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• Pre_clinical_evolution_of_haematological_malignancies

  Deep targeted sequencing of 291 peripheral blood samples taken 1-20 years prior diagnosis of a haematological malignancy alongside age- and sex-matched controls. Key objective is to distinguish indolent age-related clonal haematopoiesis from pre-cancer and to derive predictive models for early risk-stratification.

  Study EGAS00001002964

• Exome-seq, RNA-Seq, SNP array profiling of gastric tumor samples and cell lines.

  Gastric cancer is the second leading cause of worldwide cancer mortality, yet the underlying genomic alterations remain poorly understood. Here we performed exome and transcriptome sequencing and SNP array assays to characterize 51 primary gastric tumors and 32 cell lines. Meta-analysis of the exome data and previously published data sets revealed 24 significantly mutated genes in MSS tumors, and 16 in MSI tumors. More than half of the patients in our collection could potentially benefit from targeted therapies. We identified 55 splice-site mutations accompanied by aberrant splicing products, in addition to mutation-independent differential isoform usage in tumors. The ZAK kinase isoform TV1 is preferentially upregulated in gastric tumors and cell lines relative to normal samples. This pattern is also observed in colorectal, bladder, and breast cancers. Overexpression of this particular isoform activated multiple cancer-related transcription factor reporters, while depletion of ZAK in gastric cell lines inhibited proliferation. These results reveal the spectrum of genomic and transcriptomic alterations in gastric cancer, and identify isoform-specific oncogenic properties of ZAK.

  Study EGAS00001000736

• Subclonal somatic copy number alterations emerge and dominate in recurrent osteosarcoma

  Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

  Study EGAS00001007486

• RNAseq of SCCOHT patient tumors

  This data set contains BAM files of the RNAseq analysis for three SCCOHT patient tumors. Total mRNA was isolated from fresh frozen tumor samples. RNA sequencing was performed using Illumina HiSeq 4000, paired end 150 bp.

  Dataset EGAD00001007829

• Metabolism and Genetics of Hypobetalipoproteinemia

  Hypobetalipoproteinemia is characterized by extremely low levels of low-density lipoprotein cholesterol. Familial hypobetalipoproteinemia (FHBL) is a monogenic form of hypobetalipoproteinemia caused by mutations in the APOB gene. There are cases of hypobetalipoproteinemia not caused by mutations in APOB, however. The purpose of this study is to identify novel genetic causes of hypobetalipoproteinemia.

  Study phs000561

• Feasibility and Clinical Utility of Whole Genome Profiling in Pediatric and Young Adult Cancers

  Comprehensive Whole Genome Sequencing and Whole Transcriptome (RNASeq) analyses from 114 pediatric patients at Memorial Sloan Kettering. This dataset was used as a prospective clinical utility and feasibility study. By using our Isabl infrastructure for precision medicine, we developed a 2-week end-to-end pipeline to analyze cfDNA, WGS and WTS, which we refer to as cWGTS.

  Study phs002620

• Single-cell RNA sequencing of Small Intestinal Neuroendocrine Tumors (SI-NET)

  Single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from intestinal mucosa and small intestinal neuroendocrine tumors (SI-NETs) to compare their transcriptomic profiles. Tumor and adjacent normal tissues were collected from two SI-NET patients, enzymatically dissociated, and processed into single-cell suspensions. Single-cell libraries were generated using the Chromium Single Cell 3′ Reagent Kit v3 and sequenced on an Illumina platform to produce FASTQ files for downstream analysis.

  Dataset EGAD50000002265

• Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures

  Recent efforts reclassified B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) into more refined subtypes. Nevertheless, outcomes of relapsed BCP-ALL remain unsatisfactory, particularly in adult patients where the molecular basis of relapse is still poorly understood. To elucidate the evolution of relapse in BCP-ALL, we established a comprehensive multi-omics dataset including DNA-sequencing, RNA-sequencing, DNA methylation array and proteome MASS-spec data from matched diagnosis and relapse samples of BCP-ALL patients (n = 50) including the subtypes DUX4, Ph-like and two aneuploid subtypes. Relapse-specific alterations were enriched for chromatin modifiers, nucleotide and steroid metabolism including the novel candidates FPGS, AGBL and ZNF483. The proteome expression analysis unraveled deregulation of metabolic pathways at relapse including the key proteins G6PD, TKT, GPI and PGD. Moreover, we identified a novel relapse-specific gene signature specific for DUX4 BCP-ALL patients highlighting chemotaxis and cytokine environment as a possible driver event at relapse. This study presents novel insights at distinct molecular levels of relapsed BCP-ALL based on a comprehensive multi-omics integrated data set including a valuable proteomics data set. The relapse specific aberrations reveal metabolic signatures on genomic and proteomic levels in BCP-ALL relapse. Furthermore, the chemokine expression signature in DUX4 relapse underscores the distinct status of DUX4-fusion BCP-ALL.

  Study EGAS00001002856

• Landscape of somatic mutations and DNA copy number alterations and transcriptomic profiling identifies metabolic reprogramming as a hallmark of ibrutinib resistance

  Whole-exome sequencing (WES) was conducted on the clinical specimens of 14 cases that had sufficient isolated tumor DNA, including 7 ibrutinib-sensitive cases and 7 ibrutinib-resistant cases. Whole transcriptome sequencing (RNA-seq) was performed on clinical specimens isolated from 14 ibrutinib-sensitive and 7 ibrutinib-resistant cases. Unsupervised hierarchical clustering of MCL tumors using RNA-seq gene expression data showed a response-specific gene expression signature.

  Study EGAS00001003418

• Potential Modulatory Role of Osteoprotegerin in Bone Metabolism of Patients with 21-Hydroxylase Deficiency

  21-hydroxylase deficiency (21-OHD) is an inherited disorder that results from a mutation on the CYP21A2 gene. It affects the adrenal glands and is the most common cause of congenital adrenal hyperplasia (CAH). 21-OHD CAH causes the body to produce an insufficient amount of cortisol and an excess of androgen, the type of hormone that produces male characteristics. The primary treatment for 21-OHD CAH, glucocorticoid replacement therapy, has been shown to cause bone loss. However, the elevated hormone levels caused by 21-OHD CAH may increase production of the protein osteoprotegerin (OPG), which in turn may protect against bone loss. This study will compare bone density and OPG levels in women who have 21-OHD CAH and have undergone a lifetime of glucocorticoid replacement therapy to that in women who have neither of these criteria. In doing so, the study will aim to determine the relationship between OPG and bone loss. Because of the excess of androgen caused by 21-OHD CAH, women with CAH may exhibit some male-like characteristics. Glucocorticoids are a member of a class of drugs called corticosteroids, which are used in hormone replacement therapy. In order to counteract the effects of 21-OHD CAH, women with the disease are given hormone replacement therapy with glucocorticoids beginning at infancy. Glucocorticoids are known to cause bone loss. Despite many years of treatment with glucocorticoids, however, young women with 21-OHD CAH seem to be protected against bone loss. Researchers believe that the increased androgen levels in these women lead to increased estrogen levels, which in turn increase OPG production. The increase in OPG levels may protect women against bone loss. This study will evaluate bone density and OPG levels in women with and without 21-OHD CAH to determine the relationship between OPG and bone loss. Participants in this observational study will attend only one study visit. At this visit, they will undergo a blood draw; a scan of their lower spine, hip, and forearm; height and weight measurements; and a body fat analysis test. This last test will entail a weak and painless electrical signal being sent from foot to foot. Participants will not attend any follow-up visits for this study.

  Study phs001314

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 4)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of 10 B-other ALL patients (ALLT-389, ALLT-391, ALLT-393, ALLK-101, ALLK-109, ALLK-110, ALLK-113, ALLK-115, ALLK-123, ALLK-124). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002599

• WES and RNAseq dataset

  This dataset includes WES and RNAseq for 7 patients with metastatic melanoma (4), non-small cell lung adenocarcnioma (1), cervix adenocarcinoma (1), and Epidermoid nasophaeyngeal carcinoma (1), enrolled in phase I clinical trials (NCT03475134m NCT04643574 and NCT05195619). WES was performed on matched cancer and healthy tissues, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 4000/6000 and Illumina NextSeq 500/550 systems.

  Dataset EGAD50000000337

• Prospective high-throughput genome profiling in advanced cancers:

  Genomics-based tumor profiling in advanced cancers (aC) was recently demonstrated as feasible in clinical practice. After the prospective pilot PANDORA study done on advanced breast cancers, we conducted a prospective monocenter clinical trial called PERMED01 to evaluate the number patients with locally advanced or metastatic cancer for whom identification of molecular alterations in tumor samples could lead to the delivery of a targeted therapy

  Study EGAS00001004554

• The Emirati T2T-level Pangenome: A complete Diploid Graph of 58 Genomes

  This dataset is an Emirati telomere-to-telomere (T2T) pangenome graph in GBZ format built from 116 haplotype-resolved assemblies spanning 58 individuals (28 trio-based and 30 single-sample assemblies). Assemblies were generated with long-read sequencing (PacBio HiFi and ONT ultra-long) with standard polishing, then integrated into a graph representation. The genomes show high contiguity (median ≈150 Mb) and high consensus accuracy (median QV 59). The resulting GBZ graph captures globally shared and Emirati-enriched variation, including sequence in complex regions, and serves as a population-matched reference for downstream variant discovery and annotation.

  Dataset EGAD50000001756

• Diversity of the immune microenvironment and response to checkpoint inhibitor immunotherapy in mucosal melanoma

  Mucosal melanoma (MucM) is a rare cancer with a poor prognosis and low response rate to immune checkpoint inhibition (ICI) compared to cutaneous melanoma (CM). To explore the immune microenvironment and potential drivers of MucM’s relative resistance to ICI drugs, we characterized 101 MucM tumors (43 head and neck, 31 female urogenital, 13 male urogenital, 11 anorectal, and 3 other gastro-intestinal) using bulk RNA-sequencing (RNAseq). The original publication is written by JL Vos, JJH Traets, et al. and published in JCI Insight in 2024.

  Study EGAS50000000631

• Exome sequencing of synchronous colorectal cancers

  Approximately 4% of colorectal cancer (CRC) patients have at least two simultaneous cancers in the colon. Due to the shared environment, these synchronous CRCs (SCRCs) provide a unique setting to study colorectal carcinogenesis. Understanding whether these tumors are genetically similar or distinct is essential when designing therapeutic approaches. We performed exome sequencing of 47 primary cancers and corresponding normal samples from 23 patients. Additionally, we carried out a comprehensive mutational signature analysis to assess whether tumors had undergone similar mutational processes and the first immune cell score analysis (IS) of SCRC to analyze the interplay between immune cell invasion and mutation profile in both lesions of an individual. The tumor pairs shared only few mutations, favoring different mutations in known CRC genes and signaling pathways, and displayed variation in their signature content. Two tumor pairs had discordant mismatch repair statuses. In majority of the pairs, IS varied between primaries. Differences were not explained by any clinicopathological variable or mutation burden.

  Study EGAS00001003474

• Genomewide association studies in ankylosing spondylitis

  The aim of this study was to identify genes associated with ankylosing spondylitis susceptibility in British and Australian individuals of European descent.

  Study EGAS00000000104

• Spatial whole exome sequencing of metastatic melanoma

  We performed whole exome sequencing of 8 samples derived from a patient with metastatic melanoma. These represent six different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor, one pre-treatment biopsy that was treatment naive and one post-PD-1 inhibitor treated lesion. Exome sequencing data was generated using methods as previously described, including library preparation using the Agilent SureSelect XT Target Enrichment protocol (#5190-8646) prior to sequencing on an Illumina HiSeq 2000/2500 v3 system using 76bp paired-end reads. Raw sequencing data was then processed using Saturn V, the next generation sequencing data processing and analysis pipeline developed by the Department of Genomic Medicine at the UT MD Anderson Cancer Center.

  Dataset EGAD00001005819

• Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors

  Multiple congenital disorders often present complex phenotypes, but how the mutation of individual genetic factors can lead to multiple defects remains poorly understood. In the present study, we used human neuroepithelial (NE) cells and CHARGE patient-derived cells as an in vitro model system to identify the function of chromodomain helicase DNA-binding 7 (CHD7) in NE?neural crest bifurcation, thus revealing an etiological link between the central nervous system (CNS) and craniofacial anomalies observed in CHARGE syndrome. We found that CHD7 is required for epigenetic activation of superenhancers and CNS-specific enhancers, which support the maintenance of the NE and CNS lineage identities. Furthermore, we found that BRN2 and SOX21 are downstream effectors of CHD7, which shapes cellular identities by enhancing a CNS-specific cellular program and indirectly repressing non- CNS-specific cellular programs. Based on our results, CHD7, through its interactions with superenhancer elements, acts as a regulatory hub in the orchestration of the spatiotemporal dynamics of transcription factors to regulate NE and CNS lineage identities.

  Study JGAS000131

• Human PMS1-dependent non-canonical mismatch repair converges with MBD4 to repair 5-methylcytosine deamination

  CpG dinucleotides are mutational hotspots due to spontaneous deamination of 5-methylcytosine (5mC), resulting in T:G mismatches that can lead to CpG>TpG transitions. These mutations are a hallmark of aging and cancer and play a central role in the evolution of vertebrate genomes. We have previously uncovered MBD4 as the primary Base Excision Repair (BER) glycosylase responsible for 5mC deamination repair. Here, we employ an APOBEC1 deaminase fused to a catalytically dead Cas9 to induce targeted 5mC deamination independently of DNA replication, and track its repair in human cells. This approach reveals that MBD4 elicits a coordinated repair response with a non-canonical branch of Mismatch Repair (MMR) involving complexes MutLβ (MLH1-PMS1) and MutSα (MSH2-MSH6). We demonstrate that human PMS1 loss phenocopies the CpG>TpG hypermutation associated with MBD4 deficiency, revealing 5mC deamination repair as one of its main functions. Structural predictions with functional validation reveal that MBD4 activity is dependent on its physical interaction with MutLβ. In alignment with our experimental data, we show that the CpG>TpG mutational burden of MMR-deficient tumors is partly explained by replication-independent processes. Altogether, we uncover a novel function of non-canonical MMR that underscores its interplay with BER in safeguarding genomic integrity against damage to methylated DNA.

  Study EGAS50000001662

• Multidimensional and Longitudinal Immune Profiling of Sepsis in Uganda

  We conducted a prospective, observational cohort study of adults (RESERVE-U-2-TOR) admitted to Tororo General Hospital in eastern Uganda with severe, undifferentiated infection (i.e., suspected sepsis). Briefly, whole-blood samples were collected in PAXgene blood RNA tubes (PreAnalytiX, Qiagen, Germantown, MD, USA), from which RNA was extracted using PAXgene Blood RNA Kits (cat. no. 762164) (Qiagen). Sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina, after which libraries were multiplexed and sequenced on the Illumina NovaSeq X Plus platform (Illumina, Inc, San Diego, CA). Data from this study available through dbGaP include raw RNA-Seq data generated from whole-blood samples collected upon RESERVE-U-2-TOR study enrollment (N=274).

  Study phs003914

• The Genetic Landscape of Mutations in Burkitt Lymphoma

  Burkitt lymphoma (BL) is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. We sequenced exomes of 59 BL tumors, 14 of which had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a novel tumor suppressor gene.

  Study phs000562

• Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in HGSOC

  Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Long-read single-cell RNA sequencing (scRNA-seq), capturing full-length transcripts, lacked the depth to provide this information so far. Here, we increased the PacBio sequencing depth to 12,000 reads per cell, leveraging multiple strategies, including artifact removal and transcript concatenation, and applied the technology to samples from three human ovarian cancer patients. Our approach captured 152,000 isoforms, of which over 52,000 were novel, detected cell type- and cell-specific isoform usage, and revealed differential isoform expression in tumor and mesothelial cells. Furthermore, we identified gene fusions, including a novel scDNA sequencing-validated IGF2BP2::TESPA1 fusion, which was misclassified as high TESPA1 expression in matched short-read data, and called somatic and germline mutations, confirming targeted NGS cancer gene panel results. With multiple new opportunities, especially for cancer biology, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.

  Study EGAS00001006807

• Genomic profiling of paediatric glioma cell lines

  Although paediatric gliomas resemble their adult counterparts in many ways, there appear to be distinct clinical and biological differences. One important factor hampering the development of new targeted therapies is the relative lack of cell lines derived from childhood glioma patients, as it is unclear whether the well-established adult lines commonly used are representative of the underlying molecular genetics of childhood tumours. We have carried out a detailed molecular profiling of paediatric glioma cell lines KNS42, SF188, UW479, RES259 and RES186.

  Study EGAS00001003006

• Hepatocellular Carcinoma Spatial transcriptomics Data Access Committee

  This is the DAC for study ST HCC

  Dac EGAC50000000635