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• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. scRNAseq (BAM files) 38 Barrett's and normal samples

  Dataset EGAD00001005438

• He et al. WES data

  This dataset are the bam files of WES data from the paper by He et al.

  Dataset EGAD00001007134

• Dataset-linking-WGS-samples-in-ega-box-81-via-README-for-study-EGAS00001002923

  This dataset contains 318 Tumor and Control WGS files submitted in another EGA box for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007861

• SJCRH Patient-derived orthotopic xenografts of pediatric brain tumors

  Primary patient pediatric brain tumors from patients treated at SJCRH were implanted and amplified only in the brain of immunocompromised mice without tissue culture steps and referred as patient-derived orthotopic xenografts (Smith et al, Acta Neuropathologica, 2020).

  Study EGAS00001005533

• Sequencing data for oesophageal and related samples - Linossi et al

  Data supporting: "Utility of ctDNA assessment after six weeks of immunotherapy to predict radiological response in advanced oesophageal cancer" Linossi et al

  Dataset EGAD00001015434

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples

  Dataset EGAD00001010074

• Developmental Mechanisms of Human Congenital Heart Disease in Subjects with 22q11.2 Deletion Syndrome (DiGeorge Syndrome/Velocardiofacial Syndrome)

  The study is designed to identify genetic modifiers of cardiovascular defects in subjects with 22q11.2 deletion syndrome (22q11.2DS), also known as DiGeorge syndrome or velo-cardio-facial syndrome. Affymetrix 6.0 arrays were processed on 1,480 subjects with known cardiovascular anomalies or with normal structures, all with 22q11.2DS. One sample is a duplicate so it was removed. There are 1,472 samples total of unrelated, de-identified, probands. Over 90% have the same sized 3 million base pair deletion flanked by low copy repeats (LCR22) A and D, while approximately 6% have nested A to B deletions. The rest have other nested deletions, that include a deletion in the vicinity of TBX1 (between LCR22 A and B). A subset of the data was used to identify copy number variations serving as modifiers. Some data were previously published by Dr. Emanuel's team at Children's Hospital of Philadelphia in PA, USA (PMID:26742502; PMID:4896312; PMID:25892112; PMID:4570279). The de-identified DNA data from unrelated subjects come from multiple research sites in the US and Europe as part of the International 22q11.2 Consortium and the International 22q11.2 Brain and Behavior Consortium.

  Study phs001339

• Molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation (N2M2/NOA-20 phase I/IIa umbrella trial)

  Background: Patients with glioblastoma without MGMT promoter hypermethylation are unlikely to benefit from temozolomide (TMZ). Trials aiming at replacing TMZ with targeted agents in not molecularly selected patient populations have failed. Methods: This phase I/IIa umbrella trial aimed at showing safety, feasibility, and preliminary efficacy of targeted compounds in addition to standard radiotherapy initiated within 42 days postoperatively. Molecular diagnostics and bioinformatic evaluation are performed within 28 days after surgery. Stratification for treatment takes place in five subtrials, including alectinib, idasanutlin, palbociclib, vismogedib and temsirolimus, according to the best matching molecular alteration. Patients without matching alterations are randomized between subtrials without strong biomarkers using atezolizumab and asunercept and TMZ as standard of care. Primary objective of the phase I parts of the trial was dose finding or dose validation. In the phase IIa trials, centrally determined progression-free survival at six months (PFS-6) is used as endpoint for efficacy with interim analyses for futility (H0: p=0.231). Results: From May 2018 through July 2022, 301 patients were enrolled and 228 treated in 13 German NOA sites. The alectinib and vismodegib subtrials were closed since no molecularly matching patients were accrued; the idasanutlin subtrial was closed prior to the optimal dose at nine patients at discretion of the company providing the drug. The TMZ subtrial showed a PFS-6 of 18.52% (10/54 patients) (p=0.831) and a median overall survival (OS) of 12.1 months. Asunercept: PFS-6 of 15.4% (4/26) (p=0.8825) and OS of 12.8 months. Atezolizumab: PFS-6 of 21.4% (9/42) (p=0.660) and OS of 11.7 months. Palbociclib with patients demonstrating CDK4 amplification or CDKN2A/B codeletion: PFS-6 of 24.4% (10/41) (p=0.4823) and OS of 12.6 months. Temsirolimus with patients demonstrating mTOR activation: PFS-6 of 39.1% (18/46) (p=0.0109) and OS of 15.4 months. The regimen-limiting toxicity (RLT)-rate is 34.8%, which is insignificantly above the predefined unacceptable rate for RLTs of 30%. Most RLTs had severity grade 3, one RLT had severity grade 4. No RLTs resulted in death. Conclusions: N2M2 allows for elaborate molecular testing being integrated into the treatment decision and efficient determination of treatment activity for patients with newly diagnosed glioblastoma. There is clinical activity of temsirolimus in patients with tumors harboring an activated mTOR pathway although this is not positively prognostic without mTOR inhibition; there is no clinical activity for asunercept and atezolizumab in not molecularly selected patients and also palbociclib in molecularly selected patients.

  Study EGAS00001008033

• Committee of human data related to the manuscript by Germano et al. Ms2016-04-06029

  Dac EGAC00001000750

• Single-cell RNA-seq of immune cells from Melanoma tumors (Li et al, 2018) - DAC

  Dac EGAC00001001089

• Data access policy for PDTX Breast Cancer RNA-seq data from Ros et al (2020)

  Dac EGAC00001001620

• KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons (iPSC) Garcia-Swinburn et al.

  Dac EGAC50000000805

• The Diabetes Heart Study (DHS)

  The Diabetes Heart Study is a family based study enriched for type 2 diabetes (T2D). The cohort included 1220 self-reported European Americans from 475 families (Bowden et al 2010 Review of Diabetic Studies 7:188-201: PMID: 21409311; Bowden et al 2008 Annals of Human Genetics 72:598-601 PMID: 18460048) and included siblings concordant for T2D; where possible unaffected siblings were also recruited. The cohort was recruited between 1998 and 2006. Participants were extensively phenotyped for measures of subclinical CVD and other known CVD risk factors. Primary outcomes were quantified burden of vascular calcified plaque in the coronary artery, carotid artery and abdominal aorta all determined from non-contrast computed tomography scans.

  Study phs001012

• Genome-Wide Association Study of Lung Cancer Susceptibility in Never-Smoking Women in Asia

  To learn about the etiology of lung cancer among never-smoking women in Asia, we formed the Female Lung Cancer Consortium in Asia (FLCCA), which includes studies of lung cancer in Eastern Asia and conducted a GWAS. We analyzed a total of 5510 lung cancer cases and 4544 controls and identified 3 novel loci (Lan et al., 2012). Of these study subjects, 4922 lung cancer cases and 3959 controls are available for posting. Lan et al.., Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet. 2012 Dec;44(12):1330-5. doi: 10.1038/ng.2456. Epub 2012 Nov 11. PubMed PMID: 23143601.

  Study phs000716

• 1 Intratumoral genetic heterogeneity and clonal evolution following neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal tumors.

  Purpose: Neoadjuvant chemoradiotherapy (nCRT) is the standard treatment forpatients with locally advanced rectal cancer. However, little is known about the effect of nCRT in the mutational landscape and intratumoral genetic heterogeneity (ITGH) of rectal tumors. Moreover, response to nCRT vary substantially among patients and the genetic determinants of treatment response are not fully understood. Here, we sought to determine the impact of nCRT in the mutational landscape and ITGH of rectal tumors and to identify putative drivers of therapeutic resistance. Patients and Methods: We analyzed whole-exome sequencing (WES) and clinical data from 79 primary non-treated rectal cancers obtained from The Cancer Genome Atlas (TCGA). We also compared the mutational landscape of a matched set of peripheral blood cells, irradiated tumor-adjacent colonic mucosa and pre and post-treatment tumor samples to determine the iatrogenic effects of nCRT and its impact in tissue genetic heterogeneity. Finally, we performed WES of 7 matched pre and post-treatment tumor samples to examine how nCRT affects the clonal architecture of rectal tumors. Results: We show that rectal tumors exhibit remarkable ITGH, which increases with disease progression. We also show that nCRT, per se, does not introduce novel somatic mutations, nor alters the clonal architecture of the irradiated colonic mucosa. Instead, we show that it acts as a potent selective pressure, favoring the expansion of tumor cell subpopulations more prone to resist therapy and increasing ITGH in the residual tumor. Conclusion: Our results reveal the highly heterogeneous and dynamic clonal architecture of rectal tumors undergoing nCRT. Our results also uncover putative genetic determinants of response to nCRT and a possible role for ITGH in predicting treatment outcome.

  Study EGAS00001003250

• Mapping Genes for Mammographic Density

  We recruited 1,521 women from the Old Order Amish (OOA) population of Lancaster County, Pennsylvania, with the primary goal of identifying genetic factors that influence mammographic density. All women were between the ages of 40 and 88 years, with a mean of 54 years. Additional study design details, including eligibility criteria, are described elsewhere (Douglas et al., 2008). The present-day OOA of Lancaster County are the descendants of approximately 550 individuals from central Western Europe who immigrated to the U.S. in the early eighteenth century. All living individuals derive from a single, 14-generation pedigree (Lee et al., 2010). Although the OOA are a genetically closed founder population, allele frequencies and LD profiles are remarkably similar between the OOA and U.S. participants in the International HapMap project (HapMap CEU) for common SNPs (MAF>/=5%) (Van Hout et al., 2010). We recently completed genome-wide linkage and association analyses of mammographic density, including dense and non-dense areas of the breast and the ratio of dense to total area of the breast. Summary-level data from our GWAS are available here and through the Marker of DEnsity (MODE) Consortium.

  Study phs000604

• Data access policy for PDTX Breast Cancer data from Bruna et al (2016), Cell.

  Dac EGAC00001000540

• STM4 - Mouliere et al, 2018. Enhanced detection of circulating tumor DNA by fragment size analysis

  Study EGAS00001004418

• Decade-Long Leukemia Remissions with Persistence of CD4+ CAR T-Cells

  Two patients with chronic lymphocytic leukemia (CLL) were treated with CD19 targeted CAR T therapy and followed over several years. Peripheral blood from both patients at multiple time points was collected, and 5' CITE-Seq with TCR profiling was performed on sorted CD3+CAR+ T cells at multiple time points. Here, we deposit the raw sequencing data for these single-cell experiments. Processed and de-identified data (e.g. cellranger output, Seurat objects) have been made available on a separate public data repository.

  Study phs002931

• OV04 chemo prediction

  Predicting resistance to chemotherapy using chromosomal instability signatures Joe Sneath Thompson1,2,*, Laura Madrid2,*, Barbara Hernando1,*, Carolin M. Sauer3, Maria Vias3, Maria Escobar-Rey1,2, Wing-Kit Leung2,3, Diego Garcia-Lopez2, Jamie Huckstep3, Magdalena Sekowska3, Karen Hosking4,5, Mercedes Jimenez-Linan5,6, Marika A. V. Reinius3,5,6, Abhipsa Roy2, Omar Abdulle2, Justina Pangonyte3, Harry Dobson2, Amy Cullen2,3, Dilrini De Silva2, David Gómez-Sánchez1,7, Marina Torres1, Ángel Fernández-Sanromán1, Deborah Sanders3, Filipe Correia Martins3,5,6, Ionut-Gabriel Funingana3,4,5, Giovanni Codacci-Pisanelli3,4,8, Miguel Quintela-Fandino1, Florian Markowetz2,3,4, Jason Yip2, James D. Brenton2,3,4,5,6, Anna M. Piskorz#,2,3, Geoff Macintyre#,1,2 1 Spanish National Cancer Research Centre (CNIO), Madrid, Spain 2 Tailor Bio Ltd, Cambridge, UK 3 Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK 4 Department of Oncology, University of Cambridge, Cambridge, UK 5 Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK 6 Cancer Research UK Major Centre - Cambridge, University of Cambridge, Cambridge, UK 7 H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain 8 University of Rome "la Sapienza", Rome, Italy

  Dac EGAC50000000612

• Filtered variants including SLC12A2 in patients with hearing loss

  Hereditary hearing loss is challenging to diagnose because of the heterogeneity of the causative genes. Further, some genes involved in hereditary hearing loss have yet to be identified. Using whole-exome analysis of three families with congenital, severe-to-profound hearing loss, we identified a missense variant of SLC12A2 in five affected members of one family showing a dominant inheritance mode, along with de novo splice-site and missense variants of SLC12A2 in two sporadic cases, as promising candidates associated with hearing loss.

  Study JGAS000379

• Next generation sequencing of sporadic schwannomatosis samples

  Schwannomatosis (MIM #162091) is characterized by the development of multiple schwannomas without vestibular nerve involvement (which is a characteristic of neurofibromatosis type 2 - NF2). In an effort to detect novel genetic alterations predisposing to schwannomatosis, we sequenced eight tumor-blood DNA pairs from de novo schwannomatosis patients. The results of our study are present in the paper "Whole exome sequencing reveals that the majority of schwannomatosis cases remain unexplained after excluding SMARCB1 and LZTR1 germline variants" published in Acta Neuropathologica (PMID:25008767)

  Study EGAS00001000767

• Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers

  Thyroid cancer is the most common endocrine malignancy. This dataset encompasses two types of thyroid cancer : anaplastic which is the most de-differentiated and aggressive one, and papillary which is the most common one. We profiled 14 patients, including 10 papillary and 4 anaplastic thyroid carcinomas, using both single nuclei RNA sequencing and spatial transcriptomics to link single cell resolution RNA sequencing with tissue morphology and better understand inter and intratumoral thyroid cancer heterogeneity.

  Study EGAS00001007574

• Hyperdiploidy impairs fetal hematopoietic progenitor cell fitness and differentiation enabling persistence of rare preleukemic aneuploid clones

  Cells previously cryopreserved in FBS-10%DMSO were thawed and resuspended in 1mL of cold lysis buffer (10 mM Tris-HCl pH 7.4, 154 mM NaCl, 0.2% BSA, 0.1% NP-40, 1 mM CaCl₂, 0.5 mM MgCl₂ in ultra-pure water) to lyse the cell membrane and release intact nuclei. The nuclei were stained with propidium iodide (10 µg/mL) and Hoechst 33258 (10µg/mL) to facilitate sorting based on cell cycle state and viability. Single nuclei from 48 cells per sample were isolated into 96-well plates containing 5µL of freeze buffer (1X PBS, 7.5% DMSO, and 40% ProFreeze freezing medium (Lonza)) using a MoFlo Astrios cell sorter (Beckman Coulter) at the Flow Cytometry Unit of the University Medical Center Groningen (UMCG), Netherlands. The plates were centrifuged at 500 g and stored at -80°C until library preparation. Single-nuclei libraries were prepared using a Bravo Automated Liquid Handling Platform (Agilent Technologies). Nuclei were lysed, and DNA was labelled with unique 10 bp dual barcodes and amplified as previously described. Sequencing was performed on an Illumina NextSeq 2000 platform with 77bp single end reads. The generated data were subsequently demultiplexed using sample-specific barcodes and converted to FASTQ files with bcl2fastq. Sequencing reads were aligned to the GRCh38/hg38 human reference genome using Bowtie2 (v2.2.4), and duplicate reads were marked with BamUtil (v1.0.3). Single-cell karyotypes were determined by performing copy number analysis using AneuFinder (v4.3.3) (https://github.com/ataudt/aneufinder). The analysis included GC-content correction and blacklisting of artifact regions identified from euploid controls. Copy number calling was conducted with the dnacopy and edivisive algorithms, employing a bin size of 1 Mb and a step size of 500 Kb. Libraries with an average of fewer than 10 reads per chromosome copy per bin or less than 95% concordance between the two algorithms were excluded from analysis. Whole-chromosome aneuploidies were identified when over 95% of bins exhibited deviation from the disomic state. Aneuploidy scores were calculated as weighted averages of absolute copy number deviations from the euploid state. 

  Dataset EGAD50000002314

• Single cell RNAseq of stenotic, inflamed and non-inflamed transmural lesions from patients with Crohn's disease

  This dataset contains a gene-cell matrix derived from single-cell RNA sequencing (scRNA-seq) data of ileal tissue from Crohn's disease (CD) patients and colorectal cancer (CRC) patients. It includes: Crohn's Disease Patients: A trio of transmural lesions (stenotic, inflamed, and non-inflamed) from each patient. Colorectal Cancer Patients: Unaffected ileal tissue used as external non-inflamed control. Cell Level Metadata: The dataset includes relevant cell-level metadata such as cell type annotations used in the study. Experimental Details: Platform: 10x Genomics Chromium Single Cell 3' GEX Sequencing: Illumina NovaSeq Processing: Data processed with Cell Ranger software. Resulting count matrices were merged for downstream analysis, including integration and dimensionality reduction. Dataset Composition: Crohn's Disease Patients: 10 patients with 3 samples each (non-inflamed, inflamed, stenotic), totaling 30 samples. Colorectal Cancer Patients: 5 patients with 1 sample each of unaffected tissue, totaling 5 samples. Data Provided: Merged Raw Count Matrix: The final merged raw count matrix used for downstream analysis. Cell Metadata File: Contains details of sample, tissue, and patient for each cell in the count matrix. Barcodes File: Indicate each cell barcode which also encodes the sample, tissue, and patient details for each cell. CD.S_Inf: Stenotic Corhn's disease inflamed samples CD.S_Sten: Stenotic CD patient stenosis sample CD.S_Prox: Stenotic CD Patient - proximal non-inflamed sample CC.C_Prox: CRC Patient proximal unaffected sample eg: A barcode 'CC.C_1_Prox_AAGTCGTAGACCCTTA' indicates CRC Patient unaffected proximal sampe from CRC Patient no.1 and the nucleic acid sequence indicate a unique cell from this sample. Total Samples: Crohn's Disease (CD) Patients: 30 samples Colorectal Cancer (CRC) Patients: 5 samples Patient_no Sample Sample_type 1 CC.C_1 CC.C_1_Prox CC.C_Prox 2 CD.S_1 CD.S_1_Prox CD.S_Prox 3 CD.S_1 CD.S_1_Infl CD.S_Infl 4 CD.S_1 CD.S_1_Sten CD.S_Sten 5 CC.C_2 CC.C_2_Prox CC.C_Prox 6 CD.S_2 CD.S_2_Prox CD.S_Prox 7 CD.S_2 CD.S_2_Infl CD.S_Infl 8 CD.S_2 CD.S_2_Sten CD.S_Sten 9 CC.C_3 CC.C_3_Prox CC.C_Prox 10 CC.C_4 CC.C_4_Prox CC.C_Prox 11 CD.S_3 CD.S_3_Prox CD.S_Prox 12 CD.S_3 CD.S_3_Infl CD.S_Infl 13 CD.S_3 CD.S_3_Sten CD.S_Sten 14 CD.S_4 CD.S_4_Prox CD.S_Prox 15 CD.S_4 CD.S_4_Infl CD.S_Infl 16 CD.S_4 CD.S_4_Sten CD.S_Sten 17 CC.C_5 CC.C_5_Prox CC.C_Prox 18 CD.S_5 CD.S_5_Prox CD.S_Prox 19 CD.S_5 CD.S_5_Infl CD.S_Infl 20 CD.S_5 CD.S_5_Sten CD.S_Sten 21 CD.S_6 CD.S_6_Prox CD.S_Prox 22 CD.S_6 CD.S_6_Infl CD.S_Infl 23 CD.S_6 CD.S_6_Sten CD.S_Sten 24 CD.S_7 CD.S_7_Prox CD.S_Prox 25 CD.S_7 CD.S_7_Infl CD.S_Infl 26 CD.S_7 CD.S_7_Sten CD.S_Sten 27 CD.S_8 CD.S_8_Prox CD.S_Prox 28 CD.S_8 CD.S_8_Infl CD.S_Infl 29 CD.S_8 CD.S_8_Sten CD.S_Sten 30 CD.S_9 CD.S_9_Prox CD.S_Prox 31 CD.S_9 CD.S_9_Infl CD.S_Infl 32 CD.S_9 CD.S_9_Sten CD.S_Sten 33 CD.S_10 CD.S_10_Prox CD.S_Prox 34 CD.S_10 CD.S_10_Infl CD.S_Infl 35 CD.S_10 CD.S_10_Sten CD.S_Sten

  Dataset EGAD50000000559

• The Contribution of De Novo Coding Mutations to Meningomyelocele

  Meningomyelocele (MM) is considered a genetically complex disease resulting from the failure of the neural tube to close; a neural tube defect (NTD). Patients display neuromotor disability and frequent hydrocephalus requiring ventricular shunting. A few genes have been proposed to contribute to disease susceptibility, but most risk remains unexplained. 851 MM trios were recruited and we found 187 likely gene disrupting or damaging missense de novo mutations (DNMs) that are estimated to contribute to disease risk. These DNMs collectively define networks including actin cytoskeleton and microtubule-based processes, axon guidance, and histone modification. Gene validation demonstrates partial or complete loss of function, impaired signaling and defective neural tube closure in Xenopus embryos. Our results suggest DNMs make key contributions to MM risk, and highlight critical pathways required for neural tube closure in human embryogenesis. Data for 245 WES trios and 1 quad are available through dbGaP.

  Study phs003746

• Tetralogy of Fallot Exome Trios

  Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome.

  Dataset EGAD00001000344

• DAC for study CMMRD–associated high-grade glioma

  This Data Access Committee (DAC) is responsible for de-identified, summarized somatic variant call data derived from paired tumor–blood Whole-exome sequencing of human samples in a glioma research study. Access requests are approved without additional restrictions and are granted solely for health-related research purposes.

  Dac EGAC50000000855

• ICGC PCAWG Dataset: MALY-DE_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: MALY-DE.

  Dataset EGAD00001003560

• ICGC PCAWG Dataset: MALY-DE_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: MALY-DE.

  Dataset EGAD00001003561

• PacBio HiFi sequencing of telobait-captured DNA from 48 patients

  PacBio HiFi sequencing was performed on 48 barcoded patients' genomic DNA after a telobait-capture protocol to enrich for telomeric regions. The sequencing reads of each patient were de-multiplexed and presented as patient-specific PacBio CCS BAM files.

  Dataset EGAD00001008626

• Single-nucleus mRNA-Sequencing of prenatal and postnatal samples from the brain and its border regions

  Single-nucleus mRNA Sequencing of prenatal and postnatal samples from the brain and its border regions. Most samples were multiplexed with several samples run in one 10X reaction. A separate immune cell dataset was combined with published data from Braun et al 2023 and Yang et al 2021 integrated using harmony is included.

  Dataset EGAD50000000044

• Transdisciplinary Studies of Genetic Variation in Colorectal Cancer(CORECT): Axiom GWAS

  This study is part 1 of 2 for Schumacher et al, Nat Commun. 2015 Jul 7;6:7138. Part 1 is the original GWAS data for 9,259 participants on the Affymetrix Axiom platform of the studies listed below in the Inclusion Criteria.

  Study phs001856

• Whole transcriptome sequencing data of 3 histiocytic tumors with CLTC::SYK fusions

  The 3 tumor samples are PMLBM000JFR, PMLBM000JFT, and PMLBM000JFF. All samples are from different patients: Case 9 (PMLBM000JFR), Case 10 (PMLBM000JFT), and Case 12 (PMLBM000JFF) from the article by Kemps et al (Blood 2024 - In production). Methods: Total RNA was isolated and the generated libraries were sequenced on a NovaSeq 6000 (as described in Hehir-Kwa, et al. JCO Precis Oncol 2022). Data files: Provided are .cram and .crai files.

  Dataset EGAD50000000834

• Dataset contains all Single cell RNAseq data of human neurons from the study Bouwen et al Nat Comm 2025

  These documents contain the patch seq data presented in the Bouwen et al Nat Comm 2025. Human brain samples were gathered during surgery, neurons were isolated using patch clamp glass pipette. Isolated cells were processed using Smartseq2 pipeline, and sequenced using an Illumina 2500. Files are formatted in fastq format. There are a total of 12 patient samples, each with 2 replication runs.

  Dataset EGAD50000001979

• WTCCC2 Reading and Mathematics (RM) samples

  A WTCCC2 project genome-wide association study for reading and mathematics ability in 3665 12-year-old individuals from the UK, genotyped on the Affymetrix 6.0 array. Details of the WTCCC2 analysis can be found in Davis et al. [Nat. Commun. 2014 July;5:4204]

  Study EGAS00001000886

• 20210303_EGA_Melanoma Garg et al Nat Commun,  2021

  RNAseq of 55 melanoma tumors that were used as a validation dataset in Garg et al Nat Commun,  2021 Feb 18;12(1):1137. doi: 10.1038/s41467-021-21207-2.

  Dataset EGAD00001007055

• Sequencing data for ICGC / OCCAMS samples - Perner et al (WGS, sWGS, WES, mutREAD)

  Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files

  Dataset EGAD00001006170

• Sequencing data for oesophageal and related samples - Abujudeh et al (WGS, fastSeq)

  Data supporting: "Low-cost and clinically applicable copy number profiling using repeat DNA." Abujudeh et al. DNA WGS (BAM files) DNA fastSeq (fastq files) Tumours, Barrett's, normals.

  Dataset EGAD00001004289

• A novel Patient-Derived 3D Model Recapitulates Mantle Cell Lymphoma Lymph Node Signaling, Immune Profile and in vivo Ibrutinib Responses

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood Mantle Cell Lymphoma patients. These samples were unstimulated after thawing or stimulated during 7 days in culture as described in Araujo-Ayala F et. al.

  Study EGAS00001006964

• Sequencing data for oesophageal and related samples - Ganguli et al (WGS)

  Data supporting: "TBC" Ganguli et al (WGS for 1298 samples)

  Dataset EGAD00001011191

• RNA-Seq FASTQs for Tang F. et al. Chromatin accessibility profiles of castration-resistant prostate cancers reveal novel subtypes and therapeutic vulnerabilities

  This dataset contains the FASTQ files for a portion of the samples in Tang F. et al. “Chromatin accessibility profiles of castration-resistant prostate cancers reveal novel subtypes and therapeutic vulnerabilities” published in Science. It contains 51 samples sequenced with Illumina HiSeq 2500 or HiSeq 4000. The remaining samples can be found at dbGaP: phs000909.v1.p1

  Dataset EGAD00001008598

• ATAC-seq of metastatic prostate tumors

  This dataset includes Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data, in FASTQ format, from 70 metastatic castration-resistant prostate cancer tumor samples from the SU2C/PCF West Coast Dream Team (WCDT) project. The sequencing data is paired-end, 150 bp sequencing data from an Illumina NovaSeq 6000 machine. ATAC-seq libraries were prepared following the protocol described in Buenrostro et al. Nature Methods. 2013 (PMID: 24097267) and Corces et al. Nature Methods. 2017 (PMID: 28846090).

  Dataset EGAD00001009654

• Sequencing data for oesophageal and related samples - Ng, Contino et al (WGS)

  Data supporting "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. WGS (BAM files) 383 oesophageal adenocarcinoma samples 383 normal samples

  Dataset EGAD00001007808

• Sequencing data for oesophageal and related samples - Black et al (WES)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WES OACs/BOs/normals)

  Dataset EGAD00001011188

• Sequencing data for oesophageal and related samples - Mourikis et al (WGS)

  Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. WGS (BAM files) 521 samples

  Dataset EGAD00001004775

• Single-cell TCRalpha-beta sequencing of persisting human intestinal CD8 Trm clonotypes

  Single-cell TCRalpha-beta sequencing of LP CD103+ CD8 T cells from the grafted/native duodenum of two donors (Ptx#1 and Ptx#2) before and 1 year after transplantation. Single cells were sorted into 96-well plates. Paired TCRalpha and TCRbeta sequences were obtained after three nested PCR with multiplexed primers covering all TCRalpha and TCRbeta V genes, as described before (Risnes et al., 2018), and original protocol in (Han et al., 2014).

  Dataset EGAD00001005050

• Sequencing data for oesophageal and related samples - Katz-Summercorn, Jammula et al (WGS)

  Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. WGS (BAM files)

  Dataset EGAD00001006349

• Detection of early seeding of Richter transformation in chronic lymphocytic leukemia

  Dataset accompanying the study entitled “Detection of early seeding of Richter transformation in chronic lymphocytic leukemia” (Nadeu et al. Nature Medicine 2022), which includes the analysis of longitudinal samples of 19 chronic lymphocytic leukemia patients developing Richter transformation.

  Study EGAS00001006327

• HELIUS cohort gut microbiome

  The gut microbiota composition is unique to every individual but is shaped by common factors including diet, lifestyle, medication use, early-life determinants, living environment or genetics. Most of these factors may be influenced by ethnicity. This study explored variations in fecal microbiota composition in 6048 individuals with different ethnic backgrounds living in the same geographical area (Amsterdam, the Netherlands). The HELIUS data are owned by the Amsterdam University Medical Centers, location AMC in Amsterdam, The Netherlands. To allow sharing of microbiome data collected in HELIUS with (inter)national researchers, 16s rRNA sequence analysis has been stored at the European genome-phenome archive (EGA; accession code EGAD00001004106). This requires that access needs to be granted, also because the HELIUS data are stored with relevant phenotypical variables. Access is granted to all researchers affiliated with an internationally recognized research institution who request to use the HELIUS data within the EGA context, after having signed the data transfer agreement. Any researcher can request the data by submitting a proposal to the HELIUS Executive Board as outlined at http://www.heliusstudy.nl/en/researchers/collaboration, by email: heliuscoordinator at amsterdamumc dot nl. The HELIUS Executive Board will check proposals if they do not conflict with ethical approvals and informed consent forms of the HELIUS study.

  Dataset EGAD00001004106

• HELIUS cohort gut microbiome batch2

  The gut microbiota composition is unique to every individual but is shaped by common factors including diet, lifestyle, medication use, early-life determinants, living environment or genetics. Most of these factors may be influenced by ethnicity. This study explored variations in fecal microbiota composition in 6048 individuals with different ethnic backgrounds living in the same geographical area (Amsterdam, the Netherlands). The HELIUS data are owned by the Amsterdam University Medical Centers, location AMC in Amsterdam, The Netherlands. To allow sharing of microbiome data collected in HELIUS with (inter)national researchers, 16s rRNA sequence analysis has been stored at the European genome-phenome archive (EGA; accession code EGAD00001004106). This requires that access needs to be granted, also because the HELIUS data are stored with relevant phenotypical variables. Access is granted to all researchers affiliated with an internationally recognized research institution who request to use the HELIUS data within the EGA context, after having signed the data transfer agreement. Any researcher can request the data by submitting a proposal to the HELIUS Executive Board as outlined at http://www.heliusstudy.nl/en/researchers/collaboration, by email: heliuscoordinator at amsterdamumc dot nl. The HELIUS Executive Board will check proposals if they do not conflict with ethical approvals and informed consent forms of the HELIUS study.

  Dataset EGAD00001009732

• Data for paper Mold, Weissman et al. 'Clonally heritable gene expression imparts a layer of diversity within cell types'

  Dac EGAC50000000102

• DAC - organotypic co-cultures @IEO

  DAC for RNAseq data on patient-derived organotypic models (Battistini et al, CDDis 2024)

  Dac EGAC50000000238

• eQTL-CHiC DAC

  The Data Access Committee for eQTL-CHiC and related data from Ray-Jones et al., 2024.

  Dac EGAC50000000445

• NIDDK IBD Genetics Consortium Repository Exome Chip

  The Illumina Infinium HumanExome+ BeadChip contains putative functional exonic variants selected from individual exome and whole-genome sequences from diverse populations. It includes nonsynonymous variants, splice variants and stop-altering variants. It also includes tags for previous GWAS-identified loci, ancestry informative markers, markers designed for identity by descent analyses, synonymous variants, fingerprint SNPs common to major genotyping platforms, mitochondrial SNPs, chromosome Y SNPs, and HLA tag SNPs. For more information as well as a detailed description of the variant calling and QC procedures, see Li et al. (2016). Li, D., et al. (2016) A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition. Gastroenterology, 151, 1-9. PMID: 27492617.

  Study phs001723

• Resistance to Latent Mycobacterium tuberculosis Infection in South Africa: Immunologic Profiling

  Despite significant exposure to Mycobacterium tuberculosis (Mtb), some humans remain uninfected, as defined by persistently negative immune sensitization tests (tuberculin skin test, TST; interferon gamma release assays, IGRA). To explore mechanisms of natural resistance to Mtb infection, we profiled tissues from highly-exposed Mtb contacts from South Africa. The cohort in this submission were gold miners in South Africa who had worked in the mining industry ≥ 15 years with presumed high Mtb exposure, based on extreme tuberculosis incidence rates and high prevalence of latent Mtb infection (Chihota et al. 2022, PMID: 35302992; Ntshiqa et al. 2021, doi: 10.12688/gatesopenres.13191.1). TST and IGRA testing were performed at enrollment of gold miners, some of whom remained available for repeat testing at 12 months.

  Study phs002746

• Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility

  Effect of biallelic variants in genes of the piRNA pathway on biogenesis of pachytene piRNAs. RNA isolated from snap frozen testicular tissue

  Study EGAS50000000397

• Tel Aviv RNA-seq dataset of of BiPSCs and FiPSCs derived cells

  RNA-seq data obtained from directed differentiation of a subset of FiPSCs and BiPSCs cell lines towards islet-like cells. RNA was collected at two key developmental stages: definitive endoderm (DE) and pancreatic progenitors (PP).

  Dataset EGAD00001003780

• SNF_CyTOFF_20

  Matrix of normal values from 39 marker CyTOF assay performed on baseline BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011146

• TXT_Cytof_15B

  Matrix of normal values from 39 marker CyTOF assay performed on longitudinal BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011143

• Germ Cell and Associated Heme Malignancies Evolve from a Common Shared Precursor

  Germ cell tumors (GCTs) are the most common cancer in men between the ages of 15-40. While most patients are cured, those with disease arising in the mediastinum have distinctly poor outcomes. One in every 17 patients with primary mediastinal non-seminomatous GCTs develop an incurable hematologic malignancy and prior data intriguingly suggests a clonal relationship exists between hematologic malignancies and GCTs in these cases. To date however, the precise clonal relationship between GCTs and the diverse additional somatic malignancies arising in such individuals has not been determined. Here, we traced the clonal evolution and characterized the genetic features of each neoplasm from a cohort of fifteen patients with GCTs and associated hematologic malignancies. We discovered that GCTs and hematologic malignancies developing in such individuals evolved from a common shared precursor, nearly all of which harbored allelically imbalanced TP53 and/or RAS pathway mutations. Hematologic malignancies arising in this setting genetically resembled mediastinal GCTs rather than de novo myeloid neoplasms. Our findings argue that this scenario represents a unique clinical syndrome, distinct from de novo GCTs or hematologic malignancies, initiated by an ancestral precursor which gives rise to the parallel evolution of GCTs and blood cancers in these patients. Reprinted from PMID: 32897884, with permission from JCI.

  Study phs002231

• The_Genomic_Advances_in_Sepsis__GAinS__RNA_seq

  Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. This cohort comprises a subset of patients enrolled in the Genomic Advances in Sepsis (GAinS) study, an established biobank of adult sepsis patients. Patients with sepsis due to community acquired pneumonia or faecal peritonitis were recruited from 34 hospitals across the UK from 2005-2018, with samples for functional genomics and detailed clinical information collected on the first, third and/or fifth day following ICU admission. RNA was extracted from leukocytes isolated at the bedside using LeukoLOCK kits. We have previously identified sepsis response signatures (SRSs), transcriptomic endotypes that are associated with differential early mortality (Davenport et al, Lancet Respir Med, 2016; Burnham et al, AJRCCM, 2017) and response to treatment in a clinical trial (Antcliffe et al, AJRCCM, 2018). We generated RNA sequencing data on 903 samples, including 134 samples repeated from our previously released microarray data. Libraries were prepared using NEB Ultra II Library Prep kits (Illumina) and sequenced on a NovaSeq 6000. Reads were aligned to the reference genome (GRCh38) using STAR and gene counts quantified using featureCounts (annotation Ensembl v99). Counts were TMM-normalised and log-transformed. Following QC, processed data were available on 864 samples from 667 unique patients.

  Study EGAS00001003772

• Data Access Commitee for Schulte-Schrepping et al., 2020: Severe COVID-19 is marked by a dysregulated myeloid cell compartment

  Dac EGAC00001001684

• subset of DEEP IHEC release 2016 (EGAS00001001937), as used in EGAS00001001656 (bidirectional promotors paper, Fatemeh et al. 2018)

  part of the DEEP project results resulted in the publication of 'Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters', Epigenetics & Chromatin (2018), Fatemeh et al., DOI: 10.1186/s13072-018-0236-7, PMID: 30414612, PMCID: PMC6230222. This dataset contains the subset of DEEP data related to that study.

  Dataset EGAD00001005953

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (WGS)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. WGS (BAM files) 5 Barrett's samples 5 normal oesophageal samples 5 normal gastric cardia samples 5 normal duodenal samples

  Dataset EGAD00001006874

• Sequencing data for oesophageal and related samples - Scott et al (WGS, RNA)

  Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files

  Dataset EGAD00001006738

• Sequencing data for oesophageal and related samples - Xiaodun Li et al (WGS, RNA)

  Data supporting: "Esophageal adenocarcinoma organoid cultures recapitulate human disease heterogeneity and provide a model for clonality studies and precision therapeutics." Li et al. WGS (BAM files) RNAseq (BAM files) Tumours, organoids, normals

  Dataset EGAD00001004007

• Sequencing data for oesophageal and related samples - Alex Frankell et al (WGS)

  Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. WGS (BAM files) 379 matched tumour-normal pairs

  Dataset EGAD00001004417

• The genomic landscape of lung adenocarcinoma in East Asians

  We performed exome sequencing of 210 and transcriptome sequencing of 181 LUADs of Chinese patients. For more details, please see publication "Genomic landscape of lung adenocarcinoma in East Asians" by Chen J. et. al. in Nature Genetics 2020. https://www.nature.com/articles/s41588-019-0569-6.

  Study EGAS00001002941

• Sequencing data for oesophageal and related samples - Black et al (WGS)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS OACs/BOs/normals)

  Dataset EGAD00001011187

• Sequencing data for oesophageal and related samples - Abbas et al (WGS)

  Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (WGS for 1397 samples)

  Dataset EGAD00001011196

• Sequencing data for oesophageal and related samples - Izadi et al (WGS, RNA)

  Data supporting: "Genomic analysis of response to neoadjuvant chemotherapy in esophageal adenocarcinoma" Izadi et al. WGS for tumour and normal samples. RNAseq for tumour samples.

  Dataset EGAD00001007493

• Sequencing data for oesophageal and related samples - Noorani et al (WGS)

  Data supporting: "Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma." Noorani et al. WGS (BAM files) 134 samples for 18 cases Includes primary, lymph-node, distant metastatic, Barrett's and normal samples.

  Dataset EGAD00001005434

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (bulk RNA)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 12 Barrett's samples 12 normal oesophageal samples 11 normal gastric cardia samples

  Dataset EGAD00001006882

• Data Access Commitee for Dietrich and Wendisch et al., SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis (Submitted)

  Dac EGAC00001001884

• Data Access Commitee for Dietrich and Wendisch et al., SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis (Submitted)

  Dac EGAC00001002335

• Research Study into The Molecular Genetics of Hereditary Neuropathies

  Identification of genes implicated in inherited neuropathy through collecting and sequencing multiple generation families with inherited neuropathy. Patients in this study have been evaluated for demyelinating peripheral neuropathy as determined by decreased motor nerve conduction velocities in the sural nerve. Patients have also been screened for mutations in all genes implicated in demyelinating peripheral neuropathy and are expected to have previously unidentified mutations. Exome (WES) sequencing for two patients affected with inherited neuropathy. VCF files with called variants for each de-identified patient have been submitted.

  Study phs001351

• Whole exome sequencing of 184 unrelated subjects with 22q11.2 deletion syndrome (DiGeorge syndrome/velo-cardio-facial syndrome)

  Our goal is to find genetic modifiers of major phenotypes in patients with 22q11.2 deletion syndrome, also known as DiGeorge syndrome or velo-cardio-facial syndrome. Whole exome sequencing was performed as part of a contract to the NHLBI, Resequencing and Genotyping Service. We have obtained cardiac phenotype information from the de-identified subjects enrolled in the study, either by echocardiography report or medical doctor report. All of the subjects have a 3 million base pair 22q11.2 deletion flanked by low copy repeats, LCR22, A-D.

  Study phs000987

• Genetics of Antinuclear Antibodies

  Antinuclear antibodies (ANA) are antibodies that react against self-antigens in the cell. While it has been reported that 12 to 20% of the general population have a positive ANA test, the genetics of ANA positivity is unknown. We performed a genome wide-association study for positive ANA tests among individuals without an ANA related autoimmune disease in the Vanderbilt University Medical Center (VUMC) DNA biobank linked to the de-identified electronic health record (EHR) system. The study is funded by the National Institute of Arthritis and Musculoskeletal and Skin diseases (NIAMS) grant R01AR076516.

  Study phs003189

• Single-Cell Analysis of the Multiple Myeloma Microenvironment after Gamma-Secretase Inhibition and CAR T-Cell Therapy

  We examined the effects of gamma-secretase inhibition (GSI) on the bone marrow microenvironment in multiple myeloma patients before anti-B-cell maturation antigen (BCMA) CAR T-cell therapy. Single-nuclei RNA and ATAC sequencing revealed significant changes in gene expression and chromatin accessibility, especially in monocytes and tumor cells, following exposure to GSI. The findings suggest that GSI influences not only BCMA signaling but also broader cellular interactions within the tumor microenvironment. De-identified sequencing data from the study is available through dbGaP.

  Study phs003741

• Pediatric tumor in a single child of three large nuclear families

  We identify three nuclear families in which a pediatric tumor had been diagnosed in a single child and neither parent had been diagnosed with cancer. These families had 4, 5, and 7 children, respectively. Diagnoses included Wilms tumor, low-grade astrocytoma, and Burkitt’s lymphoma, respectively. We used whole-genome sequencing to profile normal cells from each family member and a linked-read technology for genomic phasing, which enabled us to identify compound-heterozygous and de novo variants in addition to simple-heterozygous and homozygous-alternate variants.

  Study EGAS00001005321

• SEAsia.Oceania.Australia

  the tar archive contains unflitered genotype data from Reich et al AJHG 2011 study in plink format

  Dataset EGAD00010002302

• SolomonIslands.Dataset

  The tar archive contains unflitered genotype data from Pugach et al 2018 in plink format

  Dataset EGAD00010002306

• Knoll et al. 2023, Identification of drug candidates targeting monocyte reprogramming in people living with HIV

  Dac EGAC50000000044

• Cardiac fibroblast DAC

  DAC for reviewing requests to access data on cardiac fibroblasts as described by Aguado-Alvaro et al (Nature Communications, 2025)

  Dac EGAC50000000479

• LOPEZ_2019.vcf.gz

  Genotype data for new samples in Lopez et al 2021

  Dataset EGAD00010002100

• Pipeline study - RNAseq dataset

  Fernandez-Cuesta et al., RNAseq data Pipline

  Dataset EGAD00001000746

• Landscape of AL mutations

  Exome Sequencing to Define the Landscape of Plasma Cells in Systemic Light chain Amyloidosis

  Dataset EGAD00001001861

• Parallel Genomic Alterations of Antigen and Payload Targets Mediate Polyclonal Acquired Clinical Resistance to the Antibody Drug Conjugate Sacituzumab Govitecan

  Sacituzumab Govitecan (SG), a novel antibody drug conjugate (ADC) incorporating the anti-TROP2 antibody hRS7 conjugated to a topoisomerase-1 inhibitor (SN-38) payload, is the first ADC to be approved for advanced triple negative breast cancer (TNBC). However, mechanisms governing therapeutic resistance to SG are not known. We sought to identify mechanisms of de novo and acquired resistance to SG through unbiased whole-exome sequencing (WES) and RNA sequencing analysis of pre-treatment and multi-site post-progression (autopsy) tumor specimens. We examined three metastatic TNBC cases exhibiting (1) de novo progression, (2) stable disease, and (3) a deep response followed by progression, then mapped the temporal and spatial genomic evolution of acquired resistance in the responding patient. We then conducted additional pre-clinical experiments to validate the observed resistance mechanisms. TROP2 RNA and gene copy number were associated with de novo resistance, as case (1) was found to have absent TROP2 expression in all specimens, case (2) expressed TROP2, while case (3) exhibited both expression and focal genomic amplification of the TACSTD2/TROP2 locus. The genomic phylogeny tree inferred from case (3) post-progression specimens revealed one branch harboring an acquired canonical E418K resistance mutation in TOP1 (encoding topoisomerase 1) and a subsequent sub-clonal TOP1 inactivating frameshift mutation, while a distinct branch exhibited acquisition of a novel T256R missense mutation in TACSTD2 (encoding TROP2). Both the TOP1- and TACSTD2-mutant clones seeded multiple distinct metastatic sites. Through reconstitution experiments in TROP2 negative cells we found that TROP2 T256R is a stable protein with defective cell membrane localization and reduced cell surface binding by RS7 compared to wild-type TROP2. Collectively, these findings underscore TROP2 as a determinant of initial response to SG, and they reveal parallel and mutually exclusive polyclonal molecular mechanisms of acquired resistance involving the direct antibody target and drug payload target in distinct metastatic subclones of a single patient. While further research is needed to extend these novel findings, this study highlights the specificity of SG and illustrates how identifying such mechanisms will inform rational therapeutic strategies to overcome ADC resistance.  

  Study phs002555

• Ethiopia_Genome_Project_high_coverage_vcf

  Integrated callset of high coverage Ethiopian genomes from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j.ajhg.2015.04.019)

  Dataset EGAD00001003294

• Patient-Derived Follicular Lymphoma Spheroids recapitulate lymph node signaling and immune profile, uncovering galectin-9 as a novel immunotherapeutic target

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood and lymph node Follicular Lymphoma patients. These samples were unstimulated after thawing and additionally, peripheral blood samples were stimulated during 7 days in culture as described in Dobaño-López C et. al.)

  Study EGAS50000000233

• Batches 1-3 prostatectomy analysis

  Whole Genome Sequencing Illumina HiSeq data from 95 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). This data is from batches 1 to 3 and is the bulk of the data used in Wedge et al, Nature Genetics 2018 (PMID: 29662167). As of September 2020, some of the studies using these data include: Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)

  Dataset EGAD00001001116

• WGS of Five Pancreatic Cancer Patients-Tumor and Normal

  We performed whole genome sequence on tumor-derived and normal cell lines from patients who had terminal pancreatic cancer and consented for rapid autopsy upon their death. The 5 samples are from Dr. Christine Iacobuzio-Donahue's rapid autopsy program as reported in Boland et al. (PLOSOne, 2024, In Press, PMID 38352348).

  Study phs003775

• WES to explore mutational landscape of blood and non blood liquids in female patients with metastatic breast cancer.

  Whole Exome Sequencing (WES) to explore mutational landscape of blood and non blood liquids in female patients with metastatic breast cancer. 11 patients. 86 liquid samples, 11 matched normal samples. Median coverage 67X. Illumina paired-end sequencing. Fastq files are provided. WES from Richard et al., Nature Communications, 2025 low-pass Whole Genome Sequencing (lpWGS) to assess the representativeness of seven body liquids from female patients with metastatic breast cancer. 216 liquid samples, 745 solid samples, 20 matched normal samples. 0.5X coverage. lpWGS from Richard et al., Nature Communications, 2025.

  Dataset EGAD50000001852

• Dense_fine_mapping_study_identifies_new_susceptibility_loci_for_primary_biliary_cirrhosis

  2,981 primary biliary cirrhosis (PBC) cases were collected by the UK PBC Consortium and genotyped on the Illumina Immunochip where 2,861 passed quality control. These cases were then compared to a UK population control to identify novel PBC risk loci and fine-map association signals. (Liu & Almarri et al., Nat Genet, 2012)

  Study EGAS00001001837

• Growth Hormone (GH) -secreting Pituitary Adenoma

  We profiled the somatic landscape of 21 growth hormone (GH) -secreting pituitary adenomas using somatic copy-number alteration (SCNA), whole-genome sequencing (WGS), bisulfate sequencing, and transcriptome approaches. See details in Valimaki et al. Genetic and epigenetic characterization of growth hormone (GH) - secreting pituitary tumors. Manuscript in preparation, 2019.

  Study EGAS00001003488

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

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

  Study EGAS00001006868

• bulk TCR-seq data IMCISION

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

  Study EGAS00001007367

• Sequencing data for oesophageal and related samples - Ogden et al (WGS, RNA)

  Data supporting: "Widespread reorganisation of the regulatory chromatin landscape facilitates resistance to inhibition of oncogenic ERBB2 signalling" Ogden et al. WGS for tumour and normal samples. RNAseq for tumour samples.

  Dataset EGAD00001007496

• Carcinoid study - WES dataset

  Fernandez-Cuesta et al, 2014, Nature Communication, Whole exome sequencing data set

  Dataset EGAD00001000820