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• Premalignant SOX2 in ovarian cancer patients

  Whole Genome Sequencing data set for the study "Premalignant SOX2 in ovarian cancer patients"

  Dataset EGAD00001002734

• Brain mets discovery cohort whole-exome sequencing raw sequencing files

  These are the raw sequencing files for the 50 brain tumour, 3 extracranial tumour and 34 matched normals for the patients in the discovery cohort.

  Dataset EGAD00001005981

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model – 2D versus 3D co-culture comparison

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions (each as biological triplicates): - wild-type cells from 2D or 3D co-cultures after 3 months of culturing (2D_WT, 3D_WT) - knock-in cells from 2D or 3D co-cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (2D_KI, 3D_KI) - 2D and 3D KI cultures treated with Bumetanide (KI_bum) or BACE IV (KI_bace) inhibitor

  Study EGAS50000001392

• Whole genome sequencing data of pediatric hypodiploid acute lymphoblastic leukemia

  Hypodiploid acute lymphoblastic leukemia (ALL) is a rare subtype of B-cell ALL characterized by chromosome number < 45 , encompassing near-haploid (24–29 chromosomes) and low-hypodiploid (30–39 chromosomes) subgroups. These subgroups display distinct genetic landscapes, including Ras and receptor tyrosine kinase pathway alterations in near-haploid ALL, and frequent IKZF2, RB1, and germline TP53 alterations in low-hypodiploid ALL. Clinically, hypodiploid ALL is associated with dismal prognosis, with 5-year overall survival rates often between 50-70% in children and markedly worse in adults. Despite advances in risk stratification and MRD-guided therapy, allogeneic stem cell transplantation remains the current standard recommendation for affected patients.

  Study EGAS50000001305

• RNA sequencing data of pediatric hypodiploid acute lymphoblastic leukemia

  Hypodiploid acute lymphoblastic leukemia (ALL) is a rare subtype of B-cell ALL characterized by chromosome number < 45 , encompassing near-haploid (24–29 chromosomes) and low-hypodiploid (30–39 chromosomes) subgroups. These subgroups display distinct genetic landscapes, including Ras and receptor tyrosine kinase pathway alterations in near-haploid ALL, and frequent IKZF2, RB1, and germline TP53 alterations in low-hypodiploid ALL. Clinically, hypodiploid ALL is associated with dismal prognosis, with 5-year overall survival rates often between 50-70% in children and markedly worse in adults. Despite advances in risk stratification and MRD-guided therapy, allogeneic stem cell transplantation remains the current standard recommendation for affected patients.

  Study EGAS50000001806

• Whole-exome sequencing of hepatocellular carcinoma biopsies

  All 122 HCC biopsies and 115 non-tumoral tissues from 114 patients were subjected to whole-exome sequencing. Whole-exome capture was performed using the SureSelectXT Clinical Research Exome (Agilent Technologies) or SureSelect Human All Exon V6+COSMIC (Agilent Technologies) platforms according to the manufacturer’s guidelines. Sequencing was performed on an Illumina HiSeq 2500 at the Genomics Facility Basel according to the manufacturer’s guidelines. Paired-end 101-bp reads were generated.

  Dataset EGAD00001008182

• 3q-capture DNA sequencing of primary AMLs with 3q26 rearrangements

  This dataset contains DNA sequencing of the chromosome 3q region in 28 primary AML cases with 3q26 rearrangements (3q26-rearranged AML). 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).

  Dataset EGAD00001006820

• Long-read sequencing for cell-free DNA analysis (human)

  In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Cell-free DNA from plasma samples of 31 pregnant women at different trimesters, 6 hepatitis B carriers, and 8 patients with hepatocellular carcinoma were sequenced with the two platforms.

  Study EGAS00001006328

• Molecular profiling of tissue autopsies and ctDNA

  The dataset contains high-throughput sequencing data derived from a cancer autopsy series of 10 patients. As part of this study, whole-exome sequencing and RNA-seq were performed for spatially distinct tissue biopsies from the patients. In addition, plasma samples from the patients were sequenced using a custom panelt to profile ctDNA. There are 106 files containing whole-exome sequencing data, 107 files containing RNA-seq data, and 9 files containing plasma sequencing data.

  Dataset EGAD00001007040

• The mutation burden of narrowband ultraviolet B phototherapy in human skin - Nanoseq

  Background: Ultraviolet radiation (UV) is used as a treatment for psoriasis, but UV can also induce mutations which may lead to development of skin cancer. Information on the mutagenicity of narrowband UVB (NBUVB) would help inform clinicians and patients who are concerned about the potential risks of this treatment.

  Dataset EGAD00001015249

• The mutation burden of narrowband ultraviolet B phototherapy in human skin - WGS

  Background: Ultraviolet radiation (UV) is used as a treatment for psoriasis, but UV can also induce mutations which may lead to development of skin cancer. Information on the mutagenicity of narrowband UVB (NBUVB) would help inform clinicians and patients who are concerned about the potential risks of this treatment.

  Dataset EGAD00001015250

• Subset of EGAS00001005112 (The INFORM Precision Medicine Study for High-Risk Pediatric Malignancies, 17 exomes) which is used in EGAS00001005243 (Radiation-induced gliomas represent H3-/IDH-wild type pediatric gliomas with recurrent PDGFRA amplification and loss of CDKN2A/B)

  Part of the project: The INFORM Precision Medicine Study for High-Risk Pediatric Malignancies resulted in the publication of this study: Radiation-induced gliomas represent H3-/IDH-wild type pediatric gliomas with recurrent PDGFRA amplification and loss of CDKN2A/B. This dataset contains the subset of 17 patient exome sequencing data.

  Dataset EGAD00001007864

• CLUSTER DAC

  The DAC for CLUSTER Consortium datasets relating to JIA and healthy controls RNAseq data and their associated clinical data.

  Dac EGAC50000000426

• WGS of cord blood hematopoietic stem and progenitor cells

  In this study, the mutational effects of prenatal chemotherapy exposure on cord blood hematopoietic stem and progenitor cells was investigated in cord blood samples taken from 10 healthy pregnant women, 4 pregnant cancer patients receiving no systemic anti-cancer treatment during pregnancy and 12 pregnant cancer patients receiving chemotherapy during pregnancy. Sequencing was performed on Illumina platforms.

  Study EGAS50000000288

• Multiple esclerosis and mixed microbial infections

  This Project deals with the sequencing of ITS1 region, which is highly variable both in length and in nucleotide sequence for different yeast using yeast-specific primers ITS1 and ITS2. A total of 19 samples involving different brain regions from patients with different conditions were analysed. Of these, 10 are controls-healthy patients and 9 multiple sclerosis (MS) patients.

  Study EGAS00001002957

• Raw sequencing data of PERMED-01 trial

  Targeted sequencing (t-NGS) of frozen advanced cancers tissue was established with three panels covering 395 to 560 candidate cancer genes. Sequencing was done using the 2x150-bp paired-end technology on the Illumina MiSeq and NextSeq500 platforms. The DNA libraries of all coding exons were done with the HaloPlex Target Enrichment System (Agilent, Santa Clara, CA, USA).

  Dataset EGAD00001006289

• Sequencing data for the Genomic Autopsy Study

  The .cram files of the Trio or Quad sequencing data used for generation of the genomic autopsy study. This contains a mix of genome sequencing and exome sequencing data for probands and their parents. A subset of families (n=32) did not provide consent to publicly sharing their data.

  Dataset EGAD00001009737

• Data of the Institute of Pathology, University Medical Center Freiburg, Germany

  DAC for proteomics data deposited in EGA by the proteomics laboratory of the Institute of Pathology, University Medical Center Freiburg, Germany

  Dac EGAC50000000048

• POLG data MS-affected co-twins

  paired-end BAM files of the sequencing analysis of the mtDNA polymerase gamma (POLG) gene in the MS-affected co-twins

  Dataset EGAD00001002189

• Targetable NOTCH1 rearrangements in reninoma - WGS

  Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

  Dataset EGAD00001010888

• Drug Resistant Hypertension in African Americans' Exome

  Resistant hypertension is defined as blood pressure that remains above goal in spite of the concurrent use of 3 antihypertensive agents of different classes or the concurrent use of 4 or more antihypertensive agents regardless of control. Its diagnosis is important for the identification of patients who are at high risk of having reversible causes of hypertension and/or patients who, because of persistently high blood pressure levels, may benefit from special diagnostic and therapeutic considerations. Resistant hypertension represents an extreme phenotype, thus, it has been predicted that genetic factors could play a larger role than for the general hypertensive population. Genetic assessments of patients with resistant hypertension have been limited. The current study assayed the exome of 91 African American patients with treatment resistant hypertension.

  Study phs000442

• Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

  We tested the efficiency and reproducibility of 10 RNA isolation methods on 5 different biofluids. Pooled human plasma and serum, bile and urine were used along with cell culture supernatants from human embryonic stem cells (hESC), primary neonatal rat ventricular myocytes (NRVM) and human cholangiocarcinoma cells (KMBC). 4 RNA isolation methods designed to isolate total RNA from bio fluids without enrichment of exRNA carriers were used. 6 methods that preferentially enriched for exRNA carriers were also compared. Small RNA libraries were constructed using the NEBNext small-RNA library prep. The efficiency and reproducibility of the different RNA isolation methods was compared using small-RNA seq.

  Study phs002143

• Massachusetts General Hospital/Eisai National Institute of Mental Health (NIMH) Genetics Initiative Alzheimer's Disease GWAS - Affymetrix GeneChip Human Mapping 500K Array Set

  This study cohort was collected as part of the National Institute of Mental Health (NIMH) Alzheimer's disease Genetics Initiative Study. Recruitment of families, predominantly sibling, for the cohort was focused on local memory disorder clinics, nursing homes, and the surrounding community. Clinical evaluation was performed at the University of Alabama at Birmingham, Johns Hopkins University, and Massachusetts General Hospital/Harvard Medical School. Informed consent was obtained from all study participants, for participants with extensive cognitive impairment, a legal guardian or caregiver with power of attorney provided consent. To determine age of onset, a creditable informer was interviewed and medical records were evaluated.

  Study phs000483

• RNAseq of GEPARSIXTO

  294 formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer’s protocol (Promega 9FB167). 279 total RNA sequencing libraries were prepared at TGL using a Bravo Automated Liquid-Handling Platform (Agilent G5562A) and the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina 20020599) following the manufacturer’s protocol (Illumina 1000000040499). RNAseq library quality and quantity were measured using a TapeStation 4200 (Agilent G2991AA) and Qubit 3.0 fluorometer (Life Technologies Q33216), pooled at equal molar ratios, and denatured following the manufacturer’s protocol (Illumina 1000000106351). 271 total RNA sequencing libraries were sequenced at TGL on NovaSeq 6000 (Illumina 20012850) S4 flow cells (Illumina 20028313) following the manufacturer’s protocol (Illumina 1000000019358) using a 2x50 bp paired-end configuration and pool sizes of 91 libraries to target a read depth of 110 million clusters per library on average.

  Dataset EGAD00001010201

• Mutation analysis using AVENIO Expanded in cfDNA

  High resolution mutation analysis using the AVENIO ctDNA Expanded Kit V2, which targets 77 cancer-associated genes, in cfDNA in metastatic breast cancer.

  Dataset EGAD50000001669