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• Somatic_evolution_in_the_psoriatic_skin

  We will use laser capture microdissection to dissect groups of a few hundred cells, from which we will isolate and sequence nucleic acids. We aim to whole-genome, whole-exome and RNA sequence the samples in effort to understand the accumulation of somatic mutations in psoriasis and their effect on transcription.

  Study EGAS00001004882

• Paediatric_CNS_tumour_autopsy_DNA_WES

  Paediatric gliomas likely have their origins in embryogenesis. This WES extension to the WGS study seeks to estimate the occurrence of driver mutations within the normal tissues of patients which have developed lethal brain tumours and compare the incidence between those that have a germline predisposition and those that don't.

  Study EGAS00001005642

• Bulk RNA sequencing of Singapore colorectal cancer patients (SG-BULK)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001005978

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-3)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006056

• Integrated Exome-seq analysis of tumor thrombus

  We prospectively enrolled 83 patients with a renal mass and TT scheduled to undergo surgical resection. To accurately integrate genomic and transcriptomic findings and enable histological co-registration, simultaneous isolation of DNA and RNA was performed from individual samples characterized histologically through immediately flanking sections

  Study EGAS00001005511

• Integrated RNA-seq analysis of tumor thrombus

  We prospectively enrolled 83 patients with a renal mass and TT scheduled to undergo surgical resection. To accurately integrate genomic and transcriptomic findings and enable histological co-registration, simultaneous isolation of DNA and RNA was performed from individual samples characterized histologically through immediately flanking sections

  Study EGAS00001005512

• Whole genome sequencing of colorectal cancer patients (SG-BULK-1)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006030

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-5)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006114

• the Yemeni-Somali 5 million SNP array dataset

  The three new samples (two from Yemen and one from Somalia) that carry a maternal lineage affiliated with the Malagasy motif were assayed for genome-wide SNP genotypes using the Illumina Human Omni5 Bead Chip (Illumina), which surveys 4,284,426 single nucleotide markers regularly spaced across the genome.

  Study EGAS00001003425

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-2)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006039

• Whole Genome sequencing of colorectal cancer patients (SG-BULK-4)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer.

  Study EGAS00001006101

• Feasibility of Ultra-Rapid Exome Sequencing in Critically Ill Infants and Children With Suspected Monogenic Conditions in the Australian Public Health Care System

  Critically ill infants and children with suspected monogenic conditions underwent ultra-rapid whole exome genetic testing. A molecular diagnosis was established in 51% of the patients. This study suggests feasibility of ultra-rapid genomic testing in critically ill pediatric patients.

  Study EGAS00001005430

• Primary_DIPG_expression_profiles

  In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG. Seventeen primary tumor samples stereotactically biopsied at diagnosis by neurosurgeons in the Necker-Enfants Malades hospital (Paris, France) and snap-frozen for RNA extraction and subsequent poly-A mRNA purification.

  Study EGAS00001007181

• Mutational signatures in single cell clone expansion samples treated with clinical stage G-quadruplex binder CX5461

  Drug induced photoreactions following exposure to UVA have been documented for several therapeutic compound classes, including psoralens and fluoroquinolones. We used whole genome sequencing to examine the mutagenic spectrum of CX5461, a quinolone-derived small molecule, in expanded retinal pigment epithelial single cell clones exposed to UVA, CX5461, or a combination of both UV and CX5461. We identified the distribution of somatic base substitutions and short indels and mutational patterns in treated samples.

  Dataset EGAD50000002513

• scRNA-seq of a 3D human cortical tissue model from human iPSCs exploring 2D versus 3D co-culturing

  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 as described in the Study section. The dataset was generated using the BD Rhapsody technology and sequenced paired-end with Illumina NovaSeq2000. Information on the multiplexing of samples is reported in the Analyses section.

  Dataset EGAD50000002021

• Genomic and clinical data from IMmotion010, a phase 3 randomised clinical trial testing adjuvant atezolizumab versus placebo for patients with renal cell carcinoma at increased risk of recurrence following resection

  778 patients were randomized in this study. Pre-treatment bulk RNAseq of primary tumors was conducted for 754 patients. For 80 patients, bulk RNAseq analysis of a metastastic biopsy was conducted. For these 80 pairs, DNA alterations were assessed in pre-treatment and at recurrence using FoundationOne.

  Dataset EGAD50000001827

• WGS data for Pancreatic Cancer samples (resection cohort)

  WGS data from pancreatic cancer samples. These are part of a resected cohort from a tandem duplicator phenotype paper (Farooq et al, NPJ Precision Oncology, 2025). The dataset includes tumour and normal BAM files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=189 tumour/normal pairs).

  Dataset EGAD50000001834

• snRNA-seq BAM files from 10x Multiome profiling of human fetal liver hematopoiesis

  This dataset provides snRNA-seq BAM files from a single-nucleus multiome study of 53 human fetal liver samples (5–18 post-conception weeks). Live CD45+CD235- cells were sorted from dissociated tissue, and isolated nuclei were processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. Raw sequencing data were processed and aligned to GRCh38-2020-A-2.0.0 using Cell Ranger ARC v2.0.2.

  Dataset EGAD50000002337

• RNA Sequencing of Control and Myotonic Dystrophy Type 1 Cells During Myogenic Differentiation

  To investigate gene expression dynamics during myogenic differentiation in myotonic dystrophy type 1, RNA was collected from immortalized control, patient-derived, and CRISPR/Cas9-corrected myoblasts at proliferation (day -2) and at days 1 and 5 of differentiation. High-quality RNA was isolated and sequenced using poly(A)-enriched or rRNA-depleted protocols, yielding 100 bp paired-end reads with high coverage. A subset of samples at day 1 underwent deeper sequencing to enhance transcriptome resolution.

  Dataset EGAD50000001647

• RIP-SeqRaw data

  This dataset contains 15 paired FASTQ files from the PTBP1 project. Sequencing data were generated using bulk directional RNA-seq and RIP-seq experiments performed on a NovaSeq 6000 platform (2×100 bp paired-end reads). The dataset comprises two groups of samples: controls and patients. For each group, both input and immunoprecipitated samples are available. Patient samples correspond to skin biopsies from individuals affected by a neurodevelopmental disorder associated with variable skeletal dysplasia and disproportionate short-limbed short stature.

  Dataset EGAD50000001723

• De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

  Dataset EGAD50000001673

• Multi-omic dataset utilized in the analysis of a phase II study of epigenetic priming followed by nivolumab in lung cancer

  This dataset includes sequence files from whole exome sequencing and bulk RNA sequencing of tissue and blood biospecimens from a phase II clinical trial investigating epigenetic priming followed by immune checkpoint blockade in non-small cell lung cancer (NSCLC; NCT01928576). There are 78 whole exome sequencing files and 36 bulk RNA sequencing files included in this dataset.

  Dataset EGAD50000001336

• Whole scRNA-seq from pre frontal cortex patient biopsy

  The single- cell RNA-seq prefrontal cortex sample was selected from a cohort of patients with hydrocephalus ≥18 years of age planning to undergo CSF diversion surgery either with a ventriculoperitoneal shunt placement (VP) or ventriculocisternostomy (VCS). The tissue was dissociated followed by red cell and debris removal and counting of the cells to be sequenced with (scRNA-seq; 10x Genomics kit v2). After dissociation only non neuronal cells were retrieved.

  Dataset EGAD50000001542

• Clinical Outcomes for 344 Diffuse Large B-Cell Lymphoma Patients

  This dataset contains clinical outcomes for 344 Diffuse Large B-Cell Lymphoma patients. For each subject we have recorded AGE (binarized: > 60, <= 60), SEX (male or female), LDH (serum lactate dehydrogenase), ECOG (Performance status 3 or 4), STAGE (Disease stage III or IV according to the Ann Arbor staging system), EXBM (Two or more extranodal sites of disease (outside of a lymph node), BSYMP (Presence of B symptoms), and BM (Bone marrow involvement). All data are delivered as a single XLSX file with one row per patient.

  Dataset EGAD50000001536

• Targeted panel sequencing of two patient-derived melanoma cell lines

  Targeted panel sequencing was conducted on patient-derived cell lines: Mel-DCC-11 (the parental line, sensitive to the BRAF inhibitor) and Mel-DCC-11-R (resistant to the BRAF inhibitor). The parental cell line was generated from disseminated cancer cells (DCCs) obtained from a lymph node sample of a melanoma patient. The resistant cell line was generated from the parental one through exposure to Vemurafenib. Normal peripheral blood lymphocytes from the same patient served as the control for comparison. Sequencing on NovaSeq6000. Fastq files.

  Dataset EGAD50000001745

• Transcriptome analysis of human iPSC-derived microglia in a novel human 3D cortical tissue model

  scRNA-seq analysis of human iPSC-derived microglia in a novel, human in vitro 3D cortical tissue model. Samples include three distinct conditions (each as biological duplicates): wild-type microglia extracted from cultures after 1 month (WT_1mo) and 3 months (WT_3mo) of culturing, as well as knock-in microglia extracted from 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 (KI_3mo).

  Dataset EGAD50000000677

• Base modification analysis using single molecule real-time sequencing

  This dataset was generated using single-molecule real-time sequencing for both training and testing purposes. The DNA samples isolated from human buffy coats or placenta of healthy individuals (n=4,) were prepared in a way that four types of base modifications were incorporated, including unmodified controls, 5mC, 5hmC, and 6mA. The sequence data for each sample consists of subreads produced by single-molecule real-time sequencing and stored in a bam format. Details of the specific experiments conducted in this study are outlined in our manuscript.

  Dataset EGAD50000000541

• Sequencing data of the ampulla and fimbriae of the fallopian tube in pre-menopausal women

  A total of 10 pre-menopausal patients were recruited for this study. Sequencing of both the fimbriae and ampullary region of the fallopian tubes was performed using 10x Genomics single-cell RNA-seq and ATAC-seq. For one patient, data were sequenced across 4 lanes, while the remaining patients' data were sequenced in 2 lanes each, resulting in a total of 44 sequencing datasets for each platform.

  Dataset EGAD50000000889

• Epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages

  Immune memory is key to effective antimicrobial responses, but the impact of mRNA vaccines on this process is not fully understood. Our research shows that SARS-CoV-2 mRNA vaccines alter the epigenetic profile of human macrophages, specifically enhancing histone acetylation, which is linked to immune training. Significant epigenetic changes, along with increased cytokine release, require two vaccine doses. However, these effects diminish over time but can be restored with a booster dose six months later, maintaining a strong pro-inflammatory response.

  Dataset EGAD50000000495

• RnaSeq data from 414 tumor samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 414 BAM files corresponding to the full total RNA-sequencing dataset.

  Dataset EGAD50000000733

• 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. Screening was performed through RNA-Seq

  Dataset EGAD50000000039

• Quantitative Exploratory Proteomics Analysis of Glioblastoma in Initial and Recurrent Tumors

  Shotgun Proteomics; Glioblastoma samples from 11 patients were obtained at initial and recurrent tumor stages. Proteins were extracted, identified and quantified via tandem mass spectrometry based on a TMT isobaric labelling approach. Quatitative proteomics reveals 146 differentially abundant proteins using a patient-matched statistical modelling. Analysis of proteolytic processing reveals differential proteolytic patterns in recurrent tumors. Proteogenomics reveals the presense of 30 single-amino acid variants present in glioblastoma tumor and 1 of those as increased in recurrent tumor.

  Dataset EGAD00010002350

• RNAseq of human breast cancer tumors from the PEARL study

  Formalin fixed, paraffin-embedded human breast cancer tumor samples had RNA extracted using the Thermo Scientific KingFisher Flex instrument and the Applied Biosystems MagMAX FFPE DNA/RNA Ultra Kit; Total RNA libraries were created using the Bravo Automated Liquid-Handling Platform and the TruSeq Stranded Total RNA Library Prep Gold Kit; libraries were sequenced on the Illumina NovaSeq 6000 machine using a 2x50 bp paired-end configuration to target a read depth of 120 million clusters per library.

  Dataset EGAD00001015613

• ICU transcriptomics: Assessing the role of the host immune response in patients with ventilator-associated pneumonia

  This is a study of 100 patients with the aim to provide transcriptomic sequencing data analysis of cells isolated from bronchioalveolar lavage and blood samples from critically ill patients with pneumonia on an intensive care unit in order to investigate the host contribution to disease. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001015407

• Combined Telomerase Vaccination and Pembrolizumab in Advanced Melanoma: WES and RNA sequencing of biopsies from a Phase I Trial

  This dataset contains whole-exome and RNA sequencing of biopsies obtained from patients enrolled in a phase I clinical trial investigating the UV1 vaccine in combination with pembrolizumab in patients with advanced melanoma.

  Dataset EGAD00001011074

• limbal stem cells from Aniridia patients

  Limbal stem cells obtained during penetrating keratoplasty from aniridia patients with congenital aniridia (Lagali Stage 4), limbal tissue was digested in collagenase A solution (4 mg/ml) in keratinocyte serum-free medium (KSFM) (Thermo Fisher Scientific; Waltham, MA) for 20 h at 37 °C. Cell suspensions were filtered through a use of Flowmi® micro strainer (SP Bel-Art; Wayne, NJ). LSC clusters were dissociated with trypsin-EDTA (0.05%) solution and cultivated in KSFM. Medium was refreshed every other day. Subconfluent (80–90%) limbal epithelial cells were harvested at passage 2

  Dataset EGAD00001011124

• pan-cancer plasma cfRNA

  Dataset contains mRNA capture sequencing data from plasma of 266 different human donors. The first, pan-cancer, cohort covers 25 high-grade to metastatic cancer types (8 cancer patients per type) and a control group (8 healthy donors). The validation cohort comprises additional plasma samples from ovarian, prostate and uterine cancer patients (12 per type) as well as additional samples from controls (22 new and 8 repeated). Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

  Dataset EGAD00001009713

• WCDT Hi-C assays performed mCRPC biopsies

  Paired FASTQ files from a Hi-C assay performed on mCRPC tumors. Sequencing was performed using 150nt paired reads generated by a Novaseq 6000 instrument.

  Dataset EGAD00001009408

• WGS data from a GBM patient PT-MS8478

  WGS data from a GBM patient PT-MS8478

  Dataset EGAD00001008524

• fibroblast RNAseq from a GINS3 patient and two parents

  RNA-seq was performed from 3 separate GINS3 patient fibroblast cultures and 1 replicate of fibroblasts derived from each of the two parents. RNA-seq libraries were generated with NEBNext Ultra II Directional RNA library prep for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and sequenced on Illumina NextSeq500 with paired-end 150 bp read length. SIRV Set 3 (Lexogen) spike-ins were added. Two fastq files are provided for each RNAseq sample.

  Dataset EGAD00001008571

• WGS and RNA-Seq data from a GBM patient PT-SS3647

  WGS and RNA-Seq data from a GBM patient PT-SS3647

  Dataset EGAD00001008530

• WGS and RNA-Seq data from a GBM patient PT-SJ5453

  WGS and RNA-Seq data from a GBM patient PT-SJ5453

  Dataset EGAD00001008529

• WGS and RNA-Seq data from a GBM patient PT-PV2594

  WGS and RNA-Seq data from a GBM patient PT-PV2594

  Dataset EGAD00001008526

• Cancer and germline exomes consisting of FASTQ reads from melanoma, lung and colon cancer samples

  Cancer and germline exomes consisting of FASTQ reads from 6 individuals (4 melanoma, 1 lung and 1 colon cancer). Exome sequencing was performed on illumina with a depth of 100x to 200x. 2 Melanoma datasets contain reads from 2 different tumor regions 2 Melanoma datasets contain reads from 1 tumor region and from a tumor derived cell line 1 Melanoma dataset contains reads from 2 healthy tissues Colon and lung datasets contain both 1 matched germline-tumor pair

  Dataset EGAD00001007950

• Resequencing (MIPS) of candidate genes for Keratoconus (2020)

  The dataset consists of the BAM-files of 745 patients and 810 controls (retained after quality control) of a set of 34 candidate genes obtained after targeted enrichment via Molecular Inversion Probes (MIPS) technology. The sequencing was performed on the NextSeq 500 (Illumina, CA, USA) using custom sequencing and index primers in three 2 x 76 bp, dual indexed runs using a 150 cycles High-Output Illumina kit (Illumina, CA, USA). Alignment of the fastq reads to the human genome was performed using BWA (v0.7.4).

  Dataset EGAD00001006825

• FFPE

  The mutational status of 112 recurrently mutated genes in B-cell lymphoma was examined by targeted next-generation sequencing (NGS). Libraries were performed with 150 ng of genomic DNA (gDNA) obtained from formalin-fixed paraffin-embedded (FFPE) biopsy using molecular-barcoded library adapters (ThruPLEX Tag-seq kit; Takara) coupled with a custom hybridization capture based method (SureSelect XT Target Enrichment System Capture strategy, Agilent Technologies Inc.) and sequenced in a MiSeq instrument (Illumina, 2x150bp).

  Dataset EGAD00001006565

• WGS and WES of Advance Prostate Cancer

  The dataset consists of BAM files of 2 pairs of matched tumor/normal samples of a men with advanced prostate cancer. One pair is whole genome sequencing: WGS_T/WGS_N for tumor and normal samples, respectively; and the other pair is whole exome sequencing: WES_T/WES_N for tumor and normal specimens, respectively. Details can be found at the publication titled: "Molecular Medicine Tumor Board: Whole Genome Sequencing to Inform on Personalized Medicine for a Man with Advanced Prostate Cancer"

  Dataset EGAD00001006487

• Detection of ctDNA in Plasma of Patients with Clinically Localised Prostate Cancer is Associated with Rapid Disease Progression

  Whole genome sequencing of tumour-normal pairs in eight patients with clinically localised disease undergoing prostatectomy. A bespoke DNA capture and amplification panel against the highest prevalence, highest confidence aberrations for each individual was designed and used to interrogate ctDNA isolated from plasma prospectively obtained pre- and post- (24 hours and 6 weeks) surgery. Tagged-amplicon deep sequencing (TAm-Seq) across the TP53 gene in ctDNA in a cohort of 189 individuals.

  Dataset EGAD00001006369

• Reference exome data for Australian Aboriginal populations from Western Australia and the Northern Territory

  Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. The data is provided as 2 VCF files, one for the WA population and one for the NT population.

  Dataset EGAD00001005189

• Pervasive H3K27 acetylation and ERV expression in H3.3K27M gliomas present a therapeutic vulnerability

  We sequenced a total of 2 H3.3K27WT (pcGBM2, G477; 3 replicates total) and 2 H3.3K27M (DIPGVI, DIPGXIII; 6 replicates total) patient-derived cell lines as well as Crispr/Cas9 H3.3K27M-KO clones for one of the cell lines (3 replicates total; DIPGXIII-KO) using ATAC-Seq. P-XX designates passages of replicates. These samples can be found at GEO under accession number GSE128744. This repository contains 1 replicate of G477 to be released under controlled access.

  Dataset EGAD00001004961

• Targeted gene panel sequencing of matched diagnosis-remission-relapse B cell precursor acute lymphoblastic leukemia samples

  Bone marrow mononuclear cells from patients diagnosed with B cell precursor acute lymphoblastic leukemia were obtained at three sequential time points: first diagnosis, remission after chemotherapy and relapse. Genomic DNA was isolated and targeted gene panel sequencing was performed using a customized biotinylated RNA oligo pool (SureSelect, Agilent, Santa Clara, California) to hybridize the target regions comprising 362 kbp on a HiSeq2000. Target regions were selected to validate mutations previously identified in these samples using whole exome sequencing.

  Dataset EGAD00001004977

• Multiple myeloma Total Therapy trial patient sequencing

  DNA was obtained from either CD138+ cells from the bone marrow of multiple myeloma patients (tumor) or from stem cell harvests or peripheral blood cells from the same patient (control). 100 ng of DNA was fragmented, end-repaired, and adapters ligated using the HyperPlus kit (KAPA Biosystems). After PCR amplification the libraries were hybridized with probes against either a targeted panel consisting of 140 genes and chromosomal regions (Nimblegen) using SeqCap reagents (Nimblegen). Hybridized libraries underwent further amplification before being sequenced on a NextSeq500 (Illumina) using 75 bp paired end reads.

  Dataset EGAD00001004373

• 33 Paired (Normal-Tumor1-Tumor2) MM whole-exome data

  Samples were sequenced from 33 multiple myeloma patients including tumor presentation and relapse samples and a matched patient control sample. Tumor DNA was isolated from CD138-positive plasma cells. Control DNA originated from peripheral blood leukapheresis products collected after induction therapy. Libraries were prepared using the SureSelectQXT sample prep kit and the SureSelect Clinical Research Exome kit (Agilent), with additional baits covering the Ig and MYC loci. Paired-end sequencing was performed to an average sequencing depth of 118× on a HiSeq2500 (Illumina).

  Dataset EGAD00001002165

• Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

  Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001307

• Genome and transcriptome sequence data from a primary unknown cancer patient

  Genome and transcriptome sequence data from a primary unknown cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001308

• Amplicon sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study".

  Amplicon sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are Illumina amplicon deep sequencing libraries (n = 118) to validate somatic predictions made in the whole genome sequencing libraries. Specifically, there are 72 tumor libraries and 46 normal libraries. Some patients may have multiple amplicon libraries sequenced.

  Dataset EGAD00001002896

• Prognostic factors in prostate cancer: deep sequencing pilot project TAPG

  This is a pilot project to determine whether the TAPG FFPE DNA's are suitable for deep sequencing. If successful an investigation of SNP distribution in a larger cohort will follow.

  Dataset EGAD00001001237

• Harnessing transposons for drug resistance gene discovery in cancer

  This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines.

  Dataset EGAD00001000980

• Massive genomic rearrangement acquired in a single catastrophic event during cancer development

  Massive genomic rearrangement acquired in a single catastrophic event during cancer development

  Dataset EGAD00001000002

• Surgical Treatment for Ischemic Heart Failure (STICH-BioLINCC)

  Data Access NOTE: Please refer to the &#8220;Authorized Access&#8221; section below for information about how access to the data from this accession differs from many other dbGaP accessions. ObjectiveTo compare medical therapy with coronary bypass surgery and/or surgical ventricular reconstruction for patients with congestive heart failure and coronary artery disease.BackgroundCoronary artery disease (CAD) is the most common cause of heart failure, which in turn is a major cause of death and disability globally. Evidence from previous clinical trials supports the use of coronary-artery bypass grafting (CABG) to relieve disabling symptoms of angina, particularly among high-risk subgroups with extensive CAD. However, the studies did not include patients with severe left ventricular dysfunction, and developments in medical therapy have since led to updated guidelines. In addition, the benefits of CABG in patients with ischemic cardiomyopathy had still not been clearly established at the time of this study. STICH sought to evaluate the role of CABG in the treatment of patients with CAD and left ventricular systolic dysfunction.Reduced left ventricular function may occur after myocardial infarction, often in conjunction with left ventricular remodeling, including left ventricular enlargement and changes in chamber geometry. Left ventricular remodeling is correlated with progression of heart failure and a poor prognosis. Therefore, a surgical approach to remodeling through left ventricular volume reduction could improve outcomes for patients with CAD and heart failure. Surgical ventricular reconstruction (SVR) has been shown to reduce the left ventricular volume, increase the ejection fraction, and improve ventricular function. There is also evidence that SVR performed with CABG may reduce the rate of hospitalization and improve ventricular function, as compared to CABG alone. As part of a second hypothesis, STICH additionally investigated whether SVR when added to CABG would improve outcomes in patients with heart failure and CAD.ParticipantsA total of 2,136 participants were enrolled in STICH. 1,212 were enrolled in the hypothesis 1 component of the trial, with 602 participants assigned to receive medical therapy alone, and 610 participants assigned to receive medical therapy plus CABG. 1,000 were enrolled in the hypothesis 2 component, with 499 participants assigned to receive medical therapy plus CABG, and 501 participants assigned to receive medical therapy plus CABG and SVR. 76 participants that were assigned to the CABG with medical therapy treatment were enrolled in both hypothesis components.DesignAfter initial determination of overall eligibility, participants were evaluated to determine which component of the STICH program was appropriate for them on the basis of suitable therapeutic options. All participants underwent cardiac imaging for assessment of left ventricular function and wall motion. Participants in the hypothesis 1 component were randomly assigned to receive either medical therapy alone or medical therapy plus CABG. Participants in the hypothesis 2 component were randomly assigned to receive either medical therapy plus CABG or medical therapy plus CABG and SVR.At baseline, demographic factors and clinical characteristics were assessed, including current medications and prior diagnostic and other cardiovascular procedures, and a physical examination was performed. Guideline-based recommendations for drug and device use were emphasized for all participants. All participants underwent follow-up evaluations at the time of discharge or at 30 days for participants still hospitalized, every 4 months for the first year, and every 6 months thereafter. The median length of follow-up was 56 months for hypothesis 1 and 48 months for hypothesis 2.For participants receiving CABG, arterial grafting for stenosis of the left anterior descending coronary artery was required for all participants without specific contraindications. The use of additional arterial conduits supplemented by vein grafts was recommended for revascularization of all major vessels with clinically significant stenoses. Concurrent mitral-valve surgery for regurgitation was performed at the discretion of the surgeon. For participants receiving SVR, the operation was most commonly performed during a single period of cardioplegic arrest after construction of bypass grafts. However, the procedure could also be performed with the heart beating in order to facilitate identification of the noncontractile zone of scarring. After an anterior left ventriculotomy was centered in the zone of anterior asynergy, a suture was placed in the interior of the ventricle to encircle the scar at the boundary between the akinetic and viable tissue. Visual inspection and palpation facilitated the judgment of whether a patch was needed to optimize the chamber size without deforming the left ventricle during closure of the ventriculotomy.The primary outcome for hypothesis 1 was the rate of death from any cause. The primary outcome for hypothesis two was a composite of death from any cause and hospitalization for cardiac causes.ConclusionsThere was no significant difference between medical therapy alone and medical therapy plus CABG for death from any cause, though participants that underwent CABG had lower rates of death from cardiovascular causes, death from any cause, or hospitalization for cardiovascular causes. Adding SVR to CABG reduced the left ventricular volume, as compared with CABG alone. However, this anatomical change was not associated with a greater improvement in symptoms or exercise tolerance, or with a reduction in the rate of death or hospitalization for cardiac causes.

  Study phs003493

• NHLBI TOPMed: SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS)

  Subpopulations and Intermediate Outcome Measures in COPD Study Description Subpopulations and intermediate outcome measures in COPD study (SPIROMICS) supports the prospective collection and analysis of phenotypic, biomarker, genetic, genomic, and clinical data from subjects with COPD for the purpose of identifying subpopulations and intermediate outcome measures. It is funded by the National Heart, Lung, and Blood Institute and is coordinated by the University of North Carolina at Chapel Hill. Molecular fingerprinting and extensive subject phenotyping will be performed to identify disease subpopulations and to identify and validate surrogate markers of disease severity, which will be useful as intermediate outcome measures for future clinical trials. Secondary aims are to clarify the natural history of COPD, to develop bioinformatic resources that will enable the utilization and sharing of data in studies of COPD and related diseases, and to create a collection of clinical, biomarker, radiographic, and genetic data that can be used by external investigators for other studies of COPD. Participating Institutions: Research participants for SPIROMICS will be enrolled, phenotyped, and followed at twelve SPIROMICS Clinical Centers: Columbia University, Temple University, Johns Hopkins University, Wake Forest University, University of Michigan, University of Illinois at Chicago, University of Iowa, University of Utah, National Jewish Health, University of California at San Francisco, and University of California at Los Angeles. The University of North Carolina at Chapel Hill serves as the Genomics and Informatics Center. The Radiology Reading Center is based at the University of Iowa. The PFT Reading Center is based at the University of California at Los Angeles. Study Design: SPIROMICS is a prospective cohort study that enrolled approximately 2,981 participants at twelve clinical centers over five years. Participants are distributed across four enrollment strata (i.e., Never-smokers, Smokers without COPD, Mild/Moderate COPD, and Severe COPD). Study Visits: Participants have up to four in-person visits (Baseline and Annual Clinic Visits at years 1, 2, 3 after Baseline). Study questionnaires and spirometry are completed at all main study visits. Blood and urine samples are collected at visits 1, 2, and 4. Sputum samples are collected at Visit 1. The CT scans are completed and Baseline and Visit 2. Participants also receive quarterly follow-up calls to assess health status and determine if an exacerbation has occurred. Substudies Bronchoscopy and Immunophenotyping Substudy The Bronchoscopy Substudy will enroll 50 subjects per site, for a total of 300 participants. These participants will be recruited across all four study strata. This substudy includes two study visits. During the first visit, sputum samples are collected for Immunophenotyping analysis at the Immunophenotyping Core Lab based at the University of Michigan. Participants then return for a second visit during which samples are collected via bronchoscopy, including bronchoalveolar lavage, epithelial brushings and bronchial biopsies. Immunophenotyping analysis is also conducted on BAL and blood collected during the bronchoscopy study visit. Repeatability Substudy The entire baseline clinic visit was repeated on 98 volunteers to determine reliability of measurement procedures. All baseline study-related procedures and questionnaires, including the CT scan, were re-administered and new samples of blood, urine, saliva, and sputum were collected. Field center staff processed these biospecimen samples according to the same protocol. Exacerbation Substudy The Exacerbation Substudy is a prospective, longitudinal observational study of up to 400 participants, which will allow the assessment of participant-driven health care utilization (HCU) events and symptom-defined exacerbation events over time. HCU-driven events are defined by change in medical treatment in response to a perceived COPD Exacerbation. Symptom-based events will be defined by using EXACT-PRO (EXacerbations of Chronic Pulmonary Disease Tool - Patient Reported Outcome), a daily symptom diary developed to measure the frequency, severity, and duration of exacerbations in clinical trials. All participants are provided with a PDA on which to complete the diary. Participants reporting a possible COPD exacerbation will be brought into the study clinic for a study visit to collect biological specimens and questionnaire data. The overall objectives of the Exacerbation Substudy are to: Obtain clinical data and specimens on SPIROMICS participants before and during an acute COPD exacerbation defined by Health care utilization triggered by the subject, or Symptomatic change (triggered by an EXACT defined threshold) Describe symptomatic changes occurring around HCU and symptom-defined (EXACT) events and their relationship to clinical and specimen data, Characterize the non-exacerbation "stable" state in COPD using the EXACT, including: Symptom variability (EXACT), Clinical data and specimen parameters during a stable state (baseline), The relationship between clinical and specimen data and symptom severity and variability. Explore the characteristics of stable patients, defined as those who do not experience HCU or symptom-defined (EXACT) events during the sub-study period, using baseline clinical data and specimens, and compare these characteristics with patients who experience HCU and/or symptom-defined events. Examine the relationship between HCU and symptom-defined exacerbation frequency during the first one-year period of follow-up for exacerbations and health outcomes, including 12-month change in lung function and COPD health status, and longer-term morbidity and mortality, with the latter derived from long-term data from the larger SPIROMICS study.

  Study phs001927

• A Heterozygous Missense Mutation in the Coiled-Coil Domain of STAT5B is Associated with Leukocytosis, Lymphadenopathy, Splenomegaly, Necrotizing Granulomas, Hyper-IgM and Thrombocytopenia

  We describe one patient with a heterozygous missense mutation in the coiled-coil domain of STAT5B. This patient presented with leukocytosis, lymphadenopathy, splenomegaly, necrotizing granulomas, hyper-IgM and autoimmune thrombocytopenia. Mutant STAT5B protein was shown to dominantly-interfere with IL2-induced transcriptional activity resulting in global downregulation of STAT5-regulated genes in patient T cells. The patient exhibited an increase in CD4+ T effector memory cells in the peripheral blood and these cells were resistant to restimulation-induced cell death in vitro.

  Study phs001479

• A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma

  In this study, we conducted a genome-wide association study (GWAS) of post-bronchodilator (BD) FEV1 (forced expiratory volume in 1 second) and FEV1/FVC (forced vital capacity) in Puerto Rican children with asthma. From September 2003 to June 2010, we recruited 618 Puerto Rican children with asthma, which was defined as physician diagnosed asthma and at least one episode of wheezing in the previous year. The recruited children include 267 from public schools in Hartford, Connecticut and 351 from randomly selected households in San Juan, Puerto Rico.

  Study phs001216

• A New CA19-9 Cut-Off Value Identifies Lewis Antigen Status and Refines Prognostic Stratification in PDAC

  This study investigates the clinical utility of serum CA19-9 levels in pancreatic ductal adenocarcinoma (PDAC), with a focus on identifying patients with Lewis antigen–negative status due to germline FUT3 variants. Using data from multicenter prospective cohorts in Taiwan, we analyzed CA19-9 classification, FUT2/FUT3 genotypes, and clinicopathological annotations. The goal of this study is to refine prognostic stratification and reduce false-negative interpretation of CA19-9 in PDAC patients. All participants provided informed consent, and the study was approved by the relevant institutional review boards.

  Study EGAS50000001575

• The DIRECT study: A roadmap for ctDNA-based risk prediction, molecular profiling and MRD detection in Diffuse Large B Cell Lymphoma

  DIRECT was a prospective, multisite study assessing the feasibility and utility of circulating tumor DNA (ctDNA) in 188 patients with aggressive B-cell non-Hodgkin lymphoma using capture panel sequencing and an open-source computational pipeline. The aims of the study were 1)baseline risk stratification, 2)genetic profiling and 3)ultrasensitive minimal residual disease (MRD) assessment. This study highlighted the considerable potential, but also the caveats and limitations, of ctDNA technology when applied to aggressive B-cell lymphoma.

  Study EGAS50000000968

• T cell repertorie analysis fom a Spanish cohort of mild and severe cases of COVID-19 recovered patients

  The cohort included 98 mild and 75 severe cases with a median age of 53 years. We amplified and sequenced the T Cell Receptor (TCR β) chain complementary determining region 3 (CDR3b) and performed bioinformatic analyses to assess repertoire diversity, clonality, allelic usage, and epitope affinity CDR3b clustering. CDR3b sequences were amplified by multiplex PCR and sequenced by Illumina. The resulting raw files were processed for clonotype assembly, filtering for coding clonotypes, removal of non-TRB alleles, and downsampling.

  Study EGAS50000000331

• ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19

  In a dual-center, two-cohort study, we performed single-cell RNA-sequencing of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 over time. This study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.

  Study EGAS00001004571

• RNA-sequencing of gluten-reactive and non-reactive T-cells from blood samples of treated CeD patients during a gluten-challenge

  Gluten-specific CD4+ T cells are drivers of celiac disease (CeD). Here we aimed to characterize such cells in blood of treated CeD patients during gluten challenge with comparison to similar cells of untreated disease. Treated CeD patients underwent a 3-day gluten-challenge with blood sampling at baseline and day 6 (d6). Blood cells were stained with HLA-DQ:gluten tetramers (Tetramer). CD4+, gut-homing Tetramer+ and Tetramer- effector-memory T (TEM) cells at d6 were subjected to bulk RNA-seq (n=7).

  Study EGAS00001004988

• A transcriptome atlas of human skeletal muscles

  We generated a large transcriptome atlas of human skeletal muscles by collecting biopsies from 6 different muscles to determine molecular signatures that may be distinct between leg muscles. The biopsies were collected from gracilis (GR), semitendinosus (ST), vastus lateralis (VL), vastus medialis (VM), rectus femoris (RF), and gastrocnemius lateralis (GL) muscles. We also investigated molecular differences within the muscle by including two biopsies from the middle and distal sides of the semitendinosus muscle (STM and STD, respectively). In total, 128 samples from 20 individuals (aged 25 ± 3.6 yr) were analyzed.

  Study EGAS00001005904

• Diagnosis of multisystem inflammatory syndrome in children by a whole-blood transcriptional signature

  To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki Disease (KD), bacterial infections and viral infections. Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020-April 2021 were prospectively recruited. Whole blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C to those from children with KD, definite bacterial and viral infections. Data deposited here comprises samples from patients recruited into the DIAMONDS study.

  Study EGAS00001007409

• Bone morphogenetic protein-9 controls pulmonary vascular growth and remodeling

  Pulmonary arterial hypertension (PAH) and hereditary hemorrhagic telangiectasia (HHT) are two distinct vascular diseases linked to impaired signaling through bone morphogenetic protein (BMP) receptor complexes in endothelial cells. Although BMP-9 plays a central role in activating this pathway by binding to ALK1 and BMPR-­II, its precise function in the pulmonary microvasculature has remained unclear. In this study, we uncover a previously unrecognized role for BMP-9 in regulating pulmonary vascular architecture and homeostasis. Our findings demonstrate that BMP-9 signaling intersects with VEGF pathways and contributes to the delicate balance between vascular growth and remodeling in the lungs. We also show that disruption of this pathway can shift vascular responses toward an HHT-­like state, potentially altering disease susceptibility. These insights offer a unique perspective on how BMP-9 and ALK1 shape pulmonary vascular biology and suggest that targeting this axis could inform future strategies for treating complex vascular diseases such as PAH.

  Dataset EGAD50000001496

• SweGen whole-genome sequencing from the Swedish Twin Registry

  The dataset contains whole-genome sequencing data (aligned read files) in CRAM-format (lossless compression) for a total of 942 DNA samples, selected to represent a cross-section of the Swedish population. The samples originate from the Swedish Twin Registry (STR) and have been obtained from different geographical regions. For each of the 942 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. All participants gave their written informed consent and the TwinGene study was approved by the regional ethics committee (Regionala Etikprövningsnämnden, Stockholm, dnr 2007-644-31, dnr 2014/521-32). Access to phenotypic information can be requested from the Swedish Twin Registry (http://ki.se/en/research/the-swedish-twin-registry).

  Dataset EGAD50000001326

• SweGen genetic variation from the Swedish Twin Registry

  The dataset contains files with single nucleotide variants in VCF format for a total of 942 DNA samples, selected to represent a cross-section of the Swedish population. The samples originate from the Swedish Twin Registry (STR) and have been obtained from different geographical regions. For each of the 942 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. All participants gave their written informed consent and the TwinGene study was approved by the regional ethics committee (Regionala Etikprövningsnämnden, Stockholm, dnr 2007-644-31, dnr 2014/521-32). Access to phenotypic information can be requested from the Swedish Twin Registry (http://ki.se/en/research/the-swedish-twin-registry).

  Dataset EGAD50000001323

• NEOPREDICT-Lung: longitudinal whole exome sequencing of non-small cell lung cancers under immunotherapy

  In 43 patients pretreatment tumor biopsies, resected tumors and normal tissue of sufficient quality and quantity were obtained to longitudinally explore the mutational profiles of a comprehensive set of cancer-related genes. For tumor samples, one to four FFPE sections (10 µm thickness, number depending on sample size) were lysed for genomic DNA isolation. Isolation was performed semi-automatically on the Maxwell purification system (Maxwell RSC DNA FFPE Kit, AS1450, Promega) as specified by the manufacturer. DNA was eluted in 50 µl RNase-free water and quantified fluorescently for library preparation using a Qubit 2.0 fluorometer (Life Technology) with its appertaining DNA broad-range assay. Corresponding normal DNA was isolated from blood or PBMCs using routinely available QIAGEN technology. DNA was stored at -20°C before use. Whole-exome sequencing (WES) was performed using the Twist Human Core + RefSeq + Mitochondrial Panel (Twist Bioscience), and 2 x 100 bp fragment sizes were sequenced using a NovaSeq6000 (Illumina). Demultiplexing of sequenced reads was achieved using bcl2fastq (version 2.2).

  Dataset EGAD00001015362

• Transcriptional consequences of SETBP1 variants in developmental disorders and malignancies

  The SETBP1 gene encodes a DNA-binding nuclear protein that regulates gene expression across multiple tissues. Precise control of SETBP1 dosage is essential for normal cellular function, as both loss- and gain-of-function variants of SETBP1 can lead to severe phenotypic consequences. De novo germline gain-of-function point mutations that prolong SETBP1 half-life result in Schinzel-Giedion syndrome (SGS), an ultra-rare and severe congenital disorder associated with extensive developmental abnormalities and health complications. These SGS-associated variants cluster within a hotspot in the SKI-homology domain of SETBP1, overlapping with somatic mutations recurrently observed in myeloid leukaemia with poor prognosis. Thus far, the precise mechanisms by which these SETBP1 mutations drive disease remain largely unclear. Here, through single-cell and single-nucleus mRNA sequencing of a rare collection of primary patient samples with SGS and myeloid leukaemia, we examined the transcriptional consequences of SETBP1 gain-of-function variants in haematopoietic cells, comparing their impacts when acquired in the germline and somatically in malignancies.

  Dataset EGAD00001015482

• Distinct embryonic phylogenies and driver events of infant Wilms tumor - RNA

  Cancers of adults typically arise through progressive rounds of clonal diversification and intratumoral selective sweeps which generate a long mutational trunk with shorter subclonal branches. Here, we investigated whether tumors of young children exhibit the same phylogenetic configuration. We studied three infants, including two newborns, with the childhood kidney cancer, Wilms tumour, through whole genome sequencing of bulk tissues, of single cell derived organoids, and of microdissections. All three cancers exhibited unusual driver events, with tumours of newborns harbouring FOXR2 rearrangements, delineating a distinct variant of Wilms tumour. Phylogenetic analyses suggest that tumors were seeded in an early, possibly confined window of development. Unusually, following seeding there was extensive polyclonal diversification with little evidence of clonal sweeps, leading to a distinct phylogenetic configuration more reminiscent of normal tissues rather than of adult cancers. These findings indicate that some childhood cancers may diversify via unorthodox phylogenetic pathways.

  Dataset EGAD00001009813

• Convergent somatic evolution from early life in a germline ribosomopathy

  Clonal tracking of stem cells and their progeny by whole genome sequencing permits exploration of evolutionary genetics in human disease. In this study, we performed phylogenetic reconstruction of haematopoiesis using somatically acquired mutations in 323 single haematopoietic stem and progenitor cell-derived colonies from 10 individuals with an inherited disorder of ribosome assembly, Shwachman-Diamond syndrome. We observed numerous clonal expansions, with recurrent acquisition of mutually exclusive mutations (EIF6, TP53, RPL5, RPL22, PRPF8, chromosomes 7 and 15) in multiple different clones in utero or early childhood converging on the p53-dependent nucleolar surveillance pathway that monitors ribosome integrity. In contrast to clones carrying biallelic TP53 mutations, genomes derived from colonies carrying mono-allelic TP53 mutations displayed no increase in mutation burden or specific mutational signatures. Our study highlights striking loss of clonal diversity with convergent somatic evolution on the p53-dependent nucleolar surveillance pathway from early life to offset the deleterious effects of a germline mutation in a Mendelian haematopoietic disorder.

  Dataset EGAD00001009061

• Targeted Myeloid DNA-Panelsequencing, DKFZ

  Targeted myeloid DNA-Panelsequencing from purified bone marrow blasts of 104 treatment naive AML patients from the discovery cohort. For more details, we refere to Jayavelu, Wolf, Buettner et al. Libraries were prepared from 40 ng DNA using the QIASeq Human Myeloid Neoplasms Panel (Qiagen) according to the manufacturer’s protocol. Samples were tagged with the QIAseq 96-Unique Dual Index Set A for Illumina platforms (Qiagen) to yield unique combinations of i5 and i7 barcodes for each sample. Sample fragment size distribution and concentration was estimated using the Agilent High Sensitivity DNA kit on a 2100 Bioanalyzer (Agilent). Samples were pooled in an equimolar fashion, denatured, and diluted to 1.5 pM according to Illumina’s recommendations. The diluted library was sequenced on a NextSeq 500 benchtop sequencer (Illumina) using NextSeq High Output cartridges. Demultiplexing was performed using the BaseSpace cloud platform (Illumina).

  Dataset EGAD00001008501

• The effect of freezing delay of cell-type specific transcriptome responses in human brain via snRNA-seq

  In other analysis in the current manuscript, we find a similar gene signature (to dissociation based artifacts in mouse and human tissue) is present in post-mortem microglia and astrocytes, across all snRNA-seq datasets analyzed, although it is highly variable between subjects. ​ Using acutely-resected neurosurgical tissue, we performed single-nucleus RNA-seq and reveal that a similar signature can be detected in microglia following prolonged exposure to room temperature. Tissue handling and methods details, as well as sequencing and analysis details) can be found in the methods section of related manuscript (Marsh et al., 2022). Together, these results suggest that the presence of this signature in post-mortem brain samples may be the result of a combination of acute pre-mortem (agonal state, cause of death, comorbidities, etc.) and post-mortem (post-mortem interval (PMI), storage time, RNA quality, etc.) variables and may not represent normally present cell state.

  Dataset EGAD00001008541

• MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas

  Temozolomide (TMZ) is an oral alkylating agent used for the treatment of glioblastoma and is now becoming a chemotherapeutic option in patients diagnosed with high-risk low-grade gliomas. The O-6-methylguanine-DNA methyltransferase (MGMT) is responsible for the direct repair of the main TMZ-induced toxic DNA adduct, the O6-Methylguanine lesion. MGMT promoter hypermethylation is currently the only known biomarker for TMZ response in glioblastoma patients. Here we show that a subset of recurrent gliomas carry MGMT genomic rearrangements that lead to MGMT overexpression, independently from changes in its promoter methylation. By leveraging the CRISPR/Cas9 technology we generated some of these MGMT rearrangements in glioma cells and demonstrated that they lead to TMZ resistance both in vitro and in vivo. Lastly we showed that such fusions can be detected in tumor-derived exosomes and could potentially represent an early detection marker of tumor recurrence in a subset of patients treated with TMZ.

  Dataset EGAD00001006281

• WES, sWGS and RNA-seq of Asian breast cancer

  The dataset contains a full genomics characterization of 527 Asian breast tumours. This includes whole-exome sequencing of tumour tissue at 80X, whole-exome sequencing of matched normal (blood) tissue at 40X, shallow-whole genome sequencing at 0.1X for copy number analyses, and RNA-seq of tumour tissue at 40X coverage (&gt;15 million reads). Whole-exome libraries were prepared using the Nextera Rapid Capture Exome Kit; exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a HiSEQ4000 platform. RNA libraries were prepared using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold as per manufacturer’s instructions and also subjected to paired end 75 sequencing on a HiSEQ4000 platform. Uploaded bam files have been mapped to the hs37d5 human genome and processed using the standard GATK pipelines. Paired clinical, demographic, genotyping, and overall survival data for these patients are available from the associated publications or by request.

  Dataset EGAD00001006399

• Single Cell RNAseq at various stages of HiPSCs differentiating toward definitive endoderm and endoderm derived lineages

  When comparing the differentiation capacities of pluripotent stem cell lines that have different genetic backgrounds, batch to batch experimental variablility poses a significant challenge, especially when trying to identify smaller effects. One way to address this issue is to differentiate several different lines in the same culture dish, thereby elimating experimental variation. In addition, it allows researchers to analyze many more lines with less experiments. Parallel single cell RNA-Seq exploits that individual cells are tagged and hence each cell can be reliably assigned to the donor of origin based on the genetic variants it contains. In addition, analyzing the genetic signature of single cells within a differentiating population can reveal differentation stages that are not easily detected in bulk RNAseq data. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001005741

• Genomic variants in 121 genes associated with ovarian cancer in cancer tissue and derived organoids

  High-grade serous ovarian cancer (HGSOC) likely originates from the fallopian tube (FT) epithelium, but advanced stages are mostly found outside the FT. We used ex-vivo cultures of HGSOC and knock-out of tumor suppressors in FT organoids to study changes in epithelial cells and niche requirements for normal and transformed FT cells. We found that transformed cells require BMP signaling and are growth arrested in Wnt rich medium. A SureSelectXT Automation Custom Capture Library (Agilent) target enrichment panel was designed. The enrichment panel comprised all coding exons of 121 genes associated with ovarian cancer. Capture was performed according to the manufacturer’s instructions using an NGS Workstation Option B (Agilent) for automated library preparation starting with 3 μg DNA per sample. Sequencing was performed on a Illumina Hiseq 2500 system gnerating 2x100bp paired end reads and a target coverage of &gt;200 per sample. Sequence reads were mapped to the haploid human reference genome (hg19) using BWA. Variants where called with FreeBayes v1.1.

  Dataset EGAD00001005279

• The mutational landscape of normal human endometrial epithelium

  All normal somatic cells are thought to acquire mutations. However, characterisation of the patterns and consequences of somatic mutation in normal tissues is limited. Uterine endometrium is a dynamic tissue undergoing cyclical shedding and reconstitution lined by a gland-forming epithelium. Whole genome sequencing of normal endometrial glands showed that most are clonal cell populations derived from a recent common ancestor, with mutation burdens differing from other normal cell types and many fold lower than endometrial cancers. Mutational signatures found ubiquitously account for most mutations. Many, in some women all, endometrial glands are colonised by cell clones carrying driver mutations in cancer genes, often with multiple drivers. Total and driver mutation burdens increase with age, but are also influenced by other factors, including body mass index and parity, and clones with drivers often originate during early decades of life. The somatic mutational landscapes of normal cells differ between cell types and are revealing the procession of neoplastic change leading to cancer.

  Dataset EGAD00001004547

• Multi-Ethnic Study of Atherosclerosis (MESA) Cohort

  MESA The Multi-Ethnic Study of Atherosclerosis (MESA) is a study of the characteristics of subclinical cardiovascular disease (disease detected non-invasively before it has produced clinical signs and symptoms) and the risk factors that predict progression to clinically overt cardiovascular disease or progression of the subclinical disease. MESA researchers study a diverse, population-based sample of 6,814 asymptomatic men and women aged 45-84. Thirty-eight percent of the recruited participants are white, 28 percent African-American, 22 percent Hispanic, and 12 percent Asian, predominantly of Chinese descent. Participants were recruited from six field centers across the United States: Wake Forest University, Columbia University, Johns Hopkins University, University of Minnesota, Northwestern University and University of California - Los Angeles. Each participant received an extensive physical exam to determine coronary calcification, ventricular mass and function, flow-mediated endothelial vasodilation, carotid intimal-medial wall thickness and presence of echogenic lucencies in the carotid artery, lower extremity vascular insufficiency, arterial wave forms, electrocardiographic (ECG) measures, standard coronary risk factors, sociodemographic factors, lifestyle factors, and psychosocial factors. Selected repetition of subclinical disease measures and risk factors at follow-up visits allows study of the progression of disease. Blood samples have been assayed for putative biochemical risk factors and stored for case-control studies. DNA has been extracted and lymphocytes cryopreserved (for possible immortalization) for study of candidate genes and possibly, genome-wide scanning, expression, and other genetic techniques. Participants are being followed for identification and characterization of cardiovascular disease events, including acute myocardial infarction and other forms of coronary heart disease (CHD), stroke, and congestive heart failure; for cardiovascular disease interventions; and for mortality. In addition to the six Field Centers, MESA involves a Coordinating Center, a Central Laboratory, and Central Reading Centers for Computed Tomography (CT), Magnetic Resonance Imaging (MRI), Ultrasound, and Electrocardiography (ECG). Protocol development, staff training, and pilot testing were performed in the first 18 months of the study. The first examination took place over two years, from July 2000 - July 2002. It was followed by four examination periods that were 17-20 months in length. Participants have been contacted every 9 to 12 months throughout the study to assess clinical morbidity and mortality. MESA Family The general goal of the MESA Family Study, an ancillary study to MESA funded by a grant from NHLBI, is to apply modern genetic analysis and genotyping methodologies to delineate the genetic determinants of early atherosclerosis. This is being accomplished by utilizing all the current organizational structures of the Multi-Ethnic Study of Atherosclerosis (MESA) and Genetic Centers at Cedars-Sinai Medical Center and University of Virginia. In the MESA Family Study, the goal is to locate and identify genes contributing to the genetic risk for cardiovascular disease (CVD), by looking at the early changes of atherosclerosis within families (mainly siblings). 2128 individuals from 594 families, yielding 3,026 sibpairs divided between African Americans and Hispanic-Americans, were recruited by utilizing the existing framework of MESA. MESA Family studied siblings of index subjects from the MESA study and from new sibpair families (with the same demographic characteristics) and is determining the extent of genetic contribution to the variation in coronary calcium (obtained via CT Scan) and carotid artery wall thickness (B-mode ultrasound) in the two largest non-majority U.S. populations. In a small proportion of subjects, parents of MESA index subjects participating in MESA Family were studied but only to have blood drawn for genotyping. The MESA Family cohort was recruited from the six MESA Field Centers. MESA Family participants underwent the same examination as MESA participants during May 2004 - May 2007. DNA was extracted and lymphocytes immortalized for study of candidate genes, genome-wide linkage scanning, and analyzed for linkage with these subclinical cardiovascular traits. While linkage analysis is the primary approach being used, an additional aspect of the MESA Family Study takes advantage of the existing MESA study population for testing a variety of candidate genes for association with the same subclinical traits. Genotyping and data analysis will occur throughout the study. MESA Air The general goal of the Multi-Ethnic Study of Atherosclerosis and Air Pollution (&#39;MESA Air&#39;) is to prospectively examine the relation between an individual level assessment of long-term ambient air pollution exposures (including PM2.5 and the progression of subclinical cardiovascular disease in a multi-city, multi-ethnic cohort. MESA Air will also prospectively examine the relationship between an individual level assessment of long-term ambient air pollution exposures and the incidence of cardiovascular disease, including myocardial infarction and cardiovascular death. MESA AIR is funded by a grant from the United States Environmental Protection Agency to the University of Washington and subcontracts from the UW to other participating institutions. MESA Air will assess if ambient air pollution is associated with changes over time in subclinical measures of atherosclerosis and plasma markers of inflammation, oxidative damage, and endothelial activation in a longitudinal data model, adjusting for age, race/ethnicity, socioeconomic status, and specific cardiovascular risk factors (such as diabetes, hypertension, smoking, and diet). The study will similarly assess if the incidence of cardiovascular events is associated with long-term exposure to ambient air pollution, using a proportional hazards model. The study includes refinement of statistical tools, and explores joint/independent effects of acute and long-term pollutant exposure in the occurrence of cardiovascular disease. The MESA Air study is built on the foundation of the ongoing MESA study. The parent MESA Study cohort is located in six geographic areas (&#39;Field Centers&#39;) that capture tremendous exposure heterogeneity, comparable to or greater than the variability in locations of prior U.S. cohort studies. In addition to the six Field Centers, the study involves a Coordinating Center, a Central Laboratory, and Reading Centers for Computed Tomography (CT), ultrasound and air pollution data. The cohort for the MESA Air study currently includes 6226 subjects: 5479 enrolled in the parent MESA study; 257 recruited specifically for this study, and 490 recruited from the MESA Family study. The entire MESA Air cohort will be followed over a 10-year project period for the occurrence of cardiovascular disease events. On two occasions over the ten-year study period, 3600 subjects from the MESA Air cohort, residing in nine locales, will undergo computed tomography scanning to assess presence and extent of coronary artery calcification (CAC), and ultrasound of the carotid artery to determine intima-media thickness (IMT). We will also repeatedly assess plasma markers of inflammation, oxidative damage, and endothelial function in 720 subjects. MESA Air adds state-of-the-art air pollution exposure assessment information to the MESA cohort study, and introduces new subjects and outcome measures to achieve our aims. The study will assess long-term individual-level exposure to ambient air pollutants for each subject using community-scale monitoring, outdoor spatial variation, subject proximity to pollution sources, pollutants&#39; infiltration efficiency, and personal time-activity information. The exposure models will be validated using detailed monitoring in a subset of subjects. The MESA Cohort is utilized in the following dbGaP substudies. To view genotypes, analysis, expression data, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" box located on the right hand side of this top-level study page phs000209 MESA Cohort. phs000420 MESA SHARe phs000283 MESA CARe phs000403 MESA ESP Heart-GO

  Study phs000209

• Accelerating Medicines Partnership-Systemic Lupus Erythematosus (AMP-RA/SLE)

  This project is analyzing tissue and blood samples from people with rheumatoid arthritis (RA) and lupus to pinpoint genes, proteins, chemical pathways, and networks involved at a single cell level. This type of modular, molecular analysis will allow comparisons across the diseases and will provide insights into key aspects of the disease process. The project will identify differences between those RA patients who respond to therapies and those who do not, as well as provide a better systems level understanding of disease mechanisms in both RA and lupus. This knowledge is essential for the development of targeted therapies and for the application of existing and future therapies to appropriate patient populations. Additional datasets can be accessed through ImmPort (http://www.immport.org/immport-open/public/home/studySearch), accession: SDY997

  Study phs001459

• Clinical Cancer Sequencing

  Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. In this study, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a "long tail" of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. Overall, this methodology may inform the widespread implementation of precision cancer medicine.

  Study phs000694

• Genomic sequencing of Pediatric Rhabdomyosarcoma

  Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood accounting for approximately 350 newly diagnosed cases yearly in the United States. With the development of multimodal chemotherapy regimens, relapse-free survival rates have improved to 70-80% in patients with localized disease albeit with significant toxicity. Unfortunately, despite aggressive treatment, patients with metastatic or recurrent disease continue to suffer from high mortality. Further characterization of the genetic events underlying this tumor type is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. In a collaborative effort between the National Cancer Institute, the Children's Oncology Group, and the Broad Institute, we use a combination of whole-genome and whole-exome sequencing to characterize the landscape of somatic alterations in 147 tumor/normal pairs.

  Study phs000720

• Defining and Overcoming Intrinsic T Cell Dysfunction to Enable Pediatric Immunotherapy

  T-cells from 71 children and young adults with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy were analyzed. These T-cells represent the pre-manufacture T-cells that were subsequently used for CAR T manufacture. Bulk RNA-Seq was performed on sorted T-cell subsets for all patients, in addition to CITE-Seq and single-cell ATAC-Seq on a subset of 6 patients. The primary clinical outcome was duration of B-cell aplasia, a surrogate measure of functional CAR T-cell persistence. From these data, molecular signatures associated with long and short-term CAR T-cell persistence were identified. This data submission includes bulk RNA-Seq, CITE-Seq, and single-cell ATAC-Seq data from this study.

  Study phs002323

• The Mood and Methylation Study (MMS)

  The Mood Methylation Study (MMS) is an observational study designed to understand epigenetic mechanisms underlying major depression symptoms (MDD) using a co-twin control design. Twins enrolled in the MMS were monozygotic (MZ) twin pairs discordant on lifetime history of MDD. All twins were members of the Washington State Twin Registry (WSTR), a community-based twin registry consisting of over 10,000 twin pairs. Lifetime and current MDD diagnoses were determined using the Structured Clinical Interview for DSM-IV Research Version (SCID-4-RV). DNA methylation in blood monocytes was measured using the Infinium HumanMethylationEPIC BeadChip. Monocyte gene expression was quantified by paired end RNA-seq (50 PE). Zygosity of the twin pairs included in the MMS was self-reported and confirmed using the polymorphic SNPs included in the DNA methylation array.

  Study phs002858

• Next Generation Sequencing of Stage IV Squamous Cell Lung Cancers Reveals an Association of PI3K Aberrations and Evidence of Clonal Heterogeneity in Patients with Brain Metastases

  Putative oncogenic pathways in squamous cell lung cancer have been recently characterized, although their biologic repercussions in patients is largely unknown. This study sought to discover potential clinical manifestations of major pathways in squamous cell lung cancer, particularly the PI3K pathway. Two key findings emerged: patients with stage IV squamous cell lung cancer whose tumors harbored upstream PI3K aberrations had significantly worse survival and a higher burden of metastatic disease. In addition, brain metastases were significantly more common in these patients than in others. Paired lung primary/brain metastasis genotyping, including RNA sequencing and whole exome sequencing, uncovered a high degree of genetic heterogeneity between lung/brain pairs, and identified potential regulators of the metastatic process to brain.

  Study phs000907

• The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

  This study was the first-known large-scale effort to uncover the mutational spectrum of head and neck cancers. We analyzed whole-exome sequence from 92 tumor-normal pairs and retained 74 of them for significance analysis. The majority exhibited a mutational profile consistent with tobacco exposure; human papilloma virus sequence was detectable in 15% of cases. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), the analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbor mutations in genes (such as NOTCH1, IRF6, TP63) that regulate squamous differentiation, implicating alterations in this process as a major driver of HNSCC carcinogenesis. Altogether, the results suggest that large-scale exome sequencing may illuminate fundamental tumorigenic mechanisms with important therapeutic implications.

  Study phs000370

• Health Professionals Follow-Up Study

  Health Professionals Follow-up Study (HPFS) is a prospective cohort study of men designed to evaluate hypotheses about men&#8217;s health related to diet and lifestyle to the incidence of serious illnesses, such as cancer, heart disease, and other vascular diseases. It consisted of 51,529 U.S. male health professionals who were 40-75 years old at baseline in 1986 and completed a mailed six-page baseline questionnaire. Information on age, height and weight, ancestry, medications, disease history, physical activity, lifestyle factors, and diet were gathered, with follow-up questionnaires sent biennially to update information and record health outcomes with every four years to update their diet. This datafile includes responses to the 2016 questionnaire, which is available at: https://cdn1.sph.harvard.edu/wp-content/uploads/sites/2471/2017/09/16L.pdf

  Study phs002460

• Single Cell Transcriptomic Data from CD4+ T Cells from Children with MIS-C

  Multisystem inflammatory syndrome in children (MIS-C) is a severe complication of SARS-CoV-2 infections in the pediatric population characterized by fever, multi-organ involvement and systemic inflammation. Single-cell RNA sequencing was used to evaluate the transcriptomic signature of CD4+ T cells obtained from the peripheral blood of patients with MIS-C before (n=3) and after (n=5) immunomodulatory treatment, along with pediatric controls (n=4). Compared to controls and treated children with MIS-C, T cells obtained from pre-treatment MIS-C patients upregulated genes associated with activation, such as NF-kB signaling. This single-cell transcriptomic data was used in the context of a larger study entitled, "Notch1-CD22-Dependent Immune Dysregulation in the SARSCoV2-Associated Multisystem Inflammatory Syndrome in Children."

  Study phs003086

• Time Lapse to Cancer-Defining the Transition from Polyp to Cancer

  In the US, CRC incidence has declined with uptake in colonoscopy for early detection and removal of polyps, the precursor lesion, can stop a cancer from developing but in spite of this, CRC remains the second leading cause of cancer death in the United States. One third of people who undergo screening colonoscopy will have adenomatous polyps, but less than 5% of the time are these polyps presumed to go on to develop into cancer. Why does one polyp develop into cancer while another one that looks very similar does not. In this proposal we will identify what molecular genetic changes in the genome, in the mRNA expression and genetic methylation patterns will distinguish a polyp that has already transformed into cancer from one that has not.

  Study phs001384

• Melanoma Brain Metastasis Single-Cell RNA Sequencing Atlas

  Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma, yet our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBM (scRNA-seq n=5; snRNA-seq n=17) and 10 extracranial melanoma metastases (ECM; all snRNA-seq), and matched spatial single-cell transcriptomics (n=16) and T cell receptor (TCR)-seq (n=5). Key observations were validated in matched bulk RNA- and ATAC-seq of isogenic MBM/ECM cell culture models (n=24; including triplicates (labeled as *-A, -B and -C) of 4 MBM- and 4 ECM-derived patient cell lines with 2 matched pairs). This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.

  Study phs002944

• Accelerating Medicines Partnership-Rheumatoid Arthritis (AMP-RA/SLE)

  This project is analyzing tissue and blood samples from people with RA and lupus to pinpoint genes, proteins, chemical pathways, and networks involved at a single cell level. This type of modular, molecular analysis will allow comparisons across the diseases and will provide insights into key aspects of the disease process. The project will identify differences between those RA patients who respond to therapies and those who do not, as well as provide a better systems level understanding of disease mechanisms in both RA and lupus. This knowledge is essential for the development of targeted therapies and for the application of existing and future therapies to appropriate patient populations. Additional datasets can be accessed through ImmPort (http://www.immport.org/immport-open/public/home/studySearch), accession: SDY998, SDY999.

  Study phs001457

• The Finland-United States Investigation of NIDDM Genetics (FUSION) Study

  The Finland-United States Investigation of NIDDM Genetics (FUSION) study is a long-term effort to identify genetic variants that predispose to type 2 diabetes (T2D) or that impact the variability of T2D-related quantitative traits. The initial effort involved linkage analysis of affected-sibling-pair (ASP) families based on over 5,000 individuals living in Finland, and association fine mapping based on these family members and additional T2D cases and controls. Recently we completed a genome-wide association scan on 1161 T2D cases and 1174 normal glucose tolerant (NGT) controls. Individual-level data is available here for the 919 T2D cases and 787 NGT controls who reconsented to the use of their data or are deceased. Version 3 adds individual-level data for additional phenotypic variables.

  Study phs000100

• GWAS for IgA Nephropathy

  IgA nephropathy (IgAN) is a common form of immune-mediated glomerulonephritis characterized by glomerular deposition of IgA-containing immune complexes and manifesting with hematuria, proteinuria, and often kidney failure. This dataset is from a genome-wide association study (GWAS) designed to identify novel genetic risk loci for IgAN. In this dataset, seven cohorts were genotyped by Illumina Multi-Ethnic Global Array, consisting of 3,337 IgAN cases and 2,177 healthy controls of European and East Asian ancestries. Three of the provided cohorts were genotyped by Illumina HumanImmuno Chip, which are composed of 2007 cases of IgAN of European ancestry. These cohorts were used in the GWAS meta-analysis, as described in the manuscript entitled "GWAS defines pathogenic signaling pathways and prioritizes drug targets for IgA nephropathy" (Nature Genetics 2022, in press).

  Study phs000431

• Sensitivity to the Subjective Effects of Amphetamine

  The goal of this study was to identify SNPs associated with subjective, physiological, and behavioral responses to d-amphetamine. The study was double-blind and placebo-controlled. 381 healthy volunteers aged 18-35 years old received oral doses of d-amphetamine (10 and 20 mg) and placebo over the course of three different phenotyping sessions. A subset of subjects received a fourth dose of d-amphetamine (5 mg). Measures of subjective, cardiovascular and behavioral responses were obtained at regular intervals (pre-drug administration and 30, 60, 90, 150, and 180 minutes post-drug administration). The subjective measures included in the study were the Profile of Mood States (POMS), Drug Effects Questionnaire (DEQ) and Addiction Research Center Inventory (ARCI). Tasks included were the Digit Symbol Substitution (DSST) and Stop Task.

  Study phs000832