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• The genomic landscape of primary cutaneous anaplastic large cell lymphoma (pcALCL)

  Primary cutaneous anaplastic large cell lymphoma (pcALCL) is the second most common variant of cutaneous T-cell lymphoma. We subjected tumor biopsies from patients with pcALCL to whole-genome sequencing, whole-exome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001004429

• Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses

  Genomic characterization of pediatric patients with acute myeloid leukemia (AML) has revealed age specific mutational spectrums, distinguishing it biologically from adult patients. While gene expression profiling signatures can differentiate subsets of pediatric AML, its clinical utility in risk stratification has remained limited.

  Study EGAS00001004701

• Targeted_sequencing_of_candidate_genes_in_calcific_aortic_valve_stenosis

  The objective is to identify new disease genes involved in calcific aortic valve stenosis (CAVS) by screening newly identified candidate genes. The recruitment of patients with CAVS has been achieved by l’institut du thorax (Nantes, France). DNA from the selected patients has been analysed by targeted capture (Agilent SureSelect) and massively parallel sequencing (Illumina).

  Study EGAS00001000308

• Whole-exome sequencing of acute erythroid leukemia

  To clarify the genomic characteristics of acute erythroid leukemia (AEL), 24 AEL cases with matched controls were analyzed using whole exome sequencing. Based on the patterns of genetic alterations, AEL were divided into 4 subgroups. EPOR/JAK/STAT pathway are frequently affected in AEL and could be a therapeutic target.

  Study EGAS00001003696

• Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure

  This study present a molecular analysis of upper urinary tract urothelial tumours (UTUC) and urines of patients with past exposure to carcinogenic aristolochic acid (AA). Tumor exome and transcriptome sequencing revealed the AA-specific mutations in UTUC and identified deleterious mutations at both the gene and transcript levels.

  Study EGAS00001005363

• Targeted sequencing of patients affected by familial or sporadic Alzheimer's disease

  The study aimed at identifying variants related to familial cases of Alzheimer's disease by comparing the mutational state of approximately 4000 genes associated to many known diseases ("clinical exome") in members of a family (n=7) of with members with dementia (n=2) and unaffected members (n=5)

  Study EGAS00001003856

• Genomic and transcriptomic landscape of aggressive thyroid cancer

  Molecular characteristics of anaplastic thyroid cancer (ATC) and advanced differentiated thyroid cancers (DTCs) have not been fully elucidated. In this study, we applied various types of massively-parallel sequencing technology to 113 advanced TCs, including 27 ATCs and 86 advanced DTCs, to reveal their genomic and transcriptomic characteristics.

  Study EGAS00001003540

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  In this study, we performed whole genome bisulfite sequencing (WGBS) to characterize the methylome of representative iBCP-ALL cases from the Interfant study discovery cohort, including 2 pools of B-cell progenitors from healthy donors, 2 MLL-AF4+, 2 MLL-AF9+ and 2 non-MLLs from iBCP-ALL patients.

  Study EGAS00001003650

• Single-cell TCR sequencing of gluten-specific T cells from 20 celiac disease patients uploaded on 2021

  To examine the T-cell receptors of the gluten-specific T cells in celiac disease, we isolated single CD4+ T cells from blood , gut biopsies or T-cell lines generated from gut biopsies using HLA-DQ2.5 tetramers and determined the sequences of rearranged TCRalpha and TCRbeta gene pairs.

  Study EGAS00001005047

• Transcriptomic signatures of CD4+ T cells from visceral leishmaniasis (VL) patients

  Bulk RNA-sequencing was performed on CD4+ T cells isolated from the blood of visceral leishmaniasis patients (n = 12) and endemic controls (EC; n = 12). CD4+ T cells were obtained by magnetic-activated cell sorting (MACS). Alterations in the transcripts of T helper (Th) cells during infection were identified.

  Study EGAS00001004152

• The genomic landscape of serrated lesion of the colorectum

  Serrated lesions of the colorectum are the precursors of 15-30% of colorectal cancers (CRCs). These lesions have a peculiar morphological appearance, and they are more difficult to detect than conventional adenomatous polyps. In this study we sought to define the genomic landscape of these lesions using high depth targeted sequencing.

  Study EGAS00001005648

• WGS_11pcw_fetus_hdbr_15951_DNA

  Mutations act as molecular barcodes detailing the origins of the cells that compose a tissue. To generate a high resolution map of the clonal origins and migration of cells during early human development, we will perform whole genome sequencing across the extensively sampled tissues of fetuses. Furthermore, the somatic mutations will reveal in utero mutational processes.

  Study EGAS00001005756

• Smart-seq3 scRNA-seq of cells from primary (OV2295) and metastatic (OV2295R2) high-grade serous ovarian cancer cell-line

  In this project, single cells extracted from two high-grade serous ovarian cancer cell-lines, one primary (OV2295) and one metastatic (OV2295R2), where split into two 384 well plates and libraries were prepared using Smart-seq3 single cell RNA sequencing (Hagemann-Jensen et al, 2020).

  Study EGAS00001006868

• The multifaceted genomic history of Ashaninka from Amazonian Peru

  Genome-wide profiles of Ashaninkas from Peruvian Amazonia reveal two genetic subgroups. Ashaninka ancestors derived from a south-north migration from southeastern South America. The Ashaninka1 subgroup testifies to an Arawakan-Caribbean genetic link in the Early Ceramic Age. The Ashaninka2 subgroup had recent interactions with Andean and Pacific Indigenous populations.

  Study EGAS00001006958

• bulk TCR-seq data IMCISION

  We performed bulk TCR sequencing (Adaptive Biotechnologies, Seattle, WA) on peripheral blood monocytic cells (PBMCs) from 9 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021) that responded to anti-PD-1 and anti-CTLA4 combination immunotherapy. DNA was extracted from PBMCs that were isolated from pre-treatment and on-treatment blood.

  Study EGAS00001007367

• Tyrol Lifestyle Atlas: Intermittent Fasting Methylation Data

  This study explored methylation, clinical, and other molecular alterations longitudinally over the course of intermittent fasting in healthy women aged 30 to 60. Here, we present methylation data from three matched sample types - buccal, cervical, and blood - longitudinally over the course of six months (baseline, month 2, month 4, and month 6).

  Study EGAS00001007840

• Tyrol Lifestyle Atlas: Smoking Cessation Methylation Data

  This study explored methylation, clinical, and other molecular alterations longitudinally over the course of smoking cessatio in healthy women aged 30 to 60. Here, we present methylation data from three matched sample types - buccal, cervical, and blood - longitudinally over the course of six months (baseline, month 2, month 4, and month 6).

  Study EGAS00001007841

• Raw microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006272

• Processed microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006275

• Risk alleles of membranous nephropathy and recurrence of the disease on the grafted kidney

  Samples are from patients enrolled in an international multicentric study aimed to define the genetic determinants of recurrence of membranous nephropathy in the kidney graft. They include 248 samples from patients with MN including 105 patients who received a graft, their 105 graft donors, and 192 controls all of Caucasian origin. Files from targeted-capture of HLA and PLA2R loci are available as fastq files.

  Dataset EGAD00001007831

• PBL whole exome and transcriptome data

  Plasmablastic lymphoma (PBL) represents a clinically heterogeneous subtype of aggressive B-cell non-Hodgkin lymphoma. Although targeted sequencing studies and a single center whole exome sequencing (WES) study in HIV+ patients recently revealed several genes, associated with PBL pathogenesis, the global mutational landscape and transcriptional profile of PBL remain elusive. To inform on disease-associated mutational drivers, mutational patterns and perturbed pathways in HIV+ and HIV- PBL we performed WES and RNA-sequencing (RNA-seq) of 34 PBL tumors.

  Dataset EGAD00001006795

• RNA-seq analysis of CCO+/CCO- hepatocytes in normal human liver

  RNAseq data from Passman et al 2023. Clonal CCO-deficient hepatocyte patches and nearby CCO-proficient hepatocytes were identified in morphologically normal human livers and sampled at varying distances along the PT-CV axis. Samples are characterised according to their location within the liver lobule, with "PT" denoting samples abutting the portal triad, "CV" denoting samples abutting the central hepatic vein, and "Mid" sampled acquired midway between these structures. Analysis was performed on an Illumina Nextseq using a high output kit and 100 single-end cycles.

  Dataset EGAD00001010033

• Processed microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006274

• TRACERx Reduced-representation bisulfite sequencing (RRBS)

  RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue. TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Dataset EGAD00001009707

• The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways

  69 OAMZL patients were sequenced on the Illumina platform. The data files are available in BAM format.

  Dataset EGAD00001011067