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• Inferring expressed genes by whole-genome sequencing of plasma DNA

  The analysis of cell-free DNA (cfDNA) in plasma represents a rapidly advancing field in medicine. cfDNA consists predominantly of nucleosome-protected DNA shed into the bloodstream by cells undergoing apoptosis. We performed whole-genome sequencing (WGS) of plasma DNA and identified two discrete regions at transcription start sites (TSS) where the nucleosome occupancy results in different read-depth coverage patterns in expressed and silent genes. By employing machine learning for gene classification we found that the plasma DNA read depth patterns from healthy donors reflected the expression signature of hematopoietic cells. In cancer patients with metastatic disease, we were able to classify expressed cancer driver genes in regions with somatic copy number gains with high accuracy. We could even determine the expressed isoform of genes with several TSSs as confirmed by RNA-Seq of the matching primary tumor. Our analyses provide functional information about the cells releasing their DNA into the circulation.

  Study EGAS00001001754

• Familial adult myoclonic epilepsy in Sri Lankan and Indian families

  Familial adult myoclonic epilepsy 1 (FAME1), first recognised in Japanese families, was recently shown to be caused by a TTTCA repeat insertion in intron 4 of SAMD12 on chromosome 8. We performed whole genome sequencing on two families with FAME, one of Sri Lankan origin and the other of Indian origin, and identified a TTTCA repeat insertion in SAMD12 in both families. Haplotype analysis revealed that both families shared the same core ancestral haplotype reported in Japanese and Chinese families with FAME1. Mutation dating, based on the length of shared haplotypes, estimated the age of the ancestral haplotype to be approximately 670 generations, or 17,000 years old. Our data extend the geographic range of this repeat expansion to Southern Asia and potentially implicate an even broader regional distribution given the age of the variant. This finding suggests patients of Asian ancestry with suspected FAME should be screened for the SAMD12 TTTCA expansion.

  Study EGAS00001004012

• PCCRC versus prevalent CRC

  To analyse genome wide DNA copy number changes in combination with mutation status of CRC-related genes, CIMP and MSI, in order to explore the biology of PCCRCs. Formalin-fixed, paraffin-embedded samples from 122 PCCRCs and 98 prevalent CRCs collected in 3 different hospitals in the region of South Limburg, the Netherlands, were used in this study. DNA was extracted for molecular analysis. Labels have been updated.

  Dataset EGAD00001006987

• WGS dataset for Unraveling mutagenic processes influencing the tumor mutational patterns of individuals with Constitutional Mismatch Repair Deficiency

  Molecular characterization of 41 tumors from 17 individuals with CMMRD to gain a better understandig of mutational processes driving subsequent tumor development. The molecular characterization includes the investigation of tumor mutational load and mutational signatures.

  Dataset EGAD00001015157

• Genome Denmark Phase II - alignments

  Alignment of Genome Denmark Phase II dataset to GRCh38. The dataset consists of 150 Danish individuals (50 trios) sequenced to 80X. The BAM-file contains data from multiple libraries created from one individual with libraries of 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The libraries were created using standard Illumina protocols for paired end reads (180-800bp libraries) and mate pair libraries (2kb-20kb).

  Dataset EGAD00001003157

• 48 EXOMES FAMILIAL MYELOID LEUKEMIA (QMUL)

  Whole exome sequencing (WES) libraries were prepared from 200ng of genomic DNA using the Agilent SureSelect XT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library coupled with the Agilent SureSelect XT Human all exon v6 capture reagent. Libraries were sequenced on a NextSeq 550 sequencer using the High output 300 cycles kit generating 150bp paired end single-indexed reads. Alignment against b37 using Novoalign (version 3.02.08).

  Dataset EGAD00001004539

• RNA-seq transcriptome of bronchial brush samples from COPD and control

  Human subjects (COPD patients or apparently healthy controls) where investigated by bronchoscopy and a 5 mm brush was used to sample the subsegment airways of the right lung. The material obtained mainly consist of bronchial epithelial cells plus some contamination with leukocytes. For further details see Ziegler-Heitbrock et al, European Respiratory Journal, 40:823-829, 2012.

  Dataset EGAD00001002003

• Cardiogenics_Custom_Pools - Agilent SureSelect

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Dataset EGAD00001000397

• Nimblegen

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Dataset EGAD00001000398

• The Spatio-Temporal Evolution of Multiple Myeloma from Baseline to Relapse-Refractory States

  In multiple myeloma, the spatio-temporal evolution patterns of cancer cells in the bone marrow remain largely unknown. Here, we applied spatial-longitudinal sequencing, including a total of 179 samples collected from 25 patients during a follow-up of up to 14 years. Our study highlights focal bone lesions (FL) as hotspots of tumor evolution and provides possible explanations for their negative prognostic impact. We show a close phylogenetic relationship between baseline FL and relapse clones. In patients with ≥3 FDG-PET-positive FL at diagnosis, relapse was driven by multiple distinct sub-clones, whereas in other patients, a single-cell expansion was typically seen (p<0.01). Applying imaging-guided sampling, we identified a novel evolutionary pattern with unique treatment-resistant sub-clones at distinct locations. We observed multiple selective clonal sweeps, resistant clones that can be hidden over years, and epigenetic modifier mutations as a new class of relapse aberrations. Here we show that imaging can enhance tumor evolution studies and response assessment. The sophisticated evolution mechanisms in myeloma and presence of single cells that can drive relapse even after 10 years of remission suggest that a prerequisite for curative therapies would be to overcome not only tumor heterogeneity but also dormancy.

  Study phs002625

• early-stage ESCC sequencing study

  We performed a comprehensive multi-omics analysis of 786 trace-tumor-samples from 154 esophageal squamous cell carcinoma phase (ESCC) patients, covering 9 histopathological stages in 3 phases as nontumor phase (NT phase), intraepithelial neoplasia phase (IEN phase), and ESCC phase. Proteogenomics elucidated the stage-specific molecular characterization and defined the cancer-driving waves along with the mutation accumulation in EC progression. The integrated multi-omics uncovered the chromosome 3q gain was the key event in the transmit from the NT to IEN phase, disclosed the top mutation of TP53 enhanced cell cycle and DNA replication in the IEN phase, and revealed the ESCC phase mutations of AKAP9 and MCAF1 elevated glycolysis and Wnt signaling, respectively. Furthermore, the trajectory analysis identified 6 major tracks related to different clinical features during ESCC progression. Growingly enhanced and hyperphosphorylated phosphoglycerate kinase 1 (PGK1, S203) was detected and considered as a drug target in ESCC progression. Collectively, this study provides insight into the understanding of ESCC molecular mechanism and a valuable resource for the development of therapeutic targets.

  Study EGAS00001006126

• Collaborative Study of Genes, Nutrients and Metabolites (CSGNM)

  While many genetic and metabolic studies focus on understanding disease states, this genome wide association study (GWAS) was designed to understand the influence of genetic variants on circulating metabolites and factors in normal, healthy individuals. Over 2500 healthy, ethnically Irish college students attending Trinity College Dublin completed a health and diet questionnaire and provided a non-fasting blood sample to be used for genetic and metabolic analysis. The questionnaire was designed to collect information on age, sex, height, weight, medical conditions, smoking, dietary habits, and consumption of alcohol, fortified foods, and supplements. Extracted DNA was genotyped using the Illumina HumanOmni1-Quad Beadchip. Metabolites were measured using a number of methods and focused on those relevant to the folate/vitamin B12 pathway.

  Study phs000789

• Establishing stable brain tumor stem cell lines and translational research for new treatments

  Choroid plexus carcinomas (CPCs) have dismal prognoses with limited clinical options. A lack of characterized cell lines has hindered the development of new treatment strategies. Here, we perform whole genome sequencing analyses of two cell lines established from CPCs. Whole genome sequencing (WGS),was performed in CCHE-45 and NGT131 cell lines. Both cell lines harbored pathogenic TP53 point mutations; CCHE-45 additionally displayed TP53 loss. Furthermore, alterations of the NOTCH and WNT pathways were also detected in both cell lines. Two protein-coding gene fusions, BZW2-URGCP, and CTTNBP2-ERBB4, mutations of two oncodrivers, GBP-4 and KRTAP-12-2, and several copy number alterations were observed in CCHE-45, but not NGT131. The discovered difference's importance and implications highlight the possible diversity of choroid plexus carcinoma and call for additional research to fully understand disease pathogenesis. Whole genome sequencing revealed that the two choroid plexus carcinoma cell lines shared TP53 mutations and other common pathway alterations and activation of NOTCH and WNT pathways. Noticeable differences were also observed. These cell lines can serve as valuable models to propose new treatments in these rare but deadly brain tumors.

  Study JGAS000657

• WXS and RNA-seq raw sequence data for TG project

  WXS sequence data from 112 samples, RNA-seq sequence data from 117 samples, all sequence data are raw sequence data in fastq format, sequenced by Illumina platform.

  Dataset EGAD00001007989

• HUG-CELL ASD Data Access Committee

  Data Access Committee for data generated by projects involving ASD and associated phenotypes by the Human Genome and Stem Cell Research Center (HUG-CELL), University of São Paulo

  Dac EGAC50000000475

• ChIP-Seq files for RMS.

  ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".

  Dataset EGAD00001006398

• Additional Sanger Sequencing and qPCR data to PSCNL samples

  Sanger sequencing and RT-qPCR data for validation used in Primary lymphomas of the central nervous system (PCNSL).

  Dataset EGAD00001008583

• ATAC-Seq of GM adipose tissue samples

  This dataset contains 28 fastq files (11 files for subcutaneous tissue and 17 files for visceral tissue) from nine individuals. All samples were initially sequenced by SEx50 mode (16 files) and some of them were also sequenced by PEx100 mode (12 files). Sequencing was done on the Illumina HiSeq2000 platform.

  Dataset EGAD00001010254

• Sequencing data for oesophageal / related samples - Kazachenka et al (DNA)

  Data supporting: "The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes" WGS for 452 samples

  Dataset EGAD00001011095

• Human Developmental Cell Atlas_HDCA - WGS (2019-04-11)

  Single cell + bulk genomics study for immune and hematopoietic organs during human fetal development . This dataset contains all the data available for this study on 2019-04-11.

  Dataset EGAD00001004953

• BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 Summary Statistics of Most Significant Associations

  BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 summary statistics of most significant association data include five molecular traits (eQTL, hQTL(H3K27ac), hQTL(H3K4me1), mQTL, and psiQTL) for three primary blood cells (Monocytes, Neutrophils, and T-cells). Each summary statistics file contains the most significant association for each phenotype ID.

  Dataset EGAD00001005200

• Genomic profiling of paediatric high grade gliomas from the HERBY clinical trial

  The HERBY trial was a phase-II open-label, randomised, multicentre trial evaluating bevacizumab in patients with newly-diagnosed non-brainstem high grade glioma (HGG) between the ages of 3-18yrs. 121 patients were randomised with 1yr event-free survival as the primary end-point. Confirmation of HGG diagnosis by reference pathology was mandatory before randomisation, followed by review with five independent expert neuropathologists. We collected specimens from 89 patients consenting to translational research, and performed Sanger sequencing for H3F3A, Illumina 450K BeadArray methylation profiling, and whole exome sequencing and RNA sequencing where possible. 7/89 patients (8%) harboured H3F3A G34R/V mutations, whilst 24/89 (27%) harboured H3F3A K27M, the latter reflecting a high proportion of the novel entity recognised in the 2016 WHO classification of diffuse midline glioma with H3K27M mutation. Both histone mutations conferred a significantly shorter progression-free (p=0.0104) and overall survival (p=0.00159). 450K methylation subtyping additionally identified a number of subgroups in histone wild-type cases. These included infrequent (4/86, 4.6%) cases with IDH1 mutation in older children, further categorised into astrocytic ATRX-mutant (n=3) or 1p19q co-deleted with TERT promoter mutation (n=1). 9/74, (12%) of cases were classified as biologically resembling pleomorphic xanthoastrocytoma (PXA) by methylation profiling, with 5/9 harbouring BRAF V600E mutations and epithelioid histology, and 3/9 NF1 mutation and giant cell features. Three cases had methylation profiles more closely resembling low grade gliomas, though were morphologically high grade, and harboured MAPK dysregulation in two cases, with the third part of an additional infant (<3yrs) cohort. Finally, four cases had a mutational burden several orders of magnitude higher than the rest, with (2197-5332) somatic coding variants/sample reflecting a hypermutator phenotype. These data provide an important insight into the wide biological diversity of ‘HGG’ found in the paediatric age group and allow for a profound refinement of clinical trial interpretation.

  Study EGAS00001002328

• Unraveling the Genetic Architecture of Diabetic Retinopathy in South India

  This study aims to understand the genetic architecture of diabetic retinopathy in the South Indian population by examining participants with South Indian ancestry and type 2 diabetes (T2D) from two sources: the Sankara Nethralaya-Diabetic Retinopathy Epidemiology and Molecular Genetic Study (SN-DREAMS) and prospective recruitment at Sankara Nethralaya affiliates. A total of 2393 patients were recruited and included in the genetic analysis, with 1588 patients having no diabetic retinopathy (DR) serving as the controls and 805 patients with any level of DR serving as the cases. Enrolled individuals had genome-wide genotyping from DNA extracted from blood samples. In addition, whole genome sequencing (WGS) was performed on 31 members from 2 families. Clinical data, such as age, duration of diabetes, and hemoglobin A1C (HbA1c) were recorded for study participants. Diabetic retinopathy was assessed by clinical exam and/or fundus photography. The grading of diabetic retinopathy followed the International Clinical Diabetic Retinopathy Severity Scale.

  Study phs002116

• Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas

  Molecular evidence of cellular heterogeneity in the human exocrine pancreas has not been established, due to the local concentration of hydrolytic enzymes that can rapidly degrade cells and RNA upon resection. Here we innovated single-nucleus RNA sequencing protocols, and profiled more than 120,000 cells from adult and neonatal human donors to create the first comprehensive atlas of human pancreas cells, including epithelial and non-epithelial constituents. Adult and neonatal pancreata shared common features, including the presence of previously undetected acinar subtypes, but also showed marked differences in the composition of the endocrine, endothelial, and immune compartments. Spatial cartography, including cell proximity mapping through in situ sequencing, revealed dynamic developmental cell topographies in the endocrine and exocrine pancreas. Our human pancreas cell atlas can be interrogated to understand pancreatic cell biology, and provides a crucial reference set for future comparisons with diseased tissue samples to map the cellular foundations of pancreatic diseases.

  Study EGAS00001004653

• Automated image-based profiling of complex drug induced phenotypes in patient-derived organoids

  We established a platform for high-throughput confocal fluorescence microscopy and automated image analysis to perform large-scale drug response profiling with patient derived organoids (PDOs). Using PDO lines newly established from colorectal cancer patients with a standardized workflow, we performed chemical perturbations with more than 500 experimental and clinically used compounds. Subsequently, we captured approx. six million images by confocal microscopy. To analyze drug-induced PDO re-organization on a single organoid level we developed SCOPE, a software framework for automated PDO high-throughput image analysis. We observed a rich variety of divergent and reoccurring compound induced phenotypes in organoids. Perturbation of cellular processes, including signaling by MEK, GSK3β, cyclin dependent kinases (CDKs) and others, led to recurring and distinct architectural changes. Highlighting the clinical relevance, PDO viability was heterogeneous after perturbation with anticancer drugs and matched clinical response of corresponding colorectal cancer patients. Our work opens new avenues for image-based profiling for accelerated drug discovery and clinical decision-making.

  Study EGAS00001003140

• Mechanism of Decitabine response in MDS/AML patients

  The dataset includes single cell RNA sequencing data from 17 AML/MDS patients undergoing a decitabine clinical trial. In total 47 samples were interrogated using 10X genomics ChromiumTM 140 Single Cell 5' Reagent Kit. The dataset includes bam files for each sample generated using CellRanger with default parameters.

  Dataset EGAD50000001354

• Single-cell/single-nucleus RNA-seq of diffuse hemispheric gliomas, H3G34-mutant.

  9 DHG-H3G34 patient samples were sequenced by paired-end scRNA-sequencing using the Smart-Seq2 protocol on a NextSeq 500 sequencer (Illumina). Illumina bcl2fastq 1.5 was used for demultiplexing. This dataset contains the resulting 9,408 fastq files of 4,704 single cells/nuclei sequenced.

  Dataset EGAD50000000760

• Piloting exome resequencing in consanguineous families with homozygosity mapping intervals

  This pilot study aims to generate pilot data to inform future study designs in consanguineous families or inbred populations by resequencing the exome of six individuals from five families with neurodevelopmental diseases. For all of these families a single mapping interval containing the causal variant has previously been identified.

  Dataset EGAD00001000341

• HV31 - 10x linked-read sequencing

  10x linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~40×. Sequencing was performed at Bart’s and the London Genome Centre on the Illumina HiSeq platform.

  Dataset EGAD00001007046

• Epichaperome - Englander Institute for Precision Medicine - Weill Cornell Medicine DAC

  This dataset accompanies the publication of Sugita M et al. "Targeting the Epichaperome As an Effective Precision Medicine Approach in a Novel PML-SYK Fusion Acute Myeloid Leukemia" Npj Precision Oncology 2021

  Dataset EGAD00001006904

• RNA-seq data for 67 patient cohort

  This dataset includes RNA-seq data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)

  Dataset EGAD00001008648

• WGS data for 67 patient cohort

  This dataset includes WGS data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)

  Dataset EGAD00001008647

• Exome data: Histone mutations in human Pre-Leukemic HSC and AML

  Exome sequencing was performed on samples from patients 064, 105, and 8760, including the remission sample for 105. Exomes were captured using the Agilent SureSelect All Exon kit v5 kit and libraries sequenced on HiSeq 2000 or 2500 or 4000.

  Dataset EGAD00001004436

• Low coverage WGS from plasma DNA

  Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002215

• Chromatin 3D interactions mediate genetic effects on gene expression (RNA-seq)

  RNA-seq data for 168 Lymphoblastoid Cell Lines (LCL) and 78 Fibroblasts (FIB) from the Gencord Cohort. This dataset was generated as part of the following study: Delaneau et al (2019). Chromatin 3D interactions mediate genetic effects on gene expression.

  Dataset EGAD00001004872

• Predictor_RIO_TNBC (2019-04-03)

  In this study, samples fom a window study of the PARP inhibitor rucaparib in patients with primary triple negative or BRCA1/2 related breast cancer (RIO trial) will be investigated. Samples will undergo whole genome sequence and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004894

• Wilms Tumour organoid sequencing WGS (2019-09-05)

  This study investigates the genomic and transcriptomic characteristics of Wilm's tumour organoids . This dataset contains all the data available for this study on 2019-09-05.

  Dataset EGAD00001005312

• Germline variants in patients with rare cancers - control samples WGS and WES

  The control samples (mostly blood) of 351 samples (paired WGS and WES sequencing) are in this dataset. The WGS was in nearly all cases at an Illumina HighSeq X Ten with the Illumina TruSeq Nano DNA Kit. The WES mostly on Illumina HighSeq 4000 with the Agilent SureSelect V5 plus UTRs Kit.

  Dataset EGAD00001010047

• Molecular counting enables accurate and precise quantification of methylated ctDNA for tumor-naive cancer therapy response monitoring

  Personalized cancer treatment can significantly extend survival and improve quality of life for many patients, but accurate and real-time therapy response monitoring remains challenging. To overcome logistical and technical challenges associated with therapy response monitoring via imaging scans or assays that track the variant allele fraction (VAF) of somatic mutations in circulating tumor DNA (ctDNA), we developed a tumor-naive liquid biopsy assay that leverages Quantitative Counting Template (QCT) technology to accurately and precisely quantify methylated ctDNA (Northstar ResponseTM).

  Study EGAS50000000734

• sWGS for 92 samples of mCRC

  Shallow Whole Genome Sequencing of 92 mCRC samples. Chromosomal copy number alterations analysis was performed with the samples to predict response to bevacizumab.

  Dataset EGAD50000000992

• Oncotrack_450K_tumor

  Oncotrack primary tumor samples using 450K. The dataset includes shared AF analysis files oncotrackDNAmAnalysis.R and oncotrackDNAmBetaScores.txt which were applied for both Oncotrack_450K_tumor (EGAD00010001162) and Oncotrack_450K_metastatic (EGAD00010001161) datasets.

  Dataset EGAD00010001162

• Sputum metagenome for COPD patients and healthy controls

  This dataset contains the sputum metagenome from 99 COPD patients and 36 healthy individuals in China.

  Dataset EGAD00001009063

• Exome sequencing of relapsed/refractory DLBCL

  This dataset consists of the exome sequencing data for 30 tumour and germline DNA pairs derived from relapsed/refractory DLBCL.

  Dataset EGAD00001003395

• ChIP-Seq files for RMS.

  ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".

  Dataset EGAD00001004312

• Whole exome sequencing of inflammatory bowel disease cases

  Whole exome sequencing of around 700 inflammatory bowel disease cases.This data can only be used for the identification of IBD/immune-mediated disease loci.

  Dataset EGAD00001001354

• Lund RNAseq data

  RNAsequencing data from human pancreatic islets from 191 donors, Lund University. Processed for the Inspire consortium.

  Dataset EGAD00001005512

• FMI data

  This dataset contains somatic alteration calls summarized at the gene level for 715 patients profiled by FoundationOne (Foundation Medicine).

  Dataset EGAD00001006616

• MGA-NUTM1 fusion in high grade spindle cell sarcoma

  NUT carcinoma (NC) with mesenchymal differentiation have rarely been described in the literature. In this report, we describe the characterization of two cases of high grade spindle cell sarcoma harboring a novel MGA-NUTM1 fusion. Whole genome sequencing identified the presence of complex rearrangements resulting in a MGA-NUTM1 fusion gene in the absence of other significant somatic mutations. The fusion protein was predicted to retain nearly the entire protein sequence of both MGA (exons 1-22) and NUTM1 (exons 3-8). In contrast to typical cases of NC, these cases were successfully treated with aggressive local control measures (surgery and radiation) and both patients remain alive without disease. These cases describe a new subtype of NUTM1-rearranged tumors warranting expansion of diagnostic testing to evaluate for the presence of MGA-NUTM1 or alternative NUTM1 gene fusions in the diagnostic workup of high grade spindle cell sarcomas or small round blue cell tumors of ambiguous lineage.

  Study EGAS00001003341

• A Genomic History of Aboriginal Australia

  The population history of Aboriginal Australians remains largely uncharacterised. We generated high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting early population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene (past c.10 kya) associated with limited gene flow from this region to the rest of Australia consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out of Africa dispersal, and subsequently admixed with different archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

  Study EGAS00001001766

• The 5-hydroxymethylcytosine Landscape of Prostate Cancer

  This dataset consists of genome-wide 5hmC methylomes at various stages of prostate cancer, including not only 93 metastases from castration-resistant prostate cancer (mCRPC) patients, but also 5hmC patterns in cell-free DNA (cfDNA). There are 2000 runs in total as fastq files.

  Dataset EGAD00001008462