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• Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

  Here, we profile the adult human CNS from distinct regions, sex and ages, for chromatin accessibility at the single-nuclei level. Tissue was collected from 20 different donors (10 male, 10 female) within the ages of 34 to 74 years old. Each donor donated fresh frozen white matter from the following three tissue regions: primary motor cortex (Brodmann area 4, BA4), arbor vitae cerebelli (CB) and fasciculi cuneatus and gracilis from and cervical spinal cord (CSC). Tissue was processed semi-randomly, ensuring that each batch of experiments had a representation of both sexes and all three tissue regions. Completed libraries were again randomly multiplexed during sequencing to minimize batch effects.

  Study EGAS50000000283

• Genetic landscape of non-Down syndrome acute megkaryoblastic leukemia

  To define the mutation spectrum in non-Down syndrome acute megkaryoblastic leukemia (non-DS-AMKL), we performed transcriptome sequencing on diagnostic blasts from 14 pediatric patients and validated our findings in a recurrency/validation cohort consisting of 34 pediatric and 28 adult AMKL leukemia samples. Our analysis identified a cryptic chromosome 16 inversion [inv(16)(p13.3q24.3)] in 27% of pediatric cases, which encodes a CBFA2T3-GLIS2 fusion protein. Expression of CBFA2T3-GLIS2 in Drosophila and murine hematopoietic cells induced bone morphogenic protein (BMP) signaling, and resulted in a marked increase in the self-renewal capacity of hematopoietic progenitors. These data suggest that expression of CBFA2T3-GLIS2 directly contributes to leukemogenesis.

  Study EGAS00001000379

• A Combined Omics and Tissue Biobank for Paediatric Cancers

  The Swedish Childhood Tumour Biobank (BTB) is a nonprofit national infrastructure for samples and genomic data collection from pediatric patients diagnosed with central nervous system and other solid tumours in Sweden. Fresh frozen tumour tissue and patient’s matched blood are collected from affected patients and genomic data is continuously generated and made available for approved medical research projects. We expect that the accessibility of biological samples and/or data to the research community will contribute to further advances in the understanding of tumour biology, which in turn will impact many aspects of clinical care of children with cancer, by refining diagnosis and/or identifying oncogenic drivers and therapeutic targets.

  Study EGAS50000000209

• MATISSE Whole-exome sequencing data

  Sample availability: WES was performed on 41 available baseline tumor and blood samples (22 CCRs/MPRs, 5 PPRs, 14 CRN/NPRs). Tumor DNA was extracted from formalin-fixed paraffin-embedded (FFPE) primary tumor and lymph node metastasis sections containing at least 10% viable tumor cells present in the sample. A pathologist (LS) scored the tumor percentage and indicated the most tumor-dense region on a hematoxylin and eosin (H&E) stain slide for subsequent DNA isolation. According to the manufacturer's protocol, five to 10 FFPE slides (10 µm) were used for DNA isolation using the AllPrep DNA FFPE isolation kit (Qiagen, 80234) and the QIAcube. Germline DNA was isolated from baseline PBMCs using the AllPrep DNA / RNA / miRNA Universal isolation kit (Qiagen, 80224) and the QIAcube, according to the manufacturer’s protocol. Genetic Diagnostics and Sequencing Services (CeGaT) performed whole-exome sequencing sequencing in Germany. Data processing: Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (v2.20). Adapters of the reads were trimmed with Skewer (v0.2.2), without quality trimming. Sequencing reads were aligned with BWA (v0.7.17) to the human reference genome GRCh38 (Ensemble, v105). Duplicated reads were marked using Picard (v2.25.0) MarkDuplicates, after which quality scores were recalibrated using GATK4 (4.2.2.0) BaseRecalibrator. FastQC (v0.12.1), MultiQC (v1.14), Mosdepth (v0.3.3) and NGScheckmate (v1.0.1) were used for assessing data quality, on FASTQ files and intermediate processing steps.

  Dataset EGAD50000001469

• Genetic landscape of pediatric Medulloblastoma

  Medulloblastoma is a heterogenous disease made up of at least four distinct subtypes of disease which appear to exploit and disrupt naturally occurring developmental pathways of cellular growth and hindbrain development. To better understand the driver mutations of this disease, we performed whole genome sequencing of 37 medulloblastomas and the corresponding normal DNA of the 37 affected children treated at St. Jude Children's Research Hospital. We have found several novel mutations which appear subtype specific. These mutations were checked for frequency in a separate tumor cohort of 56 children with medulloblastoma, also treated on the St. Jude Medulloblastoma 2003 trial, and were tested in several animal models of medulloblastoma for proof of oncogenic potential.

  Study EGAS00001000347

• Exome sequencing to identify predisposition to Wilms tumour

  To identify new Wilms tumor predisposition genes, we performed whole-exome paired-end sequencing of lymphocyte DNA from 12 affected individuals from six unrelated, non-syndromic Wilms tumor families in which known causes had been excluded.We prepared DNA libraries from 1.5 mg blood-derived genomic DNA using the Paired-End DNA Sample Preparation Kit (Ilumina). DNAwas fragmented using Covaris technology and the libraries were prepared without gel size selection. We performed target enrichment using the TruSeq Exome Enrichment Kit (Illumina) by targeting 62 mb of the human genome. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers.Sequencing was performed with an Illumina HiSeq2000 generating 2?101 bp reads.

  Study EGAS00001000904

• Comprehensive analysis of the (epi)genome of pediatric atypical teratoid/rhabdoid tumours (AT/RTs)

  Whole exome sequencing of atypical teratoid /rhabdoid tumors (AT/RTs) revealed recurrent mutations only in SMARCB1, a gene involved in chromatin remodeling. However, preliminary data from our lab using gene expression and DNA methylation arrays shows that there are three distinct molecular subgroups of AT/RTs, suggesting that other molecular alterations underlying the development of these aggressive pediatric brain tumors must be found outside the coding genome or at the epigenomic level. Identification of these (epi)genomic alterations, which we intend to address in this project, may lead to novel treatment strategies for these tumors and reveal options for meaningful patient stratification.

  Study EGAS00001001297

• Multiregion Whole Exome sequencing of paediatric High Grade Gliomas and DIPG

  Paediatric High Grade Gliomas (pHGG) are defined by unique, specific and highly recurrent mutations in genes encoding histone H3 variants which mark robust subgroups with distinct age of onset, anatomical distribution, clinical outcome, histopathological and radiological features. We have used whole exome sequencing to identify the main recurrent somatic mutations occurring within pHGG including H3 histones and the coincident mutations and DNA copy number events in order to classify clinically relevant subgroups and the molecular events within them as new targets for therapy. Analysis of sequenced cases revealed multiple tumour subclones, spatially and temporally co-existing in a stable manner as observed by multiple sampling strategies.

  Study EGAS00001001436

• Identifying causative mutations for Thrombocytopenia with Absent Radii

  Thrombocytopenia with Absent Radii is an inherited disorder that manifests itself with major limb skeletal abnormalities and low platelet count (and therefore a bleeding diathesis). The syndrome is well-characterised and defined phenotypically and there is a well-established database of UK-based families affected with ths disorder. The causative mutation for the disorder is yet to be identified. If known, it would allow for pre-natal screening and counselling avoiding life-long care for patients who are affected and are therefore severely disabled. We postulate that exon sequencing of 4 unrelated affected individuals would give enough power to narrow down potential candidate mutations which would thereafter be confirmed using DNA from other affected families.

  Study EGAS00001000054

• Samples from the Greek island of Crete, MANOLIS cohort

  Genome-wide association studies of complex traits have been successful in identifying common variant associations, but a substantial heritability gap remains. The field of complex trait genetics is shifting towards the study of low frequency and rare variants, which are hypothesised to have larger effects. The study of these variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. This work focuses on isolated populations from Greece. Sequencing is very efficient in isolated populations, because variants found in a few samples will be shared by others in extended haplotype contexts, supporting accurate imputation.

  Study EGAS00001000067