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• Aggregated panel-seq VCF for initial cohort screened for BoB

  Aggregated VCF file from cancer genes panel seq for the initial (n=500) cohort of solid tumors screened for the Basket of Baskets study

  Dataset EGAD00001008437

• Tumor heterogeneity and acquired drug resistance in FGFR2 fusion-positive cholangiocarcinoma through rapid research autopsy

  Whole exome sequencing was performed on blood and tumor specimens (collected from biopsy or rapid research autopsy) from a patient with FGFR2 fusion positive cholangiocarcinoma.

  Study phs001830

• Autosomal dominant macular dystrophy associated with THRB: identification of new families and variants 

  This study aims to refine the ophthalmologic phenotype, report a novel THRB variant, and investigate the impact of these splicing variants at the protein level.

  Study EGAS50000000861

• ACUITI

  This study assessed the feasibility and performance of a tumor-informed circulating tumor DNA (ctDNA) assay in patients with metastatic HR+/HER2- breast cancer receiving endocrine therapy and CDK4/6 inhibitors.

  Study EGAS50000000962

• Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  This study explores the evolution of tumor and blood immune microenvironment and related mechanisms that shape breast cancer progression, culminating in a heterogeneous lethal cancer.

  Study EGAS00001004956

• Clinical and molecular features of early onset pancreatic cancer

  A retrospective cohort study on the clinical and molecular features of early onset pancreatic cancers (i. e. diagnosed at <50 years old) in comparison with later onset tumors.

  Study EGAS50000000362

• BELLINI clinical trial bulk WES data: cohorts A & B

  WES data of 30 breast cancer primary tumors obtained from 30 unique patients from BELLINI clinical trial (cohorts A & B) and 30 matched blood samples. The data includes pretreatment samples. The included raw WES sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000809

• Trynka_sceQTL_genotypes

  Blood samples were obtained from 119 healthy individuals of British ancestry. Genomic DNA was isolated from a suspension of PBMCs from each individual using a DNA isolation kit (Qiagen). Genotyping was then performed using the Infinium CoreExome-24 (v1.3) chip (Illumina).

  Dataset EGAD00010002291

• Combined genetic and transcriptome analysis of patients with Systemic Lupus Erythematosus (SLE)

  A comprehensive profiling of the genomic architecture of Systemic Lupus Erythematosus (SLE) by combining genetic and transscriptomic analysis by RNA-seq.

  Study EGAS00001003662

• CLL_targeted_exome_sequencing

  Aim to characterise cancer gene landscape in CLL, particularly in cases with mutated POT1 gene. Treatment-naïve CLL cases will be interrogated by targeted exome sequencing using a cancer gene panel.

  Study EGAS00001001963

• Whole_exome_sequencing_of_additional_thyroid_disease_cases

  Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH).

  Study EGAS00001001114

• A novel subset of human CD33+ haematopoietic stem cells characterized at single-cell resolution

  This dataset comprises single-cell RNA sequencing of the human Lin-CD34+38-45RA-90+49f+ phenotype isolated from 2 normal cord donors. Library preparation was performed following a modified CEL-Seq2 protocol.

  Dataset EGAD00001003955

• Sequencing data of primary uveal melanomas and their matched metastases

  We performed targeted DNA sequencing of primary uveal melanomas and their matched metastases from 35 patients, analyzing a total of 124 tissues. Sequencing was performed on an Illumina HiSeq 2500 instrument using a panel of 538 genes commonly involved in cancer. 124 BAM files were generated.

  Dataset EGAD00001004453

• Whole Exome Sequencing of Localized Prostate Cancer Patients

  We performed whole-exome sequencing on localized prostate cancer patients to validate tumor content as part of a single-cell RNA sequencing study of localized prostate cancer patients.

  Study EGAS00001005685

• TB-DAR Whole Genome Sequencing Study

  116 Whole Genome Sequencing (WGS) samples from the TB-DAR study, which consists of a cohort of adult pulmonary tuberculosis patients recruited in Dar es Salaam, Tanzania.

  Study EGAS00001005850

• Dataset with genome-wide array data from Algerian Amazigh (Chaoui and Mozabite) and non-Amazigh individuals

  In this study we perform a genetic characterization of different Amazigh populations in Algeria and assess the impact of recent demography on their genomes.

  Study EGAS00001007235

• Deconvolution of bulk RNA-Seq using single cell RNA-Seq

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Study EGAS00001006723

• Gluten reactive and non-reactive T-cells from treated celiac disease patients on a gluten challenge sampled at day 6

  Gluten reactive T-cells from blood samples from patients undergoing a 3 day gluten challenge. Samples were collected on day 6. Both gluten reactive and non-gluten reactive T-cells were sequenced.

  Dataset EGAD00001006899

• RNA-seq data from a variety of pediatric brain tumors

  RNA-seq (n=52) data from a variety of pediatric brain tumors including ependymoma (PFA, PFB, Ste, spinal), medulloblastoma (G3, G4, SHH), high grade glioma (H3K27 and H3-WT), pilocytic astrocytoma, and more. Raw data provided as FASTQ. Data generated on Illumina HiSeq2500.

  Dataset EGAD00001007915

• Hi-C sequencing from a variety of pediatric brain tumors

  Hi-C (n=72) data from a variety of pediatric brain tumors including ependymoma (PFA, PFB, Ste, spinal), medulloblastoma (G3, G4, SHH), high grade glioma (H3K27 and H3-WT), pilocytic astrocytoma, and more. Raw data provided as FASTQ. Data generated on Illumina HiSeq2500.

  Dataset EGAD00001007914

• WES data of primary tumors and metastasis corresponding to three patients

  Fastq files of WES data. Primary tumor and/or metastasic samples of three chRCC patients. DNA libraries were produced using the SureSelect XT HumanAllExon V5 kit (Agilent Technologies), and sequencing was performed in a HiSeq instrument (Illumina) using a 100-bp paired-end mode.

  Dataset EGAD00001010173

• RNAseq data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors - SA

  The dataset includes fastq files from 2 LCNEC tumors and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.

  Dataset EGAD00001009993

• Genome and transcriptome sequence data from a infantile fibrosarcoma tumor patient

  Genome and transcriptome sequence data from a infantile fibrosarcoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015263

• Genome and transcriptome sequence data from a CNS sarcoma tumor patient

  Genome and transcriptome sequence data from a CNS sarcoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015268

• Genome and transcriptome sequence data from a ocular melanoma tumor patient

  Genome and transcriptome sequence data from a ocular Melanoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015269

• Genomic Translation for ALS Care (GTAC) - WGS

  To look for genetic correlates of disease progression, the GTAC study recruited patients with motor neuron disease from 13 academic medical center clinics and followed them longitudinally for up to 5 years. Participants were regularly assessed for changes in respiratory function, the ALS Functional Rating Scale, and the ALS Cognitive Behavioral Scale. Participants underwent PCR-free whole genome sequencing on the Illumina NovaSeq, as well as repeat-prime PCR assessment of the C9ORF72 repeat expansion. Participants had PBMCs and whole blood RNA banked for future correlative studies.

  Study phs002973

• DNA Methylation-based diagnostic biomarkers for ESCC in Han Chinese population

  DNA methylation-based biomarkers were suggested to be promising for early cancer diagnosis. However, DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC), especially in Chinese Han populations have not been identified and evaluated quantitatively. To identify the candidate DNA-methylation based biomarkers for ESCC diagnosis, we performed the targeted bisulfite sequencing analysis in this study. Based on these 94 pairs of ESCC tumors and adjacent normal tissues, we found out that ADHFE1, EOMES, SALL1 and TFPI2 could be an effective methylation-based assay for ESCC diagnosis.

  Study EGAS00001003158

• Amplicon sequencing of IPC-298 and MelJuso parental cell lines and Belvarafenib resistant IPC-298 colony

  Amplicon seqeuencing of (1) wildtype IPC298 cell line grown for 3-4 weeks with DMSO, amplified for ARAF exon 11 (2) IPC298 cells treated for 3-4 weeks with 10uM belvarafenib, isolated colony 9, amplified for ARAF exon 11 (3) MelJuso cell line grown with DMSO, amplified for ARAF exon 11

  Dataset EGAD00001007061

• NHLBI TOPMed: Boston-Brazil Sickle Cell Disease (SCD) Cohort

  This study involves sequencing of patients with a diagnosis of sickle cell disease from Brazil. No exclusionary criteria were employed and any eligible patients that consented to this study were recruited.

  Study phs001599

• Copy number profile of ctDNA in ovarian cancer patients

  This study analyzes the copy number profiles from circulating tumor DNA (ctDNA) in plasma samples withdrawn from ovarian cancer patients, in a subset of samples from the MITO16A clinical trial.

  Study EGAS00001008226

• Whole genome bisulfite sequencing of prostate cancer samples upon oral pimonidazole administration

  Whole genome bisulfite sequencing was performed using laser-capture of microdissected specimen sections comparing PIMO positive and negative carcinoma areas. A hypoxia related methylation molecular signature was generated.

  Study EGAS50000000069

• GIST Comprehensive Cancer Panel

  DNA Sequencing of 864 genes from KiCS cancer panel. Multiple family members affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene, (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877C>T; p.Arg293*, pR293X).

  Dataset EGAD50000000548

• BipEx-Landen: Bipolar Exome Sequencing

  This research project was a collaboration between the Karolinska Institute and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 5,876 Bipolar case/control samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x.

  Dataset EGAD50000000307

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids. A sequential single-cell cloning approach was adopted to measure the mutation rate in eight tumoroids obtained from five patients. WGS was also performed on their matched normal tissue and on standard tumoroids cultures without any cloning step.

  Dataset EGAD50000000411

• Serum Proteome Profiling Identifies Early Markers of Therapeutic Response to Neoadjuvant Chemotherapy of Breast Cancer

  We performed a proteomic serum profiling of patients with non-metastasized breast cancer (BC) who received neoadjuvant chemotherapy (NACT). Samples were collected at three timepoints during NACT. Furthermore, we compared serum samples of BC patients pre-NACT to a control group of healthy volunteers.

  Dataset EGAD00010002330

• Whole transcriptome sequencing of the dMMR colorectal cancer cohort

  We leveraged the ImmunoID NeXT platform, an Immune-enhanced multiomics platform to profile a cohort of patients with dMMR CRC. This sub-study includes the whole transriptome sequencing data

  Study EGAS50000001742

• Whole exome sequencing of the dMMR colorectal cancer cohort

  We leveraged the ImmunoID NeXT platform, an Immune-enhanced multiomics platform to profile a cohort of patients with dMMR CRC. This sub-study includes the whole exome sequencing data

  Study EGAS50000001744

• GENOMIC INSTABILITY IN MISMATCH REPAIR DEFICIENT COLORECTAL CANCER

  Here we performed whole exome sequencing on a series of 47 mismatch repair (MMR) deficient colorectal cancers (CRC) in order to identified key events in tumoral initiation and progression

  Study EGAS00001002477

• Human T-bet governs innate and innate-like adaptive IFN-g immunity against mycobacteria.

  We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. PBMCs from the patient was analyzed with scRNA-seq.

  Study EGAS00001004504

• Clonal_human_oesophagus_punches

  We wish we perform whole genome sequencing on known clonal libraries of human oesophagus to provide a detailed investigation into differences in mutational burden, copy number and mutational signatures both within and between individuals.

  Study EGAS00001007696

• Whole genome sequencing of patient IPSCs and tumors (organoids)

  This dataset contains whole genome sequencing data of a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) . This dataset further contains whole genome sequencing data of two tumors showing CNLOH. Tumors were isolated from organoids grown using the patient IPS cell line (Patient 1 TSC2+/- iPSCs )

  Dataset EGAD00001006333

• Analyses of RNAseq data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors

  The dataset includes RNA-seq expression R data, RNA-seq gene counts matrix, and RNA-seq gene FPKM matrix from 21 NEN tumors or metastases and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.

  Dataset EGAD00001009994

• Genome and transcriptome sequence data from a neurofibromatosis type 1 (NF1) tumor patient

  Genome and transcriptome sequence data from a neurofibromatosis type 1 (NF1) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015266

• A Randomized Multi-Institutional Phase II Trial of Everolimus as Adjuvant Therapy in Patients with Locally Advanced Squamous Cell Cancer of the Head and Neck

  This genomic study was an analysis of DNA samples from subjects enrolled in a randomized, interventional, parallel assignment trial of everolimus versus placebo in advanced Head and Neck Cancer. Next Generation Sequencing was performed on samples obtained from primary tumors before treatment. The purpose was to evaluate potential associations between intervention, mutations and outcomes.

  Study phs002986

• Inherited genetic predisposition to childhood acute lymphoblastic leukemia investigated using a genome wide association study.

  This series consists of summary data generated from a genome-wide association study (GWAS) investigating inherited genetic risk to childhood acute lymphoblastic leukemia (ALL). The GWAS comprised 784 cases recruited to the Medical Research Council UK ALL-2003 and ALL-97/99 trials and 7,385 controls. The data describe SNPtest association statistics from the case-control analysis.

  Study EGAS00001002809

• Mosaic Chromosomal Aneuploidies Detection in Clinical Samples

  Mosaic chromosomal aneuploidy occurs when only a subset of cells carries an abnormal number of chromosomes. Mosaic aneuploidy has been reported in multiple types of diseases. Here we have developed a new sequencing-based approach to identify, characterize and quantify mosaic aneuploidy events in human tissue samples. This ongoing study has begun with results from sequencing data from two clinical patients, one with autism spectrum disorder (ASD) and the other with hemihyperplasia (OMIM 235000). We captured ~100,000 common SNPs from the samples to identify the nature of the mosaic aneuploidy events in each of the samples.

  Study phs001557

• Detection of Somatic Mutations In Vitro Aging Cells

  Deep sequencing was performed to analyze the prevalence of somatic mutations during in vitro cell aging. Primary dermal fibroblasts from healthy subjects of young and advanced age, from Hutchinson-Gilford progeria syndrome, and from Xeroderma Pigmentosum complementation group A (XPA) and C (XPC), were first restricted in number and then expanded in vitro. DNA was obtained from cells pre- and post-expansion and sequenced at high depth, over a cumulative 290 kb target region, including the exons of 44 aging-related genes. Allele frequencies of 58 somatic mutations differed between the pre- and post-cell culture expansion passages.

  Study phs001867

• Systematic Analysis of Transcription Program Regulation by Transcription Factor EB (TFEB)

  In order to evaluate the effects of TFEB, a master regulator of autophagy and lysosomal biogenesis, CRISPR-Cas9 TFEB knock out cell lines were generated and reconstituted with wild-type TFEB (TFEB-WT), a vector control (TFEB-KO) or TFEB engineered to remain localized to the cytosol (TFEB-cyto) or to the nucleus (TFEB-nuc). RNA sequencing was performed on engineered cell lines at steady-state or following exogenous stimulation with autophagy inducer (Torin1 or Salmonella bacterial infection). Comparative analyses were performed to identify TFEB-dependent transcriptional response to subcellular localization at steady-state or to exogenous stimuli.

  Study phs002099

• Singapore Gastric Cancer Consortium GeoMx DSP tissue microarray (SGCC TMA) cohort

  Gastric cancer (GC) remains a significant global health challenge due to its high heterogeneity, with intratumoral heterogeneity (ITH) posing a major obstacle to effective patient outcomes. In this study, utilizing GeoMx Digital Spatial Profiler (DSP) technology, we specifically investigated ITH within GC patients by comparing tumor core regions to tumor edge regions. Our findings indicate that tumor edge regions exhibit more advanced tumor activity, akin to the G2-like progressed state, compared to tumor core regions. The findings confirm the spatial locations of G2 RNA-ITH subregions and support the conclusions drawn from the discovery cohort.

  Study EGAS50000000640

• Oncogene activated human breast luminal progenitors contribute basally located myoepithelial cells

  Basal-like breast cancer originates in luminal progenitors, frequently with an altered PI3K pathway, and focally in close association with genetically altered myoepithelial cells at the site of tumor initiation. The exact trajectory behind this bi-lineage phenomenon remains poorly understood. Here we used a breast cancer relevant transduction protocol including hTERT, shp16, shp53, and PIK3CA(H1047R) to immortalize FACS isolated luminal cells, and we identified a candidate multipotent progenitor. We found that the apparent luminal phenotype of these oncogene transduced progenitors was metastable giving rise to basal-like cells dependent on culture conditions.

  Study EGAS50000000505