoma_Targeted_Sequencing_Study

  This Study uses a focused bespoke bait pull down library method to target findings of Chordoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.

  Study EGAS00001000280

• Diseased_heart_analysis__RNA_Adult

  Samples for this project are taken from adult human hearts which have been preserved using 2 different methods (cold static storage on ice, and hypothermic perfusion). Samples have been acquired at various time points during post-preservation normothermic perfusion. The aim of the project is to assess the transcriptional changes caused by these differing methods of preservation.

  Study EGAS00001008302