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• The Xq22.3 contiguous gene deletion syndrome (ATS-ID): from genotype to further delineation of the phenotype

  Approximately 200 ng of high-quality of genomic DNA samples were used for library preparation. DNA libraries were prepared using the Human Core Exome Kit according to manufacturer’s recommendations (Twist Bioscience, San Francisco, CA, USA) and then sequenced on Illumina NovaSeq 6000 (Illumina, Inc., san Diego, CA, USA). Detailed protocol of WES data processing and variant analysis are available in Supplementary data.

  Dataset EGAD00001007740

• mapped Bam files from whole transcriptome RNA-seq

  In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 mapped Bam files form whole transcriptome RNA-seq.

  Dataset EGAD00001002718

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence

  ChIP-seq for AR, FOXA1 and H3K27ac in primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment. RNA-seq expression data of primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment.

  Dataset EGAD00001008562

• Genetic vulnerability of knockout cancer lines (2019-04-01)

  Genome-wide CRISPR/Cas9 library screen was performed in isogenic cell lines. Three biological replicates were used. Cells were harvested at initiation of screen and at specific time points following cell culture. Using this approach we aim to identify genes specifically important in cell survival in engineered cell lines. Please perform 72, instead of 36, PCR reactions as the screen performed at 200x coverage. . This dataset contains all the data available for this study on 2019-04-01.

  Dataset EGAD00001004881

• Somatic mutation and clonal evolution in the human bladder_TGS (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The study includes targeted sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006114

• Fastq and reference alignment of 19 samples for defining structural variation associated with breast cancer susceptibility by long-read genome sequencing

  Long-read genome sequencing performed on the Oxford Nanopore Technologies' PromethION to resolve variants underlying breast cancer susceptibility in sixteen individuals with pathogenic germline SVs in BRCA1, BRCA2, CHEK2 or PALB2.

  Dataset EGAD00001008690

• McGill EMC Community projects Release 7 for cell line "lung epithelial"

  Complete reference epigenome (as defined by IHEC) of a lung epithelial cell line with non-small Cell Lung Adenocarcinoma

  Dataset EGAD00001007679

• Stromal and dendritic cells from lymph nodes: single-cell RNA-seq

  Although cross-species transcriptional analysis has been generated for DCs, transcriptomic conservation between mouse and human FRCs at single-cell resolution has been unclear. To test whether GREM1+ FRCs might also play a role in DC homeostasis in humans, we performed scRNA-seq of CD45–PDPN+ stromal cells, as well as CD45+CD11c+ immune cells from healthy human LNs of three human donors. Data was generated using the 10x platform.

  Dataset EGAD00001008731

• Melanoma post mortem analysis

  Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient. This is a targeted pulldown validation in support of the whole-genome sequencing analysis of the metastatic tumours and targeted pulldown of the primary tumour.

  Dataset EGAD00001005073

• Whole genome sequencing of multifocal ileal neuroendocrine tumors

  This dataset includes whole genome sequences of 75 synchronous primary tumors, 15 metastases, and corresponding normal samples from 13 patients with multifocal ileal neuroendocrine tumors. The whole genomes were sequenced on Illumina HiSeq X Ten to generate 151-bp paired-end reads, which were aligned to GRCh38/hg38 reference assembly using BWA–MEM and duplicate-marked with Picard tools. GATK was utilized for base score recalibration and local indel re-alignments. The whole genomes are provided as CRAM files.

  Dataset EGAD00001008831

• Exome Sequencing of Poor Prognosis Acute Myeloid Leukaemia (2019-08-19)

  We plan to sequence the exomes of 4 AML cases (tumour and germline) in an effort to discover new mutations in this disease that could improve our understanding of leukaemogenesis and guide the development of new targeted therapies. The Sanger Institute will sequence the exomes of 4 Acute Myeloid Leukaemia cases including tumour and germline DNA so that somatically-acquired, AML-specific mutations can be accurately designated. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005265

• Fusion gene analysis using multiplex single primer extension-based RNA-sequencing

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains fusion gene analysis using multiplex single primer extension-based RNA-sequencing for a subset of 25 patients of the screening cohort. Data was generated on Illumina NexSeq 550 device in paired-end mode and is stored in compressed FASTQ file format.

  Dataset EGAD00001011326

• WGS data from LCNEC patient derived tumor organoids (PDTOs) and matched parental tumors - SA

  The dataset includes cram files from WGS of 2 LCNEC tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue derived organoids from the corresponding patients is included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

  Dataset EGAD00001009990

• Whole exome data from PMID27216186

  This dataset comprises complete exome data from from the study PMID27216186 (Harbst & Lauss et al, Cancer Research 2016). These data are from 49 samples (tumor and matched normal) from 8 patients representing multi-region sequencing of human melanoma. Files are in the BAM format and contain aligned and processed data used for e.g. somatic variant calling. The sequencing libraries were constructed using SureSelect target enrichment with Clinical Research Exome Panel (Agilent) and sequenced on a HiSeq2500 (Illumina).

  Dataset EGAD00001008149

• Paired-WGS Sequencing of Primary lymphomas of the central nervous system (PCNSL)

  Paired WGS samples, 24 tumor/control pairs of primary CNS lymphoma, sequenced on HiSeq X Ten using Illumina TruSeq Nano DNA for library preparation.

  Dataset EGAD00001007810

• Dataset RNA-Seq of tumors for ImmuNEO already used in study EGAS00001004813

  Sequencing data of 20 tumor runs (different tumors), which were uploaded to EGAS00001004813 and used in the ImmuNeo publication. The sequencing was always paired and run on Illumina HiSeq sequencers.

  Dataset EGAD00001009670

• Single-cell RNA and TCR sequencing of BALF from 11 ICI-pneumonitis patients and 6 controls

  Dataset containing the FASTQ files of RNA (scr*) and TCR (vdj*) sequencing of 17 bronchoalveolar lavage fluid samples collected from ICI pneumonitis (n=11) and control (n=6) patients. To comply with GDPR regulations, please note that individual sample identifiers used for this data deposit (alphabetical ID) are different from and cannot be traced back to the patient identifiers used throughout the manuscript (numerical ID).

  Dataset EGAD00001009723

• GELATO clinical trial RNA-Seq data (metastatic lesions)

  RNA-Seq data of 46 matched lobular breast cancer metastatic samples obtained from 21 unique patients from GELATO clinical trial assayed at three timepoints: at baseline (directly after patient randomization), pre-atezolizumab (after induction treatment with carboplatin for two weeks) and on atezolizumab (after two cycles of atezolizumab combined with carboplatin). The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009834

• Presentation and relapse myeloma

  Series of 56 paired presentation, relapse and control samples from newly diagnosed, uniformly treated myeloma patients. Deep of treatment response and maintenance allocation (active observation or lenaldiomide) was determined for all. All samples underwent whole exome sequencing with additional baits to cover the myc and immunoglobulin loci. There are 168 (56 presentation, 56 relapse and 56 control) samples in this study. 131 are available as part of this dataset. The remaining 37 are available with dataset accession id EGAD00001001358.

  Dataset EGAD00001004846

• Multi-region sequencing of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region whole-exome sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Dataset EGAD00001008020

• Egypt Genome Project - high coverage whole genome sequencing

  All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate high-coverage sequencing data for 3 Egyptian samples.

  Dataset EGAD00001001380

• Cancer gene panel (T200.1) sequencing analysis of adult type ovarian granulosa cell tumors (Validation cohort from Hillman, et al)

  Cancer gene panel (T200.1) sequencing data from tumor/normal pairs for adult type ovarian granulosa cell tumor sequencing project. This data set contains 55 tumor panel sequencing data and 44 matched normal panel sequencing data generated using the MD Anderson Cancer Center T200.1 cancer gene hybrid capture platform, with sequencing performed on an Illumina HiSeq 2000. This dataset contains BAM files generated by aligning paired-end reads to the hg19 reference genome.

  Dataset EGAD00001004091

• Subclonal analysis in S7RE2 and S7RE14 iPS cells

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001000608

• Sequencing data for oesophageal and related samples - Abujudeh et al (WGS, fastSeq)

  Data supporting: "Low-cost and clinically applicable copy number profiling using repeat DNA." Abujudeh et al. DNA WGS (BAM files) DNA fastSeq (fastq files) Tumours, Barrett's, normals.

  Dataset EGAD00001004289

• Dataset of PGD PGS study in CITIC Xiangya and BGI

  A total of 395 couples were subjected to IVF-PGD treatment, including 129 couples with NGS-based test and 266 couples with SNP array based test for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole genome sequencing with HiSeq 2000 platform. And the SNP array test was using Affymetrix Gene Chip Mapping Nsp I 262K. The average age of patients was 32.1 years (age range 20-44 years).

  Dataset EGAD00001001037