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• L1 Retrotransposon Sequencing in Schizophrenia - Study 1

  Schizophrenia (SZ) is a devastating psychiatric disorder with substantial global clinical and economic implications. While SZ is marked by high heritability, discovery of common variants associated with even moderate risk for SZ has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from dorsolateral prefrontal cortex NeuN+ neuronal nuclei from 63 SZ cases and 63 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001968

• Childhood Cancer Data Initiative (CCDI): Single-Cell Atlas of NF1 Nerve Sheath Tumors

  The worst outcome of NF1 is the development of the aggressive and highly metastatic malignant peripheral nerve sheath tumors (MPNST), which transform from benign plexiform neurofibroma (PN) and lack effective treatment. In this study, we performed single-cell RNA sequencing of 63 clinically annotated NF1-associated peripheral nerve sheath tumors, including 24 PN, 34 premalignant atypical neurofibromas, and 5 MPNSTs. These results improve the ability of identifying high-risk neurofibromas and provide a unique opportunity for early detection of MPNST.

  Study phs003519

• Genomic and Transcriptomic Sequencing of CAR-T-Treated Patients

  Chimeric Antigen Receptor (CAR)-T cell therapy has revolutionized the treatment of hematologic malignancies. Approximately half of patients with refractory large B-cell lymphomas achieve durable responses from CD19-targeting CAR-T treatment; however, failure mechanisms are identified in only a fraction of cases. Here we use next-generation sequencing technologies to characterize the genomic and transcriptomic features of CAR-T cells and tumors that influence therapeutic responses. Please see our submission to NCBI GEO (GSE273170) for additional data.

  Study phs002922

• Paired Analysis of Host and Pathogen Genomes Identifies Determinants of Human Tuberculosis

  The outcome of infectious diseases may depend on the interaction between human and pathogen genomic variations. This study was designed to explore and validate this relationship in tuberculosis (TB) by conducting a genome-to-genome study of paired genomes from human hosts and the infectious agent Mycobacterium tuberculosis.Blood samples were collected from 699 TB patients in Lima, Peru, as part of a 2020 cohort study during the COVID-19 pandemic. Genotyping data for these individuals are available through dbGaP.

  Study phs003718

• Targeted sequencing of genomic regions of interest in depression and obesity

  This study aimed to further explore the genetic relationship between MD and obesity taking advantage of targeted sequencing strategy. Specifically, we searched for genetic risk variants across the entire frequency spectrum in flanking genomic regions and genes previously associated with MD and obesity, assessed the contribution of those variants to the pathophysiology of comorbid MD and obesity, and provided a general overview of the cellular and molecular pathways mapped by those variants when these complex diseases co-occur.

  Study EGAS50000000330

• Patient-Derived Breast Cancer Organoid Study

  This study uses normal and tumor tissues from breast cancer patients to derive 3D cell culture models called organoids. Organoid technology is an innovative platform that can be used to study a patient's tumor in a dish ex-vivo. As part of this study we have comprehensively characterized these models using next-generation sequencing for: 1) pathogenic SNVs in a targeted gene panel 2) copy number alterations 3) transcriptome analysis using RNA sequencing and 4) single-cell RNA sequencing

  Study phs002722

• Testicular large B-cell lymphoma is genetically similar to PCNSL and distinct from nodal DLBCL

  Next generation sequencing (NGS) data analyzed in Rivas-Delgado, López, et al. HemaSphere 2024. Single nucleotide variants (SNVs) and short insertions /deletions (indels) were evaluated in 42 samples using a B-cell malignancy-oriented targeted panel covering 115 genes (SureSelectXT, Agilent Technologies and sequenced in a MiSeq instrument (Illumina; 2x150bp; mean coverage of 599x). The NGS data of 39 samples is provided here. The 3 additional samples were previously published. Please, see the original publication for additional details.

  Study EGAS50000000521

• Characterization of copy number quiet oral cancer

  Copy number quiet head and neck squamous cell carcinoma are a distinct subset with relatively good prognosis. Previous work has indicated this subset is most commonly found in the oral cavity and is highly enriched for HRAS and CASP8 mutations. TP53 mutations are much less common than in CNA-quiet oral cancers. In this study we corroborate the validity of CNA-quiet tumors as a distinct subset in a large OSCC cohort and further chart clinical, genomic, and immunological characteristics of this subset.

  Study EGAS50000000558

• Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

  The analysis of e2QTL allows for the identification of context-specific eQTL effects (Kim-Hellmuth et al. (2017), PMID: 28814792). To evaluate how inter-individual genetic variability influences the regulation of DNA damage-induced apoptosis, we performed e2QTL analysis of CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.

  Study EGAS50000000666

• Uncovering Principles of Adaptive Regulation in Cancer Resistance Through Deep Evolutionary Profiling

  A comprehensive understanding of the emergence of therapy resistance in cancer requires new approaches capable of generating and characterizing drug resistant cell lines at scale. Here, we present the EVolution Of Lineages in Vitro (EVOLV) platform, a high-throughput approach for generating diverse libraries of viable, drug-resistant cell lines from a common progenitor. EVOLV enables deeper insights into the genomics of drug resistance as well as into the complex interplay among genomic, transcriptomic, and functional layers during cancer evolution.

  Study phs003851

• Variant calling dataset from the whole-exome study of familial pulmonary fibrosis in the Canary Islands-VCF files

  Sequence reads were obtained from a set of 13 families with familial pulmonary fibrosis in the Canary Islands, Spain, using Illumina paired-end reads, respectively, at the Institute of Technology and Renewable Energy (ITER). Briefly, we used bcl2fastq v2.18 to perform sample demultiplexing and BWA-MEM v0.7.15 (https://github.com/lh3/bwa) to align reads to GRCh37/hg19 reference. Resulting BAM files were assessed with SAMtools v1.3 (http://www.htslib.org) and Picard v2.10.10 (https://broadinstitute.github.io/picard/) for quality control steps. Small insertions/deletions (< 50 bp) and single nucleotide variants (SNVs) were identified using an in-house bioinformatics pipeline based on GATK HaplotypeCaller v3.8 (https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller). This pipeline follows the Best Practices recommendations for germline variant calling and its description is publicly available (https://github.com/genomicsITER/benchmarking/tree/master/WES).

  Dataset EGAD50000001152

• Childhood Cancer Data Initiative (CCDI): CCDI Pediatric In Vivo Testing Program - Leukemia

  The goal of this study is to molecularly characterize a large panel of pediatric acute lymphoblastic leukemia (ALL) patient-derived xenografts (PDXs) previously established in immune-deficient mice. These PDXs are utilized as part of the NCI-funded Pediatric Preclinical In vivo Testing (PIVOT) program to identify novel agents and combinations. Biospecimen data include next-generation sequencing (RNAseq, whole exome sequencing, DNA copy number variation), whole-genome analysis of cytogenetic abnormalities, and DNA fingerprint for quality control.

  Study phs003164

• Molecular biomarkers in progression from refractory celiac disease to the lethal cancer variety enteropathy associated T cell lymphoma (EATL)

  Enteropathy associated T cell lymphoma (EATL) is frequently preceded by a state of refractoriness to the gluten-free diet, called “refractory celiac disease” or RCD. We aim to study which mutations and copy number aberrations are already manifest in RCD and to identify differences between RCD patients that do, and do not, develop EATL. We have applied whole exome sequencing to detect mutations and copy number aberration predictive for progression from RCD to EATL.

  Study EGAS00001006669

• Modulation of Lung Immune Responses to Viral Infection-Microbiome Interactions with Respiratory Organoids

  Here, we colonized bronchial epithelial air-liquid interface tissue cultures with 58 different individual microbes. Following 18 and 48 hours of colonization, we performed bulk RNA-seq of the host epithelial cells (n=3). Overall, we found significant microbial species-level and strain-level variation in host gene expression changes for innate immunity and epithelial barrier genes. Of particular interest, we found significant heterogeneity in stimulation of host interferon and antiviral interferon-stimulated genes.Study registered in ImmPort under accession # SDY2281.

  Study phs003627

• Genome-wide SNP data of Fulani populations from the Sahel belt

  This project seeks to uncover the genetic structure and ancestry of the Fulani populations across the Sahel/Savannah Belt. The study includes two datasets (''WGA_Fulani_Database'' and ''Saliva_Fulani_Ddatabase''), and SNP-genotyping data was generated using the Illumina Infinium H3Africa Consortium array (BeadChip type: H3Africa_2019_20037295_B1) in two genotyping batches (TE-2559_201029 and TE-2559_201020). In total, 419 were genotyped for this study and the key results were presented in Fortes-Lima et al. 2024 (doi: 10.1101/2024.06.22.600206).

  Study EGAS50000000451

• Childhood Cancer Data Initiative (CCDI): Comprehensive Genomic Sequencing of Pediatric Cancer Cases (CMRI/KUCC)

  This study provides paired tumor normal genomic sequencing data from ~ 200 children with cancer, including both solid tumors and leukemias, done by the Children's Mercy Research Institute (CMRI) and University of Kansas Cancer Center (KUCC). These data include whole genome sequencing (generally, ~20x), whole exome sequencing (generally, ~300x), bulk RNA sequencing (generally, ~80 million reads), and single-cell RNA and ATAC sequencing (>50,000 reads/cell). Additional phenotypic, pathologic, and genetic data, gathered clinically for these samples, are also provided.

  Study phs002529

• SweGen genetic variation from the Northern Sweden Population Health Study

  The dataset contains files with single nucleotide variants in VCF format for a total of 58 DNA samples originating from the Northern Sweden Population Health Study (NSPHS). For each of the 58 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. The NSPHS study was approved by the local ethics committee at the University of Uppsala (Regionala Etikprövningsnämnden, Uppsala, 2005:325 and 2016-03-09). All participants gave their written informed consent to the study including the examination of environmental and genetic causes of disease in compliance with the Declaration of Helsinki.

  Dataset EGAD50000001324

• SweGen whole-genome sequencing from the Northern Sweden Population Health Study

  The dataset contains whole-genome sequencing data (aligned read files) in CRAM-format (lossless compression) for a total of 58 DNA samples originating from the Northern Sweden Population Health Study (NSPHS). For each of the 58 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. The NSPHS study was approved by the local ethics committee at the University of Uppsala (Regionala Etikprövningsnämnden, Uppsala, 2005:325 and 2016-03-09). All participants gave their written informed consent to the study including the examination of environmental and genetic causes of disease in compliance with the Declaration of Helsinki.

  Dataset EGAD50000001325

• INCLUDE: Human Trisome Project

  The INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project is an NIH-wide collaboration that seeks to improve health and quality-of-life for people with Down syndrome. The INCLUDE Project Data Coordinating Center and partners created the INCLUDE Data Hub, a centralized data resource that allows access to large-scale clinical and multi-omics datasets specific to Down syndrome and supports collaborative, cloud-based analysis to accelerate scientific discoveries related to Down syndrome and its co-occurring conditions.

  Study phs002981

• Targeted plasma cell-free DNA sequencing for tissue-of-origin determination and donor-derived cell-free DNA quantification in organ transplant recipients and healthy controls

  The dataset comprises targeted deep methylation sequencing data used for both tissue-of-origin determination and donor-derived cfDNA quantification. It includes plasma cfDNA data from stable kidney transplant recipients (n = 31), stable liver transplant recipients (n = 20) and healthy controls (n = 23). In addition, plasma cfDNA samples collected early after transplantation were analyzed from kidney transplant recipients (n = 44) and liver transplant recipients (n = 40). The dataset also features genomic DNA data generated from whole blood (n = 10) and buffy coat (n = 3) from healthy controls, as well as from T cells (n = 1), B cells (n = 2), hepatocytes (n = 1) and kidney epithelium (n = 1). Lastly, genomic DNA data was generated from buffy coat of transplant recipients (n = 17). Here, “n” indicates the sample number.

  Dataset EGAD50000001446

• Genotyping from targeted NGS data based on a small set of SNPs correctly matches patient samples

  Mislabelling and swapping of laboratory samples are handling errors that can lead to erroneous interpretation of data and/or patient harm. Sequenced samples can be traced back to the respective donors by matching of single nucleotide polymorphisms (SNPs). Here we used sequencing data (targeted NGS) from two cohorts of patients with chronic lymphocytic leukaemia to demonstrate the possibility of selecting informative SNPs from a typical targeted NGS panel and to create an automated workflow for detection of sample handling errors.

  Study EGAS50000000532

• South African Blood Regulatory (SABR) Resource

  Functional genomics resources are critical for interpreting human genetic studies, however they are predominantly from European-ancestry individuals. Here we present the South African Blood Regulatory (SABR) resource, a map of blood regulatory variation that includes three South Eastern Bantu-speaking groups. Using paired whole genome and blood transcriptome data from over 600 individuals, we map the genetic architecture of 40 blood cell traits derived from deconvolution analysis, as well as expression, splice, and cell type interaction quantitative trait loci (QTL).

  Study EGAS50000001008

• Studies of L1-mediated Pseudogene Formation in Human HeLa Cells

  Alu elements mobilize from one genomic location to another by a "copy-and-paste" mechanism known as retrotransposition, which requires the human Long INterspersed Element-1 (LINE-1 or L1) ORF2-encoded protein (ORF2p); however, little is known about other cellular factors required for Alu retrotransposition. Isolates of HeLa cells differ in their ability to support Alu retrotransposition. Here, we generated Illumina whole genome sequencing data derived from four HeLa isolates: HeLa-H1, HeLa-CCL2, HeLa-HA, and HeLa-JVM.

  Study phs003397

• Whole Exome Sequencing of Waldenström Macroglobulinemia (WM) Precursor Conditions

  In this study we aimed to comprehensively characterize the genomic landscape of WM precursor conditions and identify potential biomarkers of progression to symptomatic WM by means of Whole Exome Sequencing (WES) of CD19-selected samples from 139 patients, primarily with IgM-MGUS and asymptomatic WM. Overall, our study shows that genomic profiling of patients’ tumor at the time of aWM diagnosis might represent an improved strategy for identifying patients at high risk to progression who could benefit from earlier intervention.

  Study EGAS50000001249

• Access to "BMP9 controls pulmonary vascular growth and remodeling"

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

  Dac EGAC50000000640

• 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

• 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 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 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 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 EGAD50000001895

• genetic analysis of carcinogenesis in GAPPS

  Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal dominant syndrome characterized by polyposis localized in the gastric body and fundus with a strong tendency for adenocarcinoma. The genetic mutations that accumulate during the progression from normal mucosa through fundic gland polyps (FGPs) to carcinoma in GAPPS remain unclear.We investigated the evolutionary process from normal mucosa to FGPs and carcinoma in GAPPS. Through comprehensive mutational and transcriptome analyses, we aimed to provide insights into the biology of this disease.

  Study JGAS000843

• RNAseq of MCL cell lines

  This study provides bulk RNA sequencing data from Mino and Jeko-1 mantle cell lymphoma (MCL) cell lines treated with CDK9 inhibitors, including the novel compound YX0798. CDK9 is a key regulator of RNA polymerase II–mediated transcription, and its inhibition disrupts transcriptional programs critical for tumor survival. The dataset captures transcriptomic changes associated with CDK9 inhibition, including downregulation of oncogenic drivers such as MYC and MCL-1. These data support mechanistic studies of transcriptional reprogramming and therapeutic vulnerability in aggressive MCL.

  Study EGAS50000001089

• Multiregional single nuclei RNA-seq and WGS of prostate cancer

  This study investigates the clonal evolution and metastatic dissemination of prostate cancer using multiregional single-nuclei RNA sequencing (snRNA-seq) and low-pass whole-genome sequencing (WGS) data from 43 spatially distinct tumor areas in five patients with locally advanced prostate cancer, including both primary and regional lymph node samples. We employed the Chromium Next GEM Single Cell 3’ Kit (v3/3.1, 10x Genomics) for single-nuclei transcriptome profiling and constructed bulk WGS libraries using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs) from the same pool of nuclei extracted from each area. snRNA-seq data were aligned to the human genome (GRCh38-1.2.0_premrna) using 10x Genomics Cell Ranger v5.0.0, while WGS reads were aligned to the human reference genome (GRCh38) with BWA MEM, achieving an average sequencing depth of 0.3X for low-pass WGS and 16X after resequencing.

  Dataset EGAD50000001357

• Spatial multiomic analyses reveal carcinogenic pathways in end-stage renal disease

  Patients with end-stage renal disease (ESRD) are at increased risk for acquired cystic kidney disease (ACKD) and renal tumours, but the molecular basis of such disorders remains elusive. Here, we performed spatial immunogenomic analyses on specimens from 43 patients with ACKD and associated tumours. In this study, we characterized the genomic and transcriptomic features of renal tumours in ESRD. Second, we elucidated the genetic background and microenvironment of cysts in ACKD via comprehensive spatial transcriptomics.

  Study JGAS000855

• Epigenome analysis of human trophoblast stem cells

  Trophoblast cells play an essential role in the interactions between the fetus and mother. Mouse trophoblast stem (TS) cells have been derived and used as the best in vitro model for molecular and functional analysis of mouse trophoblast lineages. However, attempts to derive human TS cells have so far been unsuccessful. In this study, we derived human TS cells from human blastocysts. Epigenome analysis revealed that the human TS cells maintained epigenome profiles similar to those of primary trophoblast cells. JGA submission accessions: JGA000122,JGA00000000122

  Study JGAS000112

• Genomic features of renal cell carcinoma developed in end-stage renal disease and dialysis

  Patients with end-stage renal disease (ESRD) or receiving dialysis have 3 ���24-fold higher risk for renal cell carcinoma (RCC). Long-term hemodialysis cause acquired cystic disease (ACD) and RCC.���But its carcinogenic mechanism and genomic features are not so clear. In this study, we analyzed whole genome and transcriptome of 38 RCCs, which were developed in ESRD patients receiving dialysis and characterized their genomic features and associations with their histology and dialysis or end-stage renal diseases.

  Study JGAS000533

• Integrated Exome and RNA Sequencing of Dedifferentiated Liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000177

• Analysis of genomic alterations in dedifferentiated liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000182

• Elucidation of genomic pathology of a patient with concurrent acute myeloid leukemia and mediastinal germ cell tumor

  The occurrence of a mediastinal germ cell tumor (GCT) and hematological malignancy in the same patient is very rare. Whole exome sequencing was performed for concurrent acute myeloid leukemia (acute megakaryoblastic leukemia) and mediastinal germ cell tumor. Somatic mutations, such as TP53 or PTEN, were commonly identified in both acute myeloid leukemia and mediastinal germ cell tumor, suggesting the common founder clone. Normal buccal cells were used as a control. Illumina NextSeq 500 platform were used.

  Study JGAS000211

• Immune Biomarkers in Metastatic Castration-resistant Prostate Cancer

  Background: Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease in which molecular stratification is needed to improve clinical outcomes. The identification of predictive biomarkers can have a major impact on the care of these patients, but the availability of metastatic tissue samples for research in this setting is limited. Objective: To study the prevalence of immune biomarkers of potential clinical utility to immunotherapy in mCRPC by tumour RNA sequencing, and to determine their association with overall survival (OS).

  Study EGAS50000001269

• Variability in immune response genes and prediction of severe SARS-CoV-2 infection (INMUNGEN-Cov2 project)

  Genetic factors may contribute to explain the variable clinical response to SARS-CoV-2 infection. To this end we sequenced the DNA of 392 COVID-19 patients from Spain. Whole Exome Sequencing (WES) was performed at two different sequencing centers. Half of the samples were sequenced at a commercial service, NIMGenetics, whereas the other half were sequenced by the EASI-Genomics consortium. Finally, Variant Call Format (VCF) files for each sample was also obtained.

  Study EGAS50000000066

• Access to "A Spatially Resolved Single-Cell Atlas of the Human Fetal Olfactory System"

  The human nasal region arises from neural crest and placodal lineages, yet its early development remains poorly understood owing to limited fetal tissue access and structural complexity. Here we present an integrated single-nucleus and spatial transcriptomic atlas of the human fetal nasal region, generated from 10 fetuses (males and females) between 7 and 12 post-conceptional weeks. Single-nucleus RNA sequencing resolved 32 distinct cell types, while integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) enabled spatial and temporal mapping of gene expression dynamics across the olfactory epithelium (OE) and adjacent tissues. We identify novel markers of olfactory sensory neuron differentiation and pathways governing epithelial patterning and OE morphogenesis. Notably, spatially organized expression of 169 olfactory receptor genes reveals molecular evidence for the “one neuron-one receptor” principle during the first trimester. Together, this work establishes the first molecular and spatial framework of early human olfactory development and provides a foundational resource for studies of sensory neurogenesis and congenital disorders.

  Dac EGAC50000000688

• Insights into Adult Gut Microbiota Composition Using the Estonian Cohort

  This study explores the gut microbiota of 1,826 adult individuals, predominantly from the Estonian population. The cohort includes 16S rRNA gene V4 region amplicon sequencing data along with metadata, such as age, sex, health status, anthropometric parameters, and stool consistency. The research aims to characterise the microbial community structure, identify distinct enterotypes, and examine their associations with host characteristics. The dataset provides a valuable reference for understanding gut microbiota composition and supports research in personalised nutrition and lifestyle-related health strategies.

  Study EGAS50000001611

• Whole_genome_sequence_of__third_generation_family_member__SFHS_

  Previously we performed deep WGS on 6 parents and 13 children from 3 large families from the Scottish Family Health Study to identify de novo mutations. This prelim is cover the additional sequencing of one grandchild from one of these three families. The inclusion of a third generation individual will provide additional experimental validation for the de novo mutations found in the initial trio. As in the previous study, the DNA will be WGS to a depth of approximately 25X to achieve this purpose.

  Study EGAS00001000429

• Clonal_expansion_of_mutated_cell_population_in_bladder_urothelium_

  1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference.

  Study EGAS00001001687

• Exome_sequencing_in_patients_with_Calcific_Aortic_Valve_Stenosis

  The objective is to identify new genes involved in calcific aortic valve stenosis (CAVS) by screening the exome of at least 20 patients with familial CAVS. The recruitment of patients with CAVS has been achieved by l’institut du thorax (Nantes, France). DNA from the selected patients has been analysed by exome capture (Agilent SureSelect) and massively parallel sequencing (Illumina). The data generated by this project will lead to the identification of candidate genes involved in CAVS, which can be further screened for mutation in additional patients with CAVS.

  Study EGAS00001000049

• Deep RNA sequencing in CLL

  Chronic lymphocytic leukemia (CLL) is a B-cell neoplasm with a heterogeneous clinical and biological behavior. We have performed deep RNA sequencing in different subpopulations of B-lymphocytes from healthy individuals and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. The transcriptomic architecture of CLL uncovered here refines the biological characterization of the disease and opens new perspectives for the clinical management of patients.

  Study EGAS00001000374

• Genetic_background_for_the_major_psychiatric_disorders_in_the_general_Finnish_population

  Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of 8028 samples from persons of 30 years or older, which were screened for psychotic and bipolar disorders using the Composite International Diagnostic Interview, self-reported diagnoses, medical examination, and national registers.

  Study EGAS00001000162

• Egypt_Genome_Project___high_coverage_whole_genome_sequencing

  All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate high-coverage sequencing data for 3 Egyptian samples.

  Study EGAS00001000482