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• TCRab sequencing of CML patients

  This dataset contains 15 TCRab sequencing samples from 6 CML patients before and after TKI-cessation. The raw data is available as fastq files.

  Dataset EGAD00001012841

• BLUEPRINT transcriptional profiling of normal and neoplastic plasma cells

  RNAseq profile of purified plasma cells from multiple myeloma patients and tonsils of healthy donors

  Dataset EGAD00001001212

• Gabriella Miller Kids First Pediatric Research Project in Cornelia de Lange Syndrome, Related Diagnosis and Structural Birth Defects

  This study involves a cohort of 400 individuals and family members with Cornelia de Lange Syndrome (CdLS) and CdLS-like phenotypes for which a molecular etiology has not yet been established. CdLS is a developmental disorder characterized by development delays, cognitive impairment, short stature, hearing loss, specific facial features, and structural birth defects such as differences of the limbs, heart, kidneys, and GI tract. Our approach to tease out genetic contributions to birth defects has been to identify the underlying causes of syndromic birth defects which are often Mendelian in nature and therefore lend themselves more readily to genetic causal identification. Once identified, these genetic causes of syndromic forms of birth defects can be leveraged to understand the genetic contributions to isolated birth defects seen in constellation in syndromes such as CdLS. This work will lead to the identification of genes critical in human embryonic development, provide novel insights into transcriptional regulation and help to identify genetic causes and candidate genes for isolated birth defects seen in constellation in similar diagnoses.

  Study phs002174

• Small cell number RNA-seq (400 cells per sample)

  Transcriptional profiles for stemB and proB cells harvested from either primary or secondary xenografts. This dataset contains six types of samples: - diagnostic stemB cells harvested from primary xenografts - diagnostic proB cells harvested from primary xenografts - relapse stemB cells harvested from secondary xenografts injected with stemB cells from primary xenografts - relapse proB cells harvested from secondary xenografts injected with stemB cells from primary xenografts - relapse stemB cells harvested from secondary xenografts injected with proB cells from primary xenografts - relapse proB cells harvested from secondary xenografts injected with proB cells from primary xenografts

  Dataset EGAD50000001830

• Paired-end Whole Exome-seq analysis of the 3D evolution of glioma cell populations. Part 2.

  Dataset contains paired-end Whole Exome sequencing data from 257 glioma samples from 28 patients. 26 normal blood samples are also included.

  Dataset EGAD00001009496

• Somatic Copy Number Analysis of Endometrial Carcinomas

  Endometrial cancer (EC) is the most commonly diagnosed gynecologic malignancy in the United States and is the sixth leading cause of cancer death amongst American women. The purpose of this study was to identify somatic (tumor-specific) copy number alterations in 7 clear cell ECs, 31 serous ECs, 17 endometrioid ECs, and the clear cell components of 2 endometrioid/clear cell ECs. To this end, DNAs from de-identified primary endometrial tumors and matched non-tumor tissues or blood were hybridized to high-density Illumina Infinium HumanHap650Y Beadchips or to high-density Human660W-Quad Beadchips and the data analyzed to annotate somatic copy number alterations throughout the genome.

  Study phs001690

• Understanding Rare Variant Contributions to autism: Lessons from Dystrofin-Deficient Model

  This project generated a whole-exome sequencing (WES) dataset of 83 boys with a pathogenic variant in the DMD gene, along with WES data from the parents of 38 of them, totaling 159 samples. Pathogenic DMD variants, besides causing dystrophinopathies, are also known risk factors for neurodevelopmental disorders (NDDs). However, the low penetrance of NDDs in individuals with dystrophinopathies suggests that additional factors contribute to their manifestation. This study aimed to: (1) characterize ASD in males with dystrophinopathies; (2) determine the relevance of additional de novo and inherited rare risk variants for their neurodevelopmental phenotype; and (3) clinically and functionally characterize the identified risk variants.

  Study EGAS50000000754

• Genome Wide Association Study:GR@ACE Stage I

  The Genome Research program at Fundacio ACE (GR@ACE, Barcelona, Spain), represents a new effort to study Alzheimer's Disease susceptibility. The GR@ACE study comprises 7,409 unrelated individuals. 4,120 AD cases were diagnosed at Fundació ACE Memory Clinic (Barcelona, Spain). 3,289 Controls were obtained from three collections (Fundació ACE, Barcelona; DNA National Biobank, Salamanca and HU Valme, Seville). Genotyping was carried out using the 815K Axiom Spain Biobank array (Affymetrix.) in the Spanish national center for genotyping (CEGEN, Santiago de Compostela, Spain). After genotyping, an extensive quality control was conducted, including re-sampling, gender match, stratification, relatedness, heterozygosity, differential missingness and HWD analyses.

  Study EGAS00001003424

• Molecular phenotyping of MCA/ID patients to improve diagnosis

  De novo structural variants are frequently identified in individuals with neurodevelopmental disorders, but the genes driving their phenotypes are often unknown. In this study we performed Whole Genome Sequencing, RNA-sequencing and ATAC-sequencing on samples of 51 patients with intellectual disability and/or multiple congenital anomalies and their biological parents (when available). The goals of the study were to gain more insights in the molecular consequences of (complex) genomic rearrangements and to improve the genetic diagnosis of patients carrying such rearrangements. Data is divided in four separate datasets based on type of source material and data access restrictions due to consent.

  Study EGAS00001003489

• Overrepresentation of genetic variation in the AnkyrinG interactome is related to a range of neurological disorders

  Upon the discovery of numerous genes involved in the pathogenesis of neurodevelopmental disorders, several studies showed that a significant proportion of these genes converge on common pathways and protein networks. Here, we used a reversed approach, by screening the well-characterized AnkyrinG protein-protein interaction network, implicated in a variety of neurodevelopmental disorders, for genetic variation in a large cohort of 1009 cases with neurodevelopmental disorder. We identified a significant enrichment of de novo potentially disease-causing variants in this network, confirming that this protein network plays an important role in the emergence of several neurodevelopmental disorders.

  Study EGAS00001004326

• Single cell sequencing of newly-diagnosed and recurrent GBM

  Single cell RNA and CITE sequencing of newly-diagnosed and recurrent GBM

  Dataset EGAD00001006778

• Mapping the Evolution of T Cell States During Response and Resistance to Adoptive Cellular Therapy

  We investigated single T cell transcriptional states that define donor lymphocyte infusion (DLI) response and resistance from cryopreserved bone marrow mononuclear cells from 15 patients with relapsed chronic myeloid leukemia (CML) after allogeneic hematopoietic stem cell transplant. By integrating bulk ATAC-seq data from sorted T cell populations from these bone marrow samples, we also defined gene regulatory networks that underlay these clusters.

  Study phs002877

• Collaborative Association Study of Psoriasis

  The goal of this collaborative study is to combine the resources and expertise of three groups with long-standing studies of psoriasis genetics in order to identify new genetic susceptibility factors for psoriasis, a common inflammatory skin disease that affects over 4 million Americans. Consent groups and participant set General research use (GRU): 1677 (950 cases, 692 controls, 35 others) Autoimmune disease (AD): 1198 (449 cases, 734 controls, 15 others)

  Study phs000019

• Matched_Ovarian_Cancer_Sequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 15 ovarian cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000155

• RNA sequencing data from visceral and abdominal subcutaneous adipose tissue from morbidly obese women with normal glucose tolerance or type 2 diabetes

  The study group consisted of 17 obese women with normal glucose tolerance and 15 obese women with T2DM. Adipose tissue specimens were taken from the epigastric region of the abdominal wall (SAT) and from the major omentum (VAT). RNA was isolated and RNA sequencing was used to analyse the transcriptome. Dharuri H et al, Diabetologia. 2014;57(11):2384-92.

  Study EGAS00001001872

• A GWAS meta-analysis on severe acne on a European population of 26,722 individuals

  Acne vulgaris is a highly heritable common, chronic inflammatory disease of the skin. We performed a genome-wide association study of 3,823 cases and 16,144 controls followed by meta-analysis with summary statistics from a previous study, with a total sample size of 26,722. We identified 20 independent association signals at 15 risk loci, 12 of which have not been previously implicated in the disease.

  Study EGAS00001003278

• RODAM

  The RODAM study assesses the health and wellbeing of Ghanaian residents in Ghana and Europe and follows them up over time. With this unique approach the RODAM study attempts to unravel the causes of cardiovascular disease and its risk factors among African migrants in Europe and non-migrants sub-Saharan Africa. Data are available upon reasonable request. These requests can be made to de RODAM-Pros cohort coordinator (rodamcoordinator@amsterdamumc.nl) or principal investigator, Professor Charles Agyemang (c.o.agyemang@amsterdamumc.nl).

  Dac EGAC50000000474

• WGBS dataset for lymphnode metastasis samples from prostate cancer

  This dataset contains WGBS sequencing data of lymphnode metastasis samples from prostate cancer. Sequencing was performed on Illumina HiSeq X Ten. The sequencing was always paired.

  Dataset EGAD50000001183

• Single-cell RNA sequencing of CML patients

  This dataset contains 15 single-cell RNA sequencing samples from 6 CML patients before and after TKI-cessation. The raw data is available as fastq files.

  Dataset EGAD00001012842

• The aim of this project is to identify, on 15 French Caucasian and 10 African-Caribbean men, through an integrative approach of DNA sequencing and transciptomic analyses, relevant genomic events that characterize or allow targeting the various phenotypes of aggressiveness of early stages of prostate cancer.

  Every year about 70,000 new cases of prostate cancer are diagnosed in France and 8,700 men died from this disease. But the incidence and the rate of mortality per 100,000 men in the French West Indies are respectively 1.5x and 2x upper than the rates observed in the metropolitan France. The aim of this project is to identify, on 15 French Caucasian and 10 African-Caribbean men, through an integrative approach of DNA sequencing and transciptomic analyses, relevant genomic events that characterize or allow targeting the various phenotypes of aggressiveness of early stages of prostate cancer.

  Study EGAS00001002176

• Single-cell RNA sequencing of 43 BALF samples from CAPA and COVID-19 patients

  Single-cell RNA sequencing of 43 bronchoalveolar lavage fluid (BALF) samples from 15 CAPA and 22 COVID-19 mechanically ventilated patients.

  Dataset EGAD00001011342

• Hospital for Sick Children Infant Glioma RNA Sequencing

  Whole transcriptome (n=4) and targetted RNA sequencing (n=15) .bam files of infantile glioma samples reported on at the Hospital for Sick Children

  Dataset EGAD00001005092

• Confirmation of a founder effect in a Northern European population (FRL) of a new beta-globin variant: HBB:c.23_26dup (codons 8/9 (+AGAA))

  Beta-thalassemia is a genetic disease caused by a defect in the production of the beta-like globin chain. More than 200 known different variants can lead to the disease and are mainly found in populations that have been exposed to malaria parasites. We recently described a duplication of 4 nucleotides in the first exon of beta-globin gene in several families of patients living in Nord-Pas-de-Calais (France). Using the genotypes at 12 microsatellite markers surrounding the beta-globin gene of four unrelated variant carriers plus an additional one recently discovered, we found that they shared a common haplotype indicating a founder effect that was estimated to have taken place 225 years ago (9 generations). In order to determine whether this variant arose in this region of Northern-Europe or was introduced by migrants from regions of the world where thalassemia is endemic, we genotyped the first 4 unrelated variant carriers and 32 controls from Nord-Pas-de-Calais for 97 European ancestry informative markers (EAIMs). Using these EAIMs and comparing with population reference panels, we demonstrated that the variant carriers were very similar to the controls and were closer to North European populations than to South European or Middle-East populations. Rare beta-thalassemia variants have already been described in patients sampled in non-endemic regions but it is the first proof of a founder effect in Northern Europe. The new genetic panel FRL is under registration in EGA.

  Study EGAS00001000980

• colorectal_epigenome

  Three different types of samples were used: 19 normal adjacent, 17 adenoma and 19 colorectal tumor tissue samples. This included 10 pairs of colorectal cancer and normal samples and 1 pair of adenoma-normal samples of the same patient. Tissue specimens were formalin-fixed paraffin-embedded (FFPE). DNA was isolated using the QIAamp FFPE Tissue kit (Qiagen, Hilden, DE) according to the manufacturer’s instructions. The processed DNA was run on the Illumina Human MethylEPIC® v1.0 BeadChip array.

  Dataset EGAD00010002726

• Whole exome sequencing data of germline and two independent primary leukemias of five patients

  The contribution of genetic predisposing factors to the development of pediatric acute lymphoblastic leukemia (ALL), the most frequently diagnosed cancer in childhood, has not been fully elucidated. Children presenting with multiple de novo leukemias are more likely to suffer from genetic predisposition. Here, we selected five of these patients and analyzed the mutational spectrum of normal and malignant tissues.

  Dataset EGAD00001002266