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• Osteosarcoma 3D patient derived cultures to test genome-informed personalized treatment options; a feasibility study

  Background: Improving osteosarcoma treatment beyond conventional (neo)adjuvant chemotherapy and resection remains challenging. An urgent need for novel therapeutic options, particularly personalized and targeted approaches, has emerged due to high inter-patient molecular heterogeneity. A lack of representative in vitro and in vivo models impedes therapeutic development, therefore we aimed to create 3D in vitro long term culture models directly from patient material. Methods: Tumour cells from seven osteosarcoma patients were propagated in monolayer or collagen hydrogels, while whole-exome sequencing of corresponding primary tumour tissue was performed to identify potential drug targets. Established cultures were subsequently used to assess efficacy of the identified personalized treatment options. Results: Three out of seven hydrogel cultures harboured the same genetic alterations as the corresponding primary tumours. Among these, the L6565 patient line exhibited homozygous CDKN2A loss with retained Rb expression, rendering tumour cells sensitive to CDK4/CDK6 inhibition via palbociclib. This patient line was used to evaluate genome-informed therapy and to compare cell culture models of increasing complexity. Our findings demonstrate feasibility of establishing long-term patient-derived osteosarcoma cultures with a success rate of 14%. Tumour heterogeneity was reflected in advanced culture methods producing more variability in treatment response. Conclusion: These results highlight the potential of genome-informed therapies in osteosarcoma and the importance of refining culture techniques to enhance translational research and therapeutic outcomes.

  Study EGAS50000001583

• Genomic analysis reveals novel secondary drivers and progression pathways in skin basal cell carcinoma

  Basal cell carcinoma of the skin (BCC) is the most common malignant neoplasm in humans. BCC is primarily driven by the aberrant activation of the Sonic Hedgehog (Hh) pathway. However, its extensive phenotypical variation remains to be explained. The genetic profiling of 293 BCCs revealed the highest mutation rate observed in cancer (65 Mutations/Mb), with strong prevalence of UV-light signature mutations. 85% of BCCs harbored mutations in Hh pathway genes: mutually exclusive PTCH1 (73%) and SMO (20%) (P=6.6x10-8), SUFU (8%), and in TP53 (61%). 85% of BCCs also harbored secondary driver mutations in other genes implicated in BCC tumorigenesis. Recurrent secondary driver mutations were observed in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), RAC1 (1%) and N/K/H-RAS (2%). Loss of function (LoF) and deleterious missense mutations were observed in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). In line with the mutational profiles detected by RNAseq, we observed activation of the Hh pathway as well as upregulation of target genes of the Hippo-YAP pathway and activation of MYCN target genes. The functional analysis of the novel tumorigenic driver mutations in MYCN, PTPN14 and LATS1 demonstrates their relevance in BCC tumorigenesis and provides an expanded molecular understanding of BCC.

  Study EGAS00001001540

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001895

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001894

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001893

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001892

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001891

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001889

• SPECTA: NGS Screening Program for Efficient Clinical Trial Access

  SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.

  Dataset EGAD00001000894

• Massive parallel RNA sequencing of highly purified mesenchymal cells derived from bone marrow specimens of 45 low-risk myelodysplastic syndrome cases

  Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 45 low-risk myelodysplastic syndrome (LRMDS) cases. Gene expression profiles (GEPs) of the 45 LRMDS have been compared to GEPs derived from likewise highly purified mesenchymal cells obtained from bone marrow specimens of healthy donors for the identification of inflammatory signatures. Additionally, an overlap in inflammatory signatures has been determined by comparing the GEPs of these 45 LRMDS cases to the GEPs of 4 Shwachman-Diamond syndrome and 3 Diamond-Blackfan anemia cases, both representing different subclasses of congenital pre-leukemia syndromes with a tendency of leukemic progression and perturbed niche compartment. Finally, the GEPs and gene expression signatures have been utilized for prognostication and the prediction of leukemic progression.

  Dataset EGAD00001002658

• COVID-19 Severity First Wave of Infection for Severe Patients in Madrid

  We recruited 98 hospitalised patients displaying severe COVID-19 symptoms from the first wave of infection. A stringent exclusion criteria based on non-genetic factors such as age, blood oxygen, radiologic findings and other typical COVID-19 signs was performed. Gingival or peripheral blood samples were taken for 98 individuals and whole exome sequencing performed using ExomeCapture-Seq capture KAPA HyperExome on Illumina machines.

  Dataset EGAD00001008464

• Non-viral precision T cell receptor replacement for personalized cell therapy

  The T cell receptor (TCR) provides the fine specificity of T cells to recognize mutations in cancer cells 1-3. We developed a clinical-grade approach based on CRISPR/Cas9 non-viral precision genome editing to simultaneously knock-out the two endogenous TCR genes, TCRα (TRAC) and TCRβ (TRBC), and insert in the TRAC locus the two chains of a neoantigen-specific TCR (neoTCR), isolated from the patient’s own circulating T cells using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with refractory solid cancers received up to three distinct neoTCR-transgenic cell products, each expressing a patient-specific neoTCR, in a cell dose-escalation, first-in-human phase 1 clinical trial (NCT03970382). One patient had grade 1 cytokine release syndrome, and one grade 3 encephalitis. All had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease, and the other 11 had disease progression as best response on therapy. NeoTCR-transgenic T cells were detected in tumour biopsies post-infusion at frequencies higher than the native TCRs pre-infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs recognizing mutational neoantigens, the simultaneous knock-out of the endogenous TCR and knock-in of the neoTCRs using single-step, non-viral precision genome editing, the manufacturing of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene edited neoTCR T cell products, and the ability of the transgenic T cells to traffic to the patients’ tumours.

  Study EGAS00001006898

• Avelumab or M7824 for People with Recurrent Respiratory Papillomatosis

  This submission includes genomic data derived from the study of clinical samples from two different phase II trials. These trials evaluated the clinical efficacy and safety of avelumab or M7824 in the treatment of adults with recurrent respiratory papillomatosis (RRP). Subjects with aggressive RRP were treated with three to six doses of avelumab or M7824. Pre-treatment or post-treatment snap frozen papilloma and normal mucosa samples were subjected to whole exome sequencing and bulk RNA-seq. A total of twenty subjects were enrolled and treated. 

  Study phs002373

• Genome-wide search for higher order epistasis as modifiers of treatment effects on bone mineral density in childhood cancer survivors

  Survivors of pediatric acute lymphoblastic leukemia (ALL) exposed to curative treatments that adversely affect BMD (age- and sex-adjusted BMD Z-scores, measured via QCT). Specifically, after SNP QC and annotation, we considered 75523 autosomal SNPs mapped to putative promoter or enhancer regions to restrict our search to 3-way SNP interactions that potentially reflect gene regulation events that influence BMD. We replicated 3-SNP interactions as modifiers of treatment effects in a cohort of adult survivors of non-ALL pediatric cancers (N=1428).

  Study EGAS00001002645

• Leiomyosarcoma Cancer Transcriptome Sequencing

  RNA-Seq data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 75bp paired-end protocol to a minimum mean reads of 50 million.

  Dataset EGAD00001003192

• UCSF Pediatric Bithalamic Glioma Genome Project

  Targeted next-generation sequencing of 13 pediatric bithalamic diffuse gliomas. BAM files of targeted next-generation DNA sequencing data of 13 pediatric gliomas, with multi-region sequencing data from 2 of these cases (17 total tumor samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from using the QIAamp DNA FFPE Tissue Kit (Qiagen). Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of 480 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.

  Dataset EGAD00001005499

• Precise reconstruction of the tumor microenvironment using bulk RNA-seq and a unique machine learning-based algorithm trained on artificial transcriptomes

  Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. Here, we present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of > 9,400 tissue and blood sorted cell RNA profiles to accurately reconstruct the tumor microenvironment (TME). Bioinformatic correction for technical and biological variability, aberrant cancer cell expression inclusion, and the accurate quantification and normalization of transcript expression increased the stability and robustness of Kassandra. Performance was validated on over 4,000 H&E tissue slides and more than 1,000 normal and tumor tissues by comparison with cytometric, immunohistochemical or single-cell RNA-seq measurements. Kassandra accurately deconvolved stromal and immune elements of blood and tumors, revealing the role of the TME in tumor pathogenesis. Digital TME reconstruction revealed that the presence of PD1-positive CD8+ T cells strongly correlated with immunotherapy response and increased the predictive potential of established biomarkers, indicating that Kassandra could potentially be utilized in future clinical applications.

  Dataset EGAD00001008776

• WGS of tumor and blood control samples of neuroblastoma

  high coverage whole genome sequencing of 38 samples was done on a patterned flowcell v.2.5 (150 bp paired end, HiSeq X Ten) with coverage of about 60x for the tumor and whole blood control samples. All tumors had a tumor cell content of ≥60%. Sequencing libraries were prepared using the Truseq DNA Nano kit (Illumina) according to the manufacturers’ instructions and size selected using SPRI beads (Beckman Coulter Genomics).

  Dataset EGAD00001009624

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer

  Circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) monitoring shows promise for risk stratification and decision-making in cancer patients. However, factors like background noise from non-tumor DNA, clonal haematopoiesis, and non-shedding tumors may complicate manual interpretation and limit its clinical application. In this proof-of-concept study in advanced non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs), we developed an algorithm that automatically classifies serial cell-free DNA (cfDNA) samples, thereby enabling reliable and reproducible interpretation, and preventing time-consuming manual interpretation in approximately 75% of patients. Importantly, application of the algorithm allowed early risk stratification and decision-making, specifically identifying approximately 35% of patients with short-term clinical benefit and approximately 25% of patients who may potentially benefit from treatment escalation. Simultaneous serum tumor marker (STM) monitoring further improved risk stratification and decision-making in our study, enabling accurate identification of all patients with a clinical benefit of at least one year.

  Study EGAS50000001554

• PacBio Revio WGS on 10 carriers of ring and marker chromosomes

  Bam files containing PacBio HiFi reads from carriers of ring and marker chromosomes. The reads where genereated using the PacBio Revio platform. Each individual was sequenced to roughly 30X coverage on one flow cell per individual. The chromosome of interest is indicated in the file name.

  Dataset EGAD50000002111

• Abnormal foetal development exome trios

  This project is to explore the contribution of de novo mutations to severe structural malformations diagnosed prenatally using ultrasound. These malformations include heart, CNS, renal and GI abnormalities. In this pilot project we aim to exome sequence 30 parent-foetus trios to ~50X mean coverage and identify de novo functional variants using an algorithm developed in the Hurles group

  Dataset EGAD00001001442

• whole exome sequencing (WES) data of the HIPO head and neck cancer (HNC, n=83)

  Paired whole exome sequencing data of the HIPO head and neck cancer (HNC) (n=83), using Agilent SureSelect V4+UTRs and V6+UTRs with the sequencing platforms HiSeq2000 and HiSeq2500. The reads were aligned to hg19. This is part of project H019.

  Dataset EGAD00001006336

• Pre-neoadjuvant treatment biopsy RNAseq breast cancer dataset

  This dataset contains RNAseq data of n=87 pre-treatment biopsies of triple negative and luminal- type breast cancer patients, all scheduled to receive neoadjuvant chemotherapy. Gene expression data is linked with treatment response and survival.

  Dataset EGAD00001008433

• Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers

  This project includes RNA-sequencing data from human FSHD and control skeletal muscle biopsies. This project includes data from 28 FSHD patients (total 37 samples, including vastus lateralis and tibialis anterior muscles) and 12 control individuals (total 24 samples, including vastus lateralis and tibialis anterior muscles).

  Study EGAS00001005782

• RNA-seq data of human skeletal muscle biopsies

  These datasets contain RNA-seq data of human skeletal muscle biopsies before or after exercise. This contains data of three projects on skeletal muscle. Paired Fastq files are uploaded. - HeteroFiber: Individual muscle fibers from human biopsies, collected at rest from m. vastus lateralis. (n = 1044) - ExerFiber: Individual muscle fibers from human biopsies (m. vastus lateralis), collected immediately after or 3 hours after HIIT exercise session. (n = 2096) - Bulk muscle exercise: bulk muscle biopsies at rest, immediately after or 3h after HIIT exercise session. (n = 126)

  Dataset EGAD50000000612

• Whole-exome sequencing laser capture micro-dissected biopsies of human renal cell carcinoma

  The dataset comprises whole exome sequences from laser capture micro-dissected biopsies of 10 patients diagnosed with clear cell renal cell carcinoma. In total over 100 regions are sampled to allow 'focally exhaustive' sequencing and explore the limits of intra-tumoural heterogeneity.

  Dataset EGAD00001008029

• Healthy control and lung cancer plasma cfDNA samples from various collection tubes

  The dataset contains 6 lung cancer and 60 healthy control plasma cfDNA samples collected in EDTA, PAXGene and Norgen blood collection tubes at various locations. Shallow WGS was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD00001008322

• Single cell RNAseq dataset of paired normal and tumor human prostate biopsies

  Single-cell RNAseq dataset of paired normal and tumor human prostate biopsies from n=10 participants. Fastq files corresponding to R1, R2 and I1 are uploaded and were generated from cellranger mkfastq. Data was sequenced on Illumina HiSeq 4000.

  Dataset EGAD00001008340

• cfDNA from fractionated and paired unfractionated plasma samples of lung cancer patients

  Plasma from lung cancer patients from EDTA tubes was fractionated using size exclusion chromatography. Fractions 1-5, 7-11, 12-15, 16-20 were pooled, cfDNA was extracted from the fractions and paired unfractionated samples and PE150bp sequencing was performed on an Illumina Novaseq S4 flowcell. Samples are provided as raw reads without any prior processing.

  Dataset EGAD00001009780

• WES and RNA-seq data of 11 cancer patients with multiple cancer types

  This dataset includes WES and RNAseq from 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy samples, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems. Paired-end reads are provided in fastq format.

  Dataset EGAD00001010169

• The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways

  69 OAMZL patients were sequenced on the Illumina platform. The data files are available in BAM format.

  Dataset EGAD00001011067

• Transcriptome profiling of HNSCC treated with PD1/PDL1

  Immune checkpoint inhibitors have improved survival in several solid tumors, including head and neck squamous cell carcinoma (HNSCC). However, current use of PD-1/PD-L1 inhibitors relies on PD-L1 expression, which does not reliably predict patient response. Therefore, better predictive biomarkers are needed to identify which patients benefit from immunotherapy. Previous studies suggest that genomic and transcriptomic features may help predict treatment response. This study aims to integrate genomic, transcriptomic, and methylomic data from 31 patients with recurrent/metastatic HNSCC to identify new biomarkers of resistance to anti-PD-1/PD-L1 therapy.

  Dataset EGAD50000002506

• Cellular Diversity of the Developing Human Cerebral Cortex

  We sought to characterize cellular heterogeneity in the human cerebral cortex at a molecular level during cortical neurogenesis. We captured single cells and generated sequencing libraries using the C1TM Single-Cell Auto Prep System (Fluidigm), the SMARTer Ultra Low RNA Kit (Clontech), and the Nextera XT DNA Sample Preparation Kit (Illumina). We performed unbiased clustering of the single cells and further examined transcriptional variation among cell groups interpreted as radial glia. Within this population, the major sources of variation related to cell cycle progression and the stem cell niche from which radial glia were captured. We found that outer subventricular zone radial glia (oRG cells) preferentially express genes related to extracellular matrix formation, migration, and stemness, including TNC, PTPRZ1, FAM107A, HOPX, and LIFR and related this transcriptional state to the position, morphology, and cell behaviors previously used to classify the cell type. Our results suggest that oRG cells maintain the subventricular niche through local production of growth factors, potentiation of growth factor signals by extracellular matrix proteins, and activation of self-renewal pathways, thereby contributing to the developmental and evolutionary expansion of the human neocortex. For study version 2, we have updated this data set to include additional primary cells that we infer to represent microglia, endothelial cells, and immature astrocytes, as well as additional cells from the developing neural retina, and from iPS-cell derived cerebral organoids. The genes distinguishing these cell populations may reveal biological processes supporting the diverse functions of these cell types as well as vulnerabilities of specific cell types in human genetic diseases and in viral infections. For study version 3, we have updated the data set to include additional primary cells, including those published in Nowakowski et al., 2017 (PMID:29217575). For study version 4, we have additionally performed parallel analyses of transcriptomes and physiological responses of 476 single cells isolated from developing human cortex. As a result, we were able to identify physiological response profiles of specific progenitor and neuronal cell types during human cortical development.For study version 5, we have additionally performed bulk RNA sequencing of organotypic primary cultures from the developing human cortex with or without exposure to SARS-CoV-2 to understand the infectability and transcriptomic effects of SARS-CoV-2 on the developing human cortex.For study version 6, we investigated the impact of LIFR signaling on neural proliferation and differentiation of human oRG cells. Specifically, we isolated oRG cells from the primary developing neocortex and cultured them for four weeks with and without LIF treatment. We then performed single-cell RNA sequencing using the Chromium Single Cell 3’ Reagent Kits (v3.1, Dual index) from 10x Genomics to understand the molecular and cellular changes of oRG differentiation upon LIF treatment.

  Study phs000989

• Targeted Long-Read Sequencing of the Ewing Sarcoma 6p25.1 Susceptibility Locus

  Ewing Sarcoma (EwS) is rare but the second most common cancer in children, adolescents and young adults. Recent studies suggest germline variation in or around GGAA microsatellites may interact with fusion oncoprotein binding causing changes in binding affinity and potentially impacting enhancer activity on nearby target genes. This study aims to better understand germline variation around EwS susceptibility regions by performing long-range haplotype sequencing of these regions using PacBio sequencing. Our analysis focused on characterizing variation in GGAA microsatellite length as well as germline variants in or around the microsatellite and their association with EwS risk.

  Study phs003159

• Long-read whole-genome sequencing of post-mortem sporadic PD cases and non-PD controls using gut tissue

  This study aims to enable in-depth genomic characterization of Parkinson’s disease (PD) by examining single nucleotide polymorphisms, structural variants, and quantitative trait loci. Long-read whole-genome sequencing was performed using the Oxford Nanopore PromethION platform on colon tissue collected post‑mortem from PD patients and non-PD controls. These data contribute high-resolution insights into genomic variation that may affect PD biology. The project is part of Team Voet’s efforts within the ASAP Collaborative Research Network, which promotes resource sharing and accelerates discovery in Parkinson’s disease research.

  Study EGAS50000001689

• 503 genotypes from Inner Asia used in 'Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy' publication

  Inner Asia is particularly interesting to understand human history and evolution, as two groups presenting contrasting cultural traits (notably their language, their social organisation and matrimonial system) cohabit. We sampled 503 individuals from these two groups, belonging to 17 populations from 11 distinct ethnic groups (AltaiKizhi, Kazakh, Khakas, Kyrgyz, Mongolian, Shore, Tajik, Telengit, Tubalar, Turkmen and Uzbek). The samples were then genotyped with 5 different DNA-arrays and, after quality-control, the 253,532 autosomal SNPs present in all the arrays were merged together in the present dataset.

  Study EGAS00001002951

• Transcriptional characterization of human innate lymphoid cells (ILCs) and natural killer (NK) cells from fresh umbilical cord blood

  The heterogenicity of cord blood ILCs (ILC1, ILC2, ILC3) and NK cells in humans has so far not been assessed. In this study, we sorted from fresh cord blood the respective cell types from 3 donors and performed single-cell transcriptome analysis. To achieve high resoluation, each sorted population was labelled individually via multiplexing antibodies and subsequent Abseq staining before pooling. To determine single-cell transcriptomes the BD Rhapsody pipeline was performed. This is the first data set to characterize human ILCs and NK cells at such depth.

  Study EGAS50000001204

• Transcriptomic profiling of skin biopsies from psoriasis patients following treatment with Zasocitinib

  The objective of this study is the exploratory analysis and characterization of psoriasis using RNA-seq-based profiling. Specifically, the cutaneous and serum biomarker profiles associated with the molecular, histological and clinical effects of Zasocitinib treatment in patients with moderate-to-severe plaque psoriasis were characterized. To evaluate differences between the transcriptomic profiles of Zasocitinib- and placebo-treated patients, exploratory biomarker endpoints included quantification of skin biomarkers, such as immune cell infiltration and mRNA expression levels in lesional and non-lesional skin, as well as quantification of circulating cytokines and other inflammatory biomarkers.

  Study EGAS50000001548

• Genomic Predictors of Response to Immune Checkpoint Therapy

  Immune checkpoint therapies, including monoclonal antibodies to programmed cell death-1 (PD-1) and cytotoxic % lymphocyte associated protein-4 (CTLA-4), yield durable clinical responses across many tumor types, including metastatic melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC). However, predictors of response to these therapies in RCC are still unknown. Genomic characterization of large clinical cohorts of patients treated with anti-CTLA-4 and anti-PD-1 agents in melanoma and NSCLC have suggested that high mutational burden, high neoantigen burden, and high expression of certain genes in pre-treatment tumors may be associated with patient response to these therapies. In this study, we sought to investigate genomic predictors of response to anti-PD1 therapy in metastatic RCC in two independent clinical cohorts using whole exome and whole transcriptome sequencing.

  Study phs001493

• Evolutionary Analysis of Chronic Lymphocytic Leukemia Cells During Relapse After Allogeneic Hematopoietic Stem Cell Transplant

  We investigated the molecular dynamics driving relapse of chronic lymphocytic leukemia (CLL) following allogeneic hematopoietic stem cell transplant (allo-HSCT) through an integrated analysis of whole exome, bulk transcriptome, bulk methylome and single cell transcriptional data from paired leukemic samples representing 19 patients. We found that their clinical kinetics corresponded to distinct genetic and epigenetic evolutionary trajectories and suggest that the selection pressures of the post-transplant, immunologic bottleneck are distinct from those imposed by chemotherapy.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out ribosome profiling (Ribo-seq) and RNA-sequencing on CLL samples and isolated primary B cells from healthy donors. We discovered novel or unannotated open reading frames (nuORFs), their expression levels, as well as somatic mutations within them to predict potential neoantigens.

  Study phs001998

• Long-Read Sequencing to Identify Inherited Mutations Predisposing to Breast Cancer

  We aimed to detect deeply intronic mutations within genes linked to breast/ovarian cancer that are potentially under-reported in clinical testing due to technical limitations. Current DNA and RNA tests typically exclude these regions, which harbor many variants within complex repetitive sequences that short-read sequencing cannot align. By employing targeted long read sequencing together with recent in silico prediction tools, we assessed the implications of rare deep intronic variants in severely affected patients with breast, ovarian, and/or metastatic prostate cancer, who had previously tested negative using standard genomic or cDNA methods. Through this approach, we identified participants who carried deep intronic mutations in tumor suppressor genes, resulting in abnormal transcripts causing premature truncations and loss of gene function. This study underscores the potential of long read DNA and cDNA sequencing in enhancing mutation discovery efforts.

  Study phs003638

• Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer: DNA Sequencing

  This randomized phase II trial studies how well paclitaxel with or without carboplatin and/or bevacizumab followed by doxorubicin and cyclophosphamide works in treating patients with breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, carboplatin, doxorubicin, and cyclophosphamide, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Bevacizumab may stop the growth of tumor cells by blocking blood flow to the tumor. Giving chemotherapy together with bevacizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed. All participants in this study were female. RNA sequencing data from the same patients were published under phs001863. Subject aliases are the same in the two datasets.

  Study phs003801

• ovarian cancer sample exome seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to exome sequencing on 16 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy.

  Dataset EGAD50000002057

• Sequencing data for the manuscript "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas"

  Mapping the spatial organization of DNA-level somatic copy number changes in tumors can provide insight to understanding higher-level molecular and cellular processes that drive pathogenesis. We describe an integrated framework of spatial transcriptomics, tumor/normal DNA sequencing, and bulk RNA sequencing to identify shared and distinct characteristics of an initial cohort of eleven gliomas of varied pathology and a replication cohort of six high-grade glioblastomas.

  Dataset EGAD50000001394

• FASTQ Data from In Situ Hi-C on Medulloblastoma Tissue Samples

  29 Hi-C datasets [8 G3 (MB3667, MB3687, MB3690, MB3692, MB3693, MB4010, MB4037, MB4141), 13 G4 (MB0558, MB3510, MB3670, MB3689, MB3716, MB3760, MB3761, MB3807, MB4079, MB4132, MB4174, MBSF7, SNC_2_5), 7 SHH (MB3612, MB3661, MB3662, MB3695, MB3697, MB3724, MB4143), and 1 WNT (MB4036)]. Fresh tissue samples were obtained from The Hospital for Sick Children (Toronto, ON). In situ Hi-C libraries were generated using approximately 2.5 million dissociated cells as input. All Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).

  Dataset EGAD50000000771

• Whole-genome bisulfite sequencing

  Raw reads from whole-genome bisulfite sequencing. Whole-genome bisulfite sequencing library preparations and Illumina sequencing of DNA samples from TET2 mutation carriers (Ly9, Ly11, Ly14, Id1) and their age-matched controls (Ly8, Ly10, Ly13, Id2, Id3) was done as a service at BGI (BGI Tech Solutions Co., Ltd., China). Bisulfite treatment was done with EZ DNA Methylation-Gold Kit (Zymo Research, CA, USA) for 300-400bp size-range fragments with methylated adapters in 5' and 3' ends. Sequencing was done with the HiSeq X-Ten platform using paired-end 150 base-pair read length.

  Dataset EGAD00001004779

• miRNA-seq data for Molecular Characterization of ETMR

  This dataset contains miRNA-seq data from 10 patients. Small RNAs were isolated as described previously57,58 from fresh-frozen tumour material. In brief, total RNA was extracted using guanidinium isothiocyanate/phenol extraction followed by 3′-adaptor ligation of barcoded adenylated adaptors. Samples were pooled in two sets of five samples. Subsequently, gel electrophoresis was used to isolate small RNAs (19–35 nt) and purified using ethanol precipitation. Fragments were then amplified using standard PCR, isolated using gel electropho- resis and purified using ethanol precipitation. Samples were sequenced on a HiSeq 2000 v.4 machine resulting in 10 Fastq files.

  Dataset EGAD00001006218

• RNA-seq data from 121 tumor samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). RNA-seq was performed using the QuantSeq kit FWD HT kit (Lexogen) using 500 ng input RNA from 121 tumor samples. Data provided here consist of 780 fastq files for RNA-seq.

  Dataset EGAD00001006238

• Sequence data for study: Mobilization of tissue-resident memory CD4+ T lymphocytes from bone marrow and their contribution to a systemic secondary immune reaction

  Short Description: This study contains 7 RRBS samples, including 3 ex vivo CD4+ Trm (2 x spleen and 1 x bone marrow) and 4 blood tetanus (TT) and measles (Me) antigen-reactive memory CD4+ cells before and one day post DTaP (diphtheria-tetanus-pertussis) and MMR (measles-mumps-rubella) vaccination, respectively (1 x tetanus D0, 1 x tetanus D1, 1 x measles D0, 1 x measles D1). Technology: Illumina HiSeq 2500 Filetype: fastq format

  Dataset EGAD00001007886

• Human normal esophagus and Barrett's esophagus mtDNA sequencing

  BAM files containing paired-end mtDNA sequencing data from human esophageal samples of individuals that had progressed to dysplasia or developed Barrett's esophagus (BE) post-esophagectomy. BE biopsies and the background mucosa were analysed. Each patient (JE*) has associated mtDNA sequencing data from biopsies of stroma, BE and squamous and cardia tissue. Two technical replicates, denoted "A" and "B", were analysed for each biopsy. Libraries were sequenced via the Illumina MiSeq platform v2 (Illumina, San Diego, CA, USA) 300 cycles (150 nt paired-end).

  Dataset EGAD00001008310