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• The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

  Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find novel patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a novel genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.

  Dataset EGAD00001012101

• WGS dataset of Characterization of UV DNA damage in B-cell precursor acute lymphoblastic leukemia

  We characterized B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients that present with the mutational signature SBS7a. We found clear subtype specificity, but presence of SBS7a did not seem linked to heterogeneity within subtypes. To further distinguish the incidence of SBS7a in pediatric cancer we analyzed a pan-cancer WGS cohort and identified frequent SBS7a in anaplastic large cell lymphomas. As SBS7a is commonly found in skin cancers and has been linked to UV-light induced DNA damage, we compared the features of UV-light induced DNA damage in skin cancer and SBS7a in ALL, and found high similarity. We found no defects in UV damage response pathways in SBS7a-positive samples, indicating no additional UV vulnerability. Additionally, transcriptomic data showed no differences between samples with and without SBS7a. Finally we looked into the moment of exposure to the source of SBS7a by deep sequencing of diagnosis-relapse pairs and single cell whole genome sequencing of diagnosis samples with high SBS7a.

  Dataset EGAD00001015600

• APC-related multiple salivary gland lesions

  This study aims to investigate the genetic and molecular mechanisms underlying a novel phenotype of attenuated familial adenomatous polyposis (AFAP), where affected individuals develop multiple salivary gland tumours, including basal cell adenomas and adenocarcinomas.

  Study EGAS50000001159

• Genomic and transcriptomic analysis on hepatocarcinogenesis after HCV eradication

  Little is known about the genomic and transcriptomic features of hepatocellular carcinoma developing after HCV eradication (SVR-HCC). In this study, we aimed to unveil the genomic and transcriptomic basis of hepatocarcinogenesis after SVR.

  Study JGAS000234

• Comprehensive genomic analysis for AYA with acute lymphoblastic leukemia

  AYA with B-ALL showed extremely inferior outcomes when compared to children. Genetic basis undelying AYA B-ALL is largely unknown. We performed integrated analysis of RNA-seq (hum0045���JGAS000047) and target DNA-seq.

  Study JGAS000276

• Novel compound heterozygous mutations in UHRF1 are associated with atypical immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome with distinctive genome-wide DNA hypomethylation

  Our study goal is to reveal underlying molecular pathogenesis of Immunodeficiency, Centromeric instability, and Facial anomalies (ICF) syndrome, which is characterized by hypomethylation of centromeric/pericentromeric repeats.

  Study JGAS000559

• Mitochondrial DNA Mutations at Low-level Heteroplasmy in Chronic Kidney Disease

  To explore for relationship between somatic or heteroplasmic mutations of mtDNA and kidney function, we here performed ultra-deep sequencing based on long-range PCR from DNAs of 78 CKD kidney tissues.

  Study JGAS000611

• Picuris Pueblo oral history and genomics reveal continuity in US Southwest

  Following the decision of Picuris Pueblo to study their population history using DNA, this project generated 16 ancient and 13 present-day genomes from the Pueblo, spanning 1,000 years of history.

  Study EGAS50000000855

• Diverse Cellular Composition in Alveolar Rhabdomyosarcoma Revealed by Single Cell RNA Sequencing

  Using single cell RNAseq data to characterize tumor composition and cellular states for Alveolar Rhabdomyosarcoma. We find that that ARMS tumors harbor phenotypically and transcriptionally distinct malignant subpopulations within an immune-influenced microenvironment.

  Study EGAS50000001564

• Target sequencing for 53 synovial sarcoma patients

  This dataset contains 138 .bam files sequenced with Illumina NovaSeq 6000. The files with the variant calling performed to the sequencing data, as well as the clinical data (phenotype) extracted during the sample extraction.

  Study EGAS50000000522