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• Pre-neoadjuvant treatment biopsy RNAseq breast cancer dataset

  This dataset contains RNAseq data of n=87 pre-treatment biopsies of triple negative and luminal- type breast cancer patients, all scheduled to receive neoadjuvant chemotherapy. Gene expression data is linked with treatment response and survival.

  Dataset EGAD00001008433

• Oropharyngeal Squamous Cell Carcinoma Mutanome

  This dataset comprises genetic variation data (as somatic indels and snvs VCFs) of 38 OPSCC tumors. WES was done using NextSeq 500 System running in 150 cycles (2x 75bp paired-end) mode. Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422. VCFs were generated using the Strelka package.

  Dataset EGAD00001009167

• Dataset for MCPlus_WES

  WES/WGS sequencing data of 75 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009276

• Dataset for negative_WES

  WES/WGS sequencing data of 242 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009278

• HDBR exome sequencing data (November 2022)

  Exome sequencing data from seven phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2

  Dataset EGAD00001009715

• PacBio HiFi sequencing of telobait-captured DNA from 68 patients

  PacBio HiFi sequencing was performed on 68 barcoded patients' genomic DNA after a telobait-capture protocol to enrich for telomeric regions. The sequencing reads of each patient were de-multiplexed and presented as patient-specific PacBio CCS BAM files. There are 56 new samples and 12 repeated samples from run 1.

  Dataset EGAD00001009397

• Germline variants in childhood melanoma

  Whole-exome sequencing was performed on DNA extracted from blood samples of 50 children diagnosed with cutaneous melanoma prior to 18 years of age. Patients were all diagnosed in Queensland, Australia, and self-reported as of European descent. Sequencing was done the Illumina platform using SureSelct V7 Post capture kits.

  Dataset EGAD00001010039

• Primary_DIPG_expression_profiles

  In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG. Seventeen primary tumor samples stereotactically biopsied at diagnosis by neurosurgeons in the Necker-Enfants Malades hospital (Paris, France) and snap-frozen for RNA extraction and subsequent poly-A mRNA purification.

  Dataset EGAD00001011080

• Germline genome sequencing samples from the Hereditary Cancer Syndromes (ICCon) Cancer Flagship

  A prospective study of individuals with suspicion of a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or was not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing and a comprehensive cancer virtual gene panel analysis were undertaken.

  Dataset EGAD00001011260

• scRNAseq data from ALI cultures of healthy donors and patients with asthma, infected with RSV

  This dataset contains the count matrices and corresponding metadata for our study on bronchial epithelial cells response to RSV in healthy and in asthma. This scRNAseq data is from primary cells, that have been differentiated in ALI cultures and infected with RSV.

  Dataset EGAD00001011264