The data contains single-cell gene sequencing data (10x Genomics) from FACS-purified CD8 T lymphocytes from two Austrian patients. The cells were stimulated with one MHC class I peptides obtained from a common (wild type) variant and an emerging mutant variant of the SARS-Cov-2 virus. Then the samples were multiplexed using hashtag oligos. We provide the raw and aligned sequence data for: i. The single-cell experiments ii. The PCR-amplified samples for enrichment of the hashtag oligo multiplexing barcodes iii. The PCR-amplified samples for enrichment of the T Cell Receptor (TCR) VDJ region for immuno-profiling. The samples and libraries were processed and obtained in collaboration between St. Anna Children's Cancer Research Institute (CCRI), CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, and the Medical University of Vienna. The cell barcodes and processed data has been submitted to the GEO database with GEO accession GSE166651.
In the context of research, this dataset contains 423 IRD samples; 411 of them analyzed with Clinical Exome Sequencing solutions, and 12 with Whole Exome Sequencing.
Profiling of co-mutations was done by targeted resequencing using the TruSight Myeloid assay (Illumina, Chesterford, UK) covering 54 genes recurrently mutated in AML: BCOR, BCORL1, CDKN2A, CEBPA, CUX1, DNMT3A, ETV6, EZH2, IKZF1, KDM6A, PHF6, RAD21, RUNX1, STAG2, ZRSR2, ABL1, ASXL1, ATRX, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CSF3R, FBXW7, FLT3, GATA1, GATA2, GNAS, HRAS, IDH1, IDH2, JAK2, JAK3, KIT, KRAS, MLL, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PTEN, PTPN11, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, TET2, TP53, U2AF1 and WT1. For each reaction, 50 ng of genomic DNA was used. Library preparation was done as recommended by the manufacturer (TruSight Myeloid Sequencing Panel Reference Guide 15054779 v02, Illumina). Samples were sequenced paired-end (150 bp PE) on NextSeq- (Illumina) or (300 bp PE) MiSeq-NGS platforms, with a median coverage of 3076 reads (range 824–30565). Sequence data alignment of demultiplexed FastQ files, variant calling and filtering was done using the Sequence Pilot software package (JSI medical systems GmbH, Ettenheim, Germany) with default settings and a 5% variant allele frequency (VAF) mutation calling cut-off. Human genome build HG19 was used as reference genome for mapping algorithms.
26 Tumor/Control pairs of WGS data of PCNSL tumors, sequenced on either Illumina HiSeq2000/2500 instruments or HiSeq X Ten. The controls are blood or buffy coat samples in most cases.
We analyzed 34 AGCTs (19 primary and 15 recurrent) and the KGN cell line by RNA-Seq. Our cohort comprised of 3 AGCTs WT for FOXL2, 28 heterozygous and 3 homo/hemizygous for the pathogenic variant. Fresh-frozen AGCTs were selected from OVCARE’s Gynecological Tissue Bank in Vancouver, Canada for bulk RNA-seq. RNA was extracted from frozen tissue and sections adjacent to the scrolls submitted for RNA-seq were stained with hematoxylin and eosin (H&E) to evaluate tumour cell purity. Cases with >80% tumour cell purity were selected for sequencing with the majority of cases (29 of 34 patients) containing >90% tumour cells. Ribodepleted RNA libraries were constructed and paired-end sequencing (125 base pair reads) was performed.
Tumor Total RNA Seq data of primary neuroblastomas. This is an update of the „Berlin Neuroblastoma Dataset” (EGAS00001004022). This data was used for the analysis of circular RNA expression and regulation in neuroblastoma.
Cancers of adults typically arise through progressive rounds of clonal diversification and intratumoral selective sweeps which generate a long mutational trunk with shorter subclonal branches. Here, we investigated whether tumors of young children exhibit the same phylogenetic configuration. We studied three infants, including two newborns, with the childhood kidney cancer, Wilms tumour, through whole genome sequencing of bulk tissues, of single cell derived organoids, and of microdissections. All three cancers exhibited unusual driver events, with tumours of newborns harbouring FOXR2 rearrangements, delineating a distinct variant of Wilms tumour. Phylogenetic analyses suggest that tumors were seeded in an early, possibly confined window of development. Unusually, following seeding there was extensive polyclonal diversification with little evidence of clonal sweeps, leading to a distinct phylogenetic configuration more reminiscent of normal tissues rather than of adult cancers. These findings indicate that some childhood cancers may diversify via unorthodox phylogenetic pathways.
Rare cancer sequencing data of 95 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired
Whole genome sequencing of sick children in neonatal and paediatric intensive care units, aligned to reference assembly GRCh37.
This dataset contains .fastq files generated by targeted DNA sequencing of 542 cancer-associated and cadidate genes (52 individuals), and targeted duplex sequencing of PIK3CA and TP53 genes (4 individuals).
