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• cfDNA Methylomes for HCC Detection and Postoperative Monitoring

  To overcome the limitations of current ctDNA-based HCC detection, specifically mutational profiling, we propose quantifying cfDNA methylation levels using cfMeDIP-seq and evaluating its capacity for HCC detection and post-surgery recurrence monitoring. This approach aims to reveal the clonal dynamics of HCC during surgery and upon relapse. Our preliminary data and analyzed results demonstrate that tumor-agnostic cfDNA methylomes can accurately detect HCC and predict recurrence after liver resection or transplantation. This method could have significant implications for the diagnosis, treatment, and monitoring of HCC.

  Study EGAS50000000450

• Characterization of Autosomal CNV Among the Negrito from Peninsular Malaysia

  Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However the CNV data from diverse populations is rather limited. Here we report the first investigation of copy number variation (CNV) in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 62 putative novel CNVs, consisting of 25 gains and 37 losses. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), as well as the metabolic pathways (GO:0001852). Copy number gains in CNVRs enriched with genes were significantly higher than the losses (P value <0.001). Therefore, in view of the small population size, relative isolation and semi-normadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.

  Study phs000664

• Kids First: The Genomic Architecture of Hirschsprung Disease (HSCR)

  Hirschsprung disease (HSCR) is a male biased developmental disorder associated with a lack of innervation of the gastrointestinal tract. Genetic studies have been instrumental in understanding its multifactorial inheritance, high heritability, syndromic associations, and genetic heterogeneity with variable penetrance and expressivity. At least 24 genes and 9 loci with pathogenic alleles (PAs) are known to underlie HSCR pathogenesis and explain 62% of its population attributable risk (PAR). Despite this heterogeneity, there is functional unity in HSCR: ~53% of HSCR PAs disrupt RET and EDNRB signaling in the developing enteric nervous system (ENS) in which 11 genes comprising a gene regulatory network control RET and EDNRB gene expression. We propose to identify the remaining 30% PAR by studying 857 unrelated HSCR cases, their 125 affected and 1,446 unaffected firstdegree relatives by whole genome sequencing to increase statistical power of gene discovery through improved detection of all types of coding and regulatory PAs. HSCR arises from cell autonomous defects in enteric neural crest cell precursors (ENCCs) affecting their proliferation, differentiation and migration in the ENS, functional studies that will guide our detection of novel genes.

  Study phs003662

• The proliferative history shapes the DNA methylome of B-cell tumor and predicts clinical outcome

  Here, we provide access to CLL and DLBCL DNA methylation and gene expression data in the context of a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. This approach showed that differential methylation among tumor entities relates to differences in cellular origin and to de novo epigenetic alterations, which allowed us to build an accurate machine learning-based diagnostic algorithm. We identify extensive patient-specific methylation variability in silenced chromatin associated with the proliferative history of normal and neoplastic B cells. Mitotic activity generally leaves both hyper- and hypomethylation imprints, but some B-cell neoplasms preferentially gain or lose DNA methylation. Subsequently, we construct a DNA methylation-based mitotic clock called epiCMIT, whose lapse magnitude represents a strong independent prognostic variable in B-cell tumors and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracer of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of clinical outcome.

  Study EGAS00001004640

• Discovery of a highly widespread bacteriophage family and its associations to metabolic syndrome gut microbiomes

  There is significant interest in altering the course of cardiometabolic disease development via the gut microbiome. Nevertheless, the highly abundant phage members of the complex gut ecosystem -which impact gut bacteria- remain understudied. Here, we characterized gut virome changes associated with metabolic syndrome (MetS), a highly prevalent clinical condition preceding cardiometabolic disease, in 196 participants with a combination of whole genome shotgun and virus like particle sequencing. MetS gut virome populations exhibited decreased richness and diversity, but larger inter-individual variation. These populations were enriched in phages infecting Bacteroidaceae and depleted in those infecting Ruminococcaeae. Differential abundance analysis identified eighteen viral clusters (VCs) as significantly associated with either MetS or healthy viromes. Among these are a MetS-associated Roseburia VC that is related to healthy control-associated Faecalibacterium and Oscillibacter VCs. Further analysis of these VCs revealed the Candidatus Heliusviridae, a highly widespread gut phage lineage found in 90+% of the participants. The identification of the temperate Ca. Heliusviridae provides a novel starting point to a better understanding of the effect that phages have on their bacterial hosts and the role that this plays in MetS

  Study EGAS00001006260

• Context-specific regulatory genetic variation in MTOR dampens neutrophil-T cell crosstalk in pneumonia-associated sepsis, modulating disease

  Sepsis is a heterogeneous clinical syndrome with a high mortality, requiring personalised stratification strategies. Here, we characterise genetic variation that modulates MTOR, a critical regulator of metabolism and immune responses in sepsis. The effects are highly context specific, involving a regulatory element that affects MTOR expression in activated T cells with opposite direction of effect in neutrophils. We show that the G-allele of the lead variant, rs4845987, associated with decreased risk of T2D, reduces MTOR expression in T cells and improves survival in sepsis due to pneumonia, with effects specific to sepsis endotype. Using ex vivo models, we demonstrate that activated T cells promote immunosuppressive sepsis neutrophils through released cytokines, a process dampened by hypoxia and the mTOR inhibitor rapamycin. Our work demonstrates a novel epigenetic mechanism that fine-tunes MTOR transcription and T cell activity via the variant-containing regulatory element, which further exhibits an allelic effect upon vitamin C treatment. These findings reveal how genetic variation interacts with disease state to modulate immune cell-cell communication, providing a patient stratification strategy to inform more effective sepsis treatment.

  Study EGAS50000000894

• ChIP-seq in KMS11 and TKO cells

  Histone chIP-seq in t(4;14) Myeloma cell line KMS11 and KMS11 cells with knock-out of translocated NSD2 allele (KMS11 TKO).

  Study EGAS50000000077

• Clonal hematopoiesis in metastatic urothelial and renal cell carcinoma

  This study aimed to determine the prevalence and clinical relevance of clonal hematopoiesis in metastatic urothelial and renal cell carcinoma.

  Study EGAS50000000870

• RISE-UP study: riboflavin supplementation in Crohn's disease

  Taxonomic classification of the fecal microbiota of Crohn's disease patients showing the shift in the gut bacterial community after riboflavin supplementation.

  Study EGAS50000000982

• Integrated Multiomics Uncovers Distinct Macrophage Alterations in Human Metabolic dysfunction-Associated Steatohepatitis Progression

  We report single-nuclei RNA sequencing data from human livers in metabolic dysfunction-associated steatotic liver disease (MASLD) patients.

  Study EGAS50000000768

• RNA-seq data from iCAF (sorted) and myCAF cluster 0 (spread) CAF-S1 fibroblasts maintained in culture

  RNA-seq data from iCAF (sorted) and myCAF cluster 0 (spread) CAF-S1 fibroblasts maintained in culture

  Study EGAS00001004031

• Epigenome-wide association study of cocaine use disorder in postmortem human brain tissue

  We aimed to identify cocaine use disorder associated DNA methylation alterations in the Brodmann Area 9 brain region.

  Study EGAS00001006826

• Fastq files from target enrichment

  Fastq files generated during target sequencing of 10MB genomic region surrounding top hits in GWAS in a subset of 86 individuals in case families. Paired end sequencing performed on Illumina NextSeq.

  Dataset EGAD00001007801

• DNA polymerase and mismatch repair exert distinct microsatellite instability signatures in normal and malignant human cells

  Whole genome sequencing data used in the manuscript: DNA polymerase and mismatch repair exert distinct microsatellite instability signatures in normal and malignant human cells.

  Dataset EGAD00001006593

• Epigenetic subtypes of neuroblastoma - ChIPseq

  In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide genome wide H3K27ac profiles in 60 primary neuroblastoma samples.

  Dataset EGAD00001006285

• ChIP sequencing in Cancer Cell Lines

  The project is to evaluate the genomic binding sites of the histone demethylase JARID1C. This gene was recently identified in CGP as a novel recessive cancer gene in human renal cell carcinoma.

  Dataset EGAD00001001453

• Development and Validation of Patient-Derived Xenografts from Fibrolamellar Carcinoma Human Tissue

  We developed and validated Patient-Derived Xenografts (PDX) of Fibrolamellar Carcinoma human tissue from surgical resections. Human tissues from primary liver tumor, recurrent liver, and liver metastases were implanted into NOD-SCID-Gamma (NSG) mice (Jackson laboratories) and monitored for tumor growth. Some of the original tissues were frozen for further analysis including RNA sequencing. Tumors that grew were then harvested and passaged into additional mice. Some tumor tissues from the PDX samples were frozen for RNA-Seq analysis. The PDX was validated by histologic, transcriptomic and proteomic analysis. The RNA-Seq analysis was performed on original tissue samples including primary liver tumor, recurrent liver, liver metastases, normal liver, and the derived PDX.

  Study phs002435

• Sequencing data of tumor tissue obtained from GANNET53 study patients

  The GANNET53 clinical trial evaulated novel treatment options for ovarian cancer patients with platinum-resistant relapse. Archival fresh-frozen paraffin embedded tissue was available from 131 of the 133 enrolled patients. NGS sequencing aimed at assessing the mutational spectrum of key ovarian cancer genes (with a focus on TP53), and their relevance for therapy resistance. From available FFPE samples, DNA was extracted and NGS sequenced using the SureSeq™ Ovarian Cancer Panel and the NGS Library Preparation kit covering all exons of 7 key ovarian cancer genes BRCA1, BRCA2,TP53, PTEN, ATM, ATR, NF1 for single nucleotide variants (SNV) and indels. Finally, sequence data from 118 individual FFPE tumor tissue samples were generated.

  Study EGAS50000000935

• The European Bank for Induced Pluripotent stem cells (EBiSC) is designed to address the increasing demand by iPSC researchers for quality-controlled, disease-relevant research grade iPSC lines, data and cell services.In this study Whole Genome Sequencing was performed on a selection of lines from the project.

  Induced pluripotent stem (iPS) cells have the potential to significantly advance drug development and health research, yet collections of stem cells are scattered across the world, their quality cannot always be guaranteed, and accessing them is often difficult. The goal of EBiSC is to establish a European iPS cell bank that will be the ‘go-to’ resource for the characterisation, storage and distribution of high quality iPS cells. Ultimately, EBiSC will become an independent organisation, distributing high quality iPS cells on a not-for-profit basis to scientists worldwide.

  Study EGAS00001002755

• Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

  We have used next generation sequencing to sequence genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient.

  Study EGAS00000000054

• Mitochondrial DNA mosaicism in human somatic cells

  Genomic alterations accumulate in the somatic cells throughout an individual’s lifetime. Recent sequencing studies have documented widespread mutations in the nuclear genome and the frequent clonal competition of normal cells carrying mutations. However, the landscape of mitochondrial DNA (mtDNA) heteroplasmy in normal human tissues is poorly understood. This study investigated the whole genome sequences (WGSs) of 2,096 clones established from non-neoplastic healthy single cells obtained from 31 donors. In addition, we analyzed 31 WGSs of neoplastic cells, including 12 clones established from adenomatous polyps from one individual with MUTYH-associated polyposis and 19 matched colorectal carcinomas from individuals who donated normal colorectal clones.

  Dataset EGAD50000000373

• Childhood Cancer Data Initiative (CCDI): Clonal Evolution During Metastatic Spread in High-Risk Neuroblastoma

  The goal of this study is to deliver a detailed characterization of the patterns of disease dissemination at diagnosis, during progression and in response to therapy in high-risk neuroblastoma. Longitudinal and spatially distinct tumors were collected from patients. Clinical data includes diagnosis and treatment information. Biospecimen data includes whole genome sequencing (WGS) and whole transcriptome sequencing (WTS).

  Study phs003111

• Whole-exome sequencing data of ovarian clear cell carcinoma in East Asia

  This is a genomic study to uncover the molecular landscape of ovarian clear cell carcinoma (OCCC) in East Asia. This dataset contains normal-tumor paired samples of 104 patients with OCCC diagnosed in two branches of Chang Gung Memorial Hospital, Taiwan. These are paired-end, whole-exome sequencing data, sequenced by Illumina NovaSeq with target depth of 150X.

  Study EGAS50000000031

• Subclonal variation in patients with pediatric T-lymphoblastic leukemia (T-ALL)

  Variations in TP53 and KRAS genes indicate a particularly poor prognosis in relapsed pediatric T-ALL. We hypothesized that these variations might be subclonally present at disease onset and contribute to relapse risk. To test this, we examined 386 children diagnosed with T-ALL, including more than 100 patients who relapsed as well as matched non-relapsing controls.

  Study EGAS50000000794

• Single-cell profiling reveals monocyte mitochondrial dysfunction in patients with cirrhosis progressing to acute-on-chronic liver failure

  We performed single-cell RNA-seq and CITE-seq in PBMC samples derived from patients with acutely decompensated cirrhosis at risk of developing ACLF, as well as from Healthy Donors. We identified a population of monocytes associated with disease progression. We also explored the presence of this cell population in blood samples by bulk RNA-sequencing.

  Study EGAS50000001127