Search Results - EGA European Genome-Phenome Archive

Primary Cytotoxic T Cell Lymphomas Harbor Recurrent Targetable Alterations in the JAK-STAT Pathway

Cytotoxic cutaneous T cell lymphomas (CTCLs) are uncommon but highly aggressive cancers of skin-homing cytotoxic T cells. These include the established World Health Organization (WHO) entity primary cutaneous gamma delta T cell lymphomas (PCGDTLs), the provisional WHO entity primary cutaneous CD8+ aggressive epidermotropic T cell lymphoma (PCAETCL), and samples that do not currently fit into a WHO category, referred to as cytotoxic CTCL-NOS (not otherwise specified). In this study, 35 CTCL cases were examined, and 9 PCAETCL cases were confirmed by CD8 expression and full-thickness epidermotropism. Whole genome sequencing (WGS) and bulk RNA sequencing were performed on these samples.  

Study phs002499

Human Epilepsy Genetics: Mosaic Mutations in Focal Epilepsy

This study investigates the role of somatic mosaic mutations in human focal epilepsies, including focal cortical dysplasia (FCD) and mesial temporal lobe epilepsy (mTLE). It leverages genomic and single-cell transcriptomic data from surgically resected brain tissue to identify pathogenic variants and characterize their effects on specific cell types and molecular pathways. The study employs methods such as deep whole-exome and targeted sequencing, single-nucleus RNA sequencing (snRNA-seq), and integrated genotype-transcriptome profiling (e.g., GO-TEN) to define the cellular architecture and functional consequences of mosaic mutations. Data generated under this project aim to elucidate mechanisms of epileptogenesis and support discovery of potential therapeutic targets.

Study phs004124

Genetic mutation profiling of lymphomas arising in the uterine cervix and vagina

Follicle center lymphoma (FCL) of the lower female genital tract (LFGT) is a rare lymphoma, with fewer than 20 cases reported to date. Since the genetic features of FCL of the LFGT have not been well characterized, we aimed to identify genetic alterations in this tumor through whole-exome sequencing or targeted gene panel analysis. Genomic DNA was extracted from a frozen tissue sample obtained from a surgically resected uterine cervical tumor. Whole-exome sequencing was performed using the Illumina NovaSeq X Plus platform. Library preparation was conducted with the SureSelect Human All Exon V6 kit, and sequencing was carried out with 150 bp paired-end reads.

Study JGAS000823

Mutational signatures in head and neck cancer (H019)

Genomic alterations are a driving force in the multistep process of head and neck cancer (HNC) and result from the interaction of exogenous environmental exposures and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome providing the unique opportunity to decipher specific signatures of mutational processes operative during HNC pathogenesis and to address their prognostic value. Computational analysis of whole exome sequencing data of the HIPO-HNC (n=83) and TCGA-HNSC (n=506) cohorts revealed five common mutational signatures (COSMIC signature 1, 2, 3, 13 and 16), and demonstrated their significant association with etiological risk factors (tobacco, alcohol and HPV16).

Study EGAS00001004588

Ethiopia Genome Project (low coverage)

The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.

Dataset EGAD00001000598

Ethiopia Genome Project (high coverage)

The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity. This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum. The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.

Dataset EGAD00001000696

Fetal origins of malignant germ cell tumours

Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells (PGCs). They are uniquely able to generate embryonic and extraembryonic tissues, which in malignant GCTs carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we studied the phylogenetic and transcriptional diversity of 15 malignant gonadal GCTs and four normal testis biopsies by sequencing 131 whole genomes and 416 transcriptomes from 14 gonadal histologies, excised by laser capture microdissection. Our findings demonstrate that tumours were initiated by whole genome duplication likely in embryogenesis, within ~5-8 cell divisions post-PGC specification, followed by chromosome 12p gains associated with invasive disease. Of note, 12p imbalances were not only generated through GCT-typical isochromosomes, but also through non-isochromosomic configurations. Whilst tumours developed along homogenous phylogenetic pathways, they spawned manifold tissues independent of genetic subclonal diversification. A key feature of GCT tissues was the expression of fetal-specific genes. The transcriptional diversity notwithstanding, we found universal transcriptional elements correlated with hallmark 12p gains. Overall, our study reveals stereotyped phylogenies and transcriptomes underpinning the development of GCT that originate in fetal life and may lend themselves to therapeutic manipulation.

Dataset EGAD00001007038

300BCG study: human population variation of trained immunity

To investigate human population variation of trained immunity, we immunized healthy individuals with Bacillus Calmette-Guérin (BCG). This live attenuated vaccine induces not only an adaptive immune response against tuberculosis, but also triggers innate immune activation and memory. We established personal chromatin accessibility maps over a time course of BCG vaccination in the 300BCG cohort using ATAC-seq.

Study EGAS50000000090

RNA Sequencing of ECOG-E1308

This study reports the RNA sequencing of HPV positive oropharyngeal squamous cell carcinoma samples from patients with HPV-associated stage III or stage IV cancer of the oropharynx that was surgically resectible. These patients participated in the ECOG-E1308 trial, a phase II trial that studied paclitaxel, cisplatin, and cetuximab followed by cetuximab and two different doses of intensity-modulated radiation therapy.

Study phs003320

National Cancer Institute (NCI) Waldenstrom Macroglobulinemia Genome-wide Association Study

A discovery GWAS is performed, consisting of genotyping 221 Waldenstrom macroglobulinemia (WM) cases on the Illumina Omni Express 12v1.1 platform and analyzing the genotypes together with those of 3798 previously genotyped controls in a model taking into account gender, age, and principal components of ancestry (i.e., significant eigenvectors). Directly genotyped data are supplemented by imputation using the Haplotype Reference Consortium.

Study phs001284

RNA-seq of der(1;7)(q10;p10) & control MDS patients

The study examined the RNA profiles of MDS cases. This study utilized BAM files of RNA-seq of der(1;7)(q10;p10) MDS cases, -7/del(7q) MDS cases, and OTHER MDS cases to analyze gene expression. In particular, the study profiled der(1;7)(q10;p10) MDS cases compared to non-der(1;7)(q10;p10) MDS cases.

Study EGAS50000000705

Elucidating the development of cervical cancer and identifying therapeutic targets based on cancer genome analysis.

The objective of this project is to analyze genomic aberrations and gene expression changes, such as mutations, deletions, and amplifications, in human cervical cancer cells at the somatic cell level, and to contrast these with clinicopathological information to elucidate the molecular mechanisms and characteristics of lcervical cancer development and progression at the genetic level.

Study JGAS000803

The Adhesion GPCR ADGRL2 Engages Galpha13 to Enable Epidermal Differentiation

We sought to determine the role of ADGRL2 in epidermal homeostasis. Primary neonatal foreskin keratinocytes were obtained from discarded surgical samples at a California hospital. Samples were anonymous and not selected. ADGRL2, working through GNA13, was found to promote epidermal differentiation through the ADGRL2 intracellular loop 3 (ICL3) loop, using the methods of RNA-seq and Perturb-seq.

Study phs004223

Whole blood transcriptomics analysis in Antiphospholipid syndrome in patients with Systemic Lupus Erythematosus

We analyzed whole-blood RNA-sequencing data from 299 SLE patients (108 SLE-aPL-positive, including 67 SLE-APS; 191 SLE-aPL-negative) and 72 matched healthy controls (HC). Pathway enrichment analysis, unsupervised WGCNA analysis and machine learning were applied to distinguish disease endotypes. Deconvolution analysis was performed to characterize the peripheral blood immune cell profile.

Study EGAS00001007750

Fecal microbiome predicts treatment response after the initiation of semaglutide or empagliflozin uptake

To investigate the effect of semaglutide and empagliflozin initiation on the gut microbiome of type 2 diabetes patients. In addition, to analyze whether the pre-treatment gut microbiome can predict the treatment efficacy. Gut microbiome fecal samples donated at four timepoints (Baseline, Month 1, Month 3; Month 12) were studied using 16S ribosomal RNA gene sequencing and analysis.

Study EGAS50000000531

CLUSTER consortium RNAseq CD19 B cell dataset of UK JIA patients.

This study examines B cell transcriptomic profiles in Juvenile Idiopathic Arthritis (JIA) patients to investigate molecular mechanisms underlying disease heterogeneity. CD19+ B cells were isolated from peripheral blood samples and subjected to RNA sequencing to characterise gene expression patterns. The dataset includes patients with documented uveitis status to enable investigation of B cell contributions to the common JIA comorbidity.

Study EGAS50000001123

Single-cell multi-omics and mtDNA genotyping of human peripheral blood cells

In this study, we characterize human peripheral blood cells using mitochondrial single-cell ATAC-seq (mtscATAC-seq), which simultaneously profiles mitochondrial genomes and chromatin accessibility at single-cell resolution. This submission includes PBMCs from one healthy pediatric donor and one 80-year-old patient diagnosed with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome.

Study EGAS50000001020

Whole-genome and transcriptome sequencing of primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma

Primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (pcAECyTCL) is a rare variant of cutaneous T-cell lymphoma with an aggressive clinical course and a very poor prognosis. We subjected tumor biopsies from patients with pcAECyTCL to whole-genome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

Study EGAS00001004332

The Gut Microbiome of renal transplant recipients – Cross-sectional

TransplantLines is designed as a single-center, prospective cohort study and biobank including all different types of solid organ transplant recipients as well as living organ donors. In the TransplantLines gut microbiome study the gut microbiome of solid organ transplant recipients is characterized and linked to clinical phenotypes. This batch contains the cross-sectional data from renal transplant recipients is.

Study EGAS00001006257

Grey_Platelet_Syndrome__GPS_

As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such pedigree, Grey Platelet Syndrome (GPS) is a rare congenital bleeding disorder caused by a reduction or absence of alpha granules in platelets. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

Study EGAS00001000091

WGS___Mutant_clone_mapping_in_normal_oesohagus_and_skin

We will use whole genome sequencing to examine normal appearing oesophageal epithelium and skin to determine the mutational burden. DNA will be extracted from epithelia of a defined size and we will overlay positional information from the epithelial pieces to give clone maps over a wide area. This will be done in both oesophageal epithelium and skin

Study EGAS00001002416

The study provides comprehensive access to the set of EGA studies which may be useful as controls.

The subjects studies in these datasets were selected due to being healthy control individuals or otherwise provide well characterised phenotype or exclude certain disease phenotype categories such that they may be useful as control population, such as to derive allele frequencies from a known reference population.

Study EGAS00001000646

Molecular analysis of giant cell lesions

Giant cell lesions of the jaws are aggressive proliferative conditions that affect young and adult patients. The genetic profile of the tumour has not been established yet. In this project we performed whole exome sequencing of 18 samples and RNAseq (n=6) of giant cell lesions of the jaws. All the tumours are sporadic and only non-syndromic patients were included.

Study EGAS00001002910

Histone acetylome-wide association study on tuberculosis infection

Epigenetic mechanisms are thought to play an important role in the pathogenesis of infectious diseases. Here, we describe the first histone acetylome-wide association study (HAWAS) of an infectious disease, based on genome-wide H3K27 acetylation profiling of peripheral granulocytes and monocytes from subjects with active Mycobacterium tuberculosis (Mtb) infection and healthy controls (135 ChIP-seq datasets).

Study EGAS00001003118

Mutant_clone_mapping_in_normal_oesohagus_and_skin

We will use targeted exome sequencing to examine normal appearing oesophageal epithelium and skin to determine the mutational burden. DNA will be extracted from epithelia of a defined size and we will overlay positional information from the epithelial pieces to give clone maps over a wide area. This will be done in both oesophageal epithelium and skin

Study EGAS00001001933

Genetic landscape of pediatric Adrenocortical Tumor

Paediatric adrenocortical carcinoma is a rare malignancy with poor prognosis. Here we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing. Collectively, these findings demonstrate the nature, timing and potential prognostic significance of key genetic alterations in paediatric ACT and outline a hypothetical model of paediatric adrenocortical tumorigenesis.

Study EGAS00001000257

RRBS MDACC Lung PreCancer

To study the evolution of DNA methylation at genome level and methylation intra-tumor heterogeneity (ITH) during early lung carcinogenesis, we performed multiregional reduced representation bisulfite sequencing (RRBS) of 62 resected lung nodules from 39 patients including atypical adenomatous hyperplasia (AAH, n=14), adenocarcinoma in situ (AIS, n=15), minimally invasive adenocarcinoma (MIA, n=22), and invasive adenocarcinoma (ADC, n=11).

Study EGAS00001004610

High intensity sequencing of plasma cfDNA and WBC gDNA

We sought to define the technical feasibility of a high-intensity sequencing assay of cfDNA and matched white-blood cell (WBC) DNA covering a large genomic region (508 genes, 2Mb, 60,000x raw-depth) in a prospective study of 124 metastatic cancer patients, with contemporaneous matched metastatic tumor tissue biopsies, and age-matched 47 non-cancer controls.

Study EGAS00001003755

The genomic landscape of childhood acute lymphoblastic leukaemia with intrachromosomal amplification of chromosome 21 (iAMP21-ALL)

Intrachromosomal amplification of chromosome 21 (iAMP21) results from breakage-fusion-bridge cycles and chromothripsis defines a cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukemia (B-ALL) cases associated with a poor prognosis. To systematically characterize the mechanism of somatic alternations in iAMP21, we perform integrated genomic, cytogenetic and transcriptomic analysis of 128 cases.

Study EGAS00001004998

Exome Sequencing of Spanish Patients with rare genetic diseases.

Whole exome sequencing of Spanish patients suffering from a rare genetic disease. The study was carried out in 2013 as a part of a public call from CNAG (Centro Nacional de Análisis Genómico), where data of eight spanish families were sent to analyse. The study concluded with three solved cases: two of aniridia and one syndromic RP.

Study EGAS00001004028

mutational landscape of normal human breast

The accumulation of somatic mutations in the healthy breast throughout life and pregnancy is poorly understood. Here we describe whole genome sequencing analysis of epithelial and stromal compartments from the normal breast. We aimed to study how pregnancy and age affect both the mutational burden and the clonality of the healthy breast, and the subsequent implications on breast cancer risk.

Study EGAS00001004672

Separation, characterization, and identification of individuals from multi-person blood mixtures with single cell transcriptome sequencing and a novel bioinformatics pipeline

We report a deconvolution and identification strategy of scRNA-seq datasets using mixed PMBCs data. After sequencing the data were processed with the de-goulash pipeline and analyzed with aim to identify and aquire biogeogrpahical ancestry of the involved individuals. The study includes samples of biological mixtures and in silico mixtures.

Study EGAS00001006202

Whole genome analysis of pediatric patients with medulloblastoma

Cancer genomes often contain structural variations (SVs) in non-coding regions, while its impact on tumorigenesis is still unclear. Our goal is to discover genome folding changes resulted from SVs using InfoGenomeR and InfoHiC frameworks, which may reveal novel therapeutic targets. We applied our frameworks to five pediatric patients with medulloblastoma, revealing 3D genome changes of medulloblastoma driver genes.

Study EGAS00001006653

Neoadjuvant Chemo or Combined Chemo-Radiation Therapy of Pancreatic Ductal Adenocarcinoma Yields Fundamentally Different Proteome Biology of the Residual Tumor Mass

We performed data independent acquisition (DIA)-based proteomics to characterize the proteomes of 67 PDAC resection specimens. Patients received either neoadjuvant chemotherapy or neoadjuvant combined chemo-radiation therapy. We employed DIA, yielding a proteome coverage in excess of 3,500 proteins. The two neoadjuvant therapies yielded highly distinguishable proteome profiles of the residual tumor mass.

Study EGAS00001006739

UKF_Paediatric_Tumours_Behjati_WellcomeCore_RNA_Managed_Access

Children born with DS have a substantially higher risk of developing childhood leukaemia. Approximately 10% are diagnosed with a preleukemic condition at birth; transient abnormal myelopoiesis (TAM). Of these, 20% - 30% of cases may progress to myeloid leukaemia associated with DS (MLDS) by the age of five. We are interested in directly characterizing the transcriptional changes underlying this stepwise development of TAM and MLDS.

Study EGAS00001007524

3q-capture DNA sequencing of atypical 3q26 cases

3q-capture DNA sequencing was performed as we described previously 13. In summary, genomic DNA was fragmented using the Covaris shearing device (Covaris), and sample libraries were assembled following the TruSeq DNA Sample Preparation Guide (Illumina). After ligation of adapters and an amplification step, target sequences of chromosomal regions 3q21.1-q26.2 were captured using custom in-solution oligonucleotide baits (Nimblegen SeqCap EZ Choice XL). The design of target sequences was based on the human genome assembly hg19: chr3q21.1:126036241-130672290 - chr3q26.2:157712147-175694147. Amplified captured sample libraries were paired-end sequenced (2x100 bp) on the HiSeq 2500 platform (Illumina) and aligned against the hg19 reference genome using the Burrows-Wheeler Aligner (BWA)25

Dataset EGAD00001006123

Spinocerebellar ataxia 15 (SCA15) derived iPSC WGS

A collection of four induced pluripotent stem cell models (iPSC) derived from patients diagnosed with Spinocerebellar ataxia 15 (SCA15) . Spinocerebellar ataxia 15 (SCA15) is a neurological condition characterised by progressive gait and limb ataxia as well as abnormalities in eye movement and difficulties with balance, speech and swallowing (Synofzik et al., 2011). Whole Genome Sequencing was performed to confirm the presence of a heterozygous deletions in the inositol 1,4,5-triphosphate receptor gene (ITPR1), characteristic of the disease. Cell models names: HPSI0216i-vieg_5 or Vieg_5 (WTSIi472-A), HPSI0216i-vieg_3 or Vieg_3 (WTSIi472-B), HPSI0216i-dacv_6 or Dacv_6 (WTSIi554-A), HPSI0216i-boho_3 or Boho_3 (WTSIi502-A). All iPSC models are available via ECACC-Culture Collections.

Dataset EGAD00001009851

Single-cell RNA sequencing of breast cancer lung metastasis and adjacent normal tissue

This dataset contains single-cell RNA sequencing data from two samples: L1 (breast cancer metastasis to lung) and N3 (adjacent normal lung tissue) from a female patient. The samples were processed using 10X Chromium 3' technology and sequenced on Illumina NextSeq 500. This data supports the study "Endocrine therapy reprogramming of breast cancer facilitates metastatic escape via upregulation of P-Rex1/Rac1 signalling" which investigates how endocrine therapy reprograms breast cancer cells, leading to upregulation of P-Rex1/Rac1 signalling pathways that facilitate metastatic escape. The single-cell analysis reveals cellular reprogramming mechanisms in endocrine therapy-resistant breast cancer cells that form metastases in the lung.

Dataset EGAD00001015769

Single cell RNA-seq, TCR-seq and bulk TCR-seq on HNSCC patients treated with ICB

We performed single cell RNA- and TCR-sequencing (10x Genomics) on immune infiltrates (CD45+ cells) from 18 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021). Viable immune cells were isolated from pre-treatment and post-treatment primary tumor biopsies of 10 patients responding (1 partial pathological response and 9 major pathological responses) and 7 patients non-responding to anti-PD-1 and anti-CTLA4 combination immunotherapy. One patient treated with anti-PD-1 monotherapy (1 major pathological response) was included in the dataset. Bulk TCR-seq was performed on the PBMCs of responding patients, pre- and post-treatment.

Dataset EGAD00001011311

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