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• Whole genome and RNA sequencing of cutaneous melanoma metastases

  Whole genome sequencing of cutaneous melanoma skin and brain metastases and matched normal DNA, as well as RNA sequencing of material from the skin and brain metastases. In addition, RNA sequencing was performed for Dabrafenib and Trametinib treated patient-derived xenografts, together with untreated and vehicle treated controls.

  Dataset EGAD00001004130

• Haplotype Reference Consortium Release 1.1

  Haplotype Reference Consortium Release 1.1 - subset for release via the EGA

  Dataset EGAD00001002729

• Sequencing data for ICGC / OCCAMS samples - Perner et al (WGS, sWGS, WES, mutREAD)

  Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files

  Dataset EGAD00001006170

• RRBS profiling for a cohort including 88 precancer specimens from 62 resected lung nodules from 39 patients including atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (ADC) and 39 matched normal lung tissues.

  To study the evolution of DNA methylation at genome level and methylation intra-tumor heterogeneity (ITH) during early lung carcinogenesis, we performed multiregional reduced representation bisulfite sequencing (RRBS) of 127 resected lung samples from 39 patients using single end library Hiseq3000.

  Dataset EGAD00001006367

• 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

• 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

• 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

• Spectrum of Response to Platinum and PARP Inhibitors in Germline BRCA Associated Pancreatic Cancer in the Clinical and Pre-clinical Setting

  Whole genome sequencing data for germline BRCA pancreatic cancer

  Dataset EGAD00001011129

• Genomic landscapes of endometrioid and mucinous ovarian cancers and morphologically similar tumor types

  While endometrioid and mucinous ovarian cancers represent nearly a quarter of ovarian cancers, their molecular characteristics and pathologic origins are poorly understood. To characterize the genomic and epigenomic alterations of these ovarian cancer subtypes and evaluate links to morphologically similar tumors from other sites, we performed sequence, copy number, mutation signature, rearrangement, and methylation analyses from tumor samples and matched normal tissues of 133 patients. These analyses included patients with ovarian endometrioid (n=44), ovarian mucinous (n=43), uterine endometrial (n=15), and gastrointestinal mucinous cancers (n=31). In addition to identifying genes previously known to be involved in these tumors, we identified alterations in RAD51C, NOTCH4, SMARCA1/4 and JAK1 in ovarian endometrioid, ESR1 in uterine endometrioid, and SMARCA4 in ovarian mucinous cancers. Whole genome sequencing revealed rearrangements involving PTEN, NF1, and NF2 in ovarian endometrioid tumors, and NF1 and MED1 in ovarian mucinous cancers. The number of alterations and affected genes in ovarian and uterine endometrioid cancers were similar as were genome-wide methylation profiles, suggesting that these tumors may have a similar tissue of origin. By contrast, methylation patterns in ovarian mucinous cancers were more similar to other gastrointestinal mucinous cancers, including mucinous cancers of the stomach, colon, and pancreas. These analyses provide insights into the genomic landscapes and origins of mucinous and endometrioid ovarian carcinomas, providing new avenues for early clinical intervention and management of patients with these cancers.

  Study EGAS50000000523

• Germline variants collaborate with somatic mutations and initiate and/or drive disease in primary myelodysplastic syndrome (MDS) and therapy-related myeloid neoplasms (t-MN)

  Therapy-related myeloid neoplasms (T-MN) are poorly characterized secondary hematological malignancies following chemotherapy/radiotherapy exposure. We compared the clinical and mutational characteristics of T-MN (n=129) and primary myelodysplastic syndrome (P-MDS, n=108) patients. Although the somatic mutation frequency was similar between T-MN and P-MDS patients (93% in both groups), the pattern was distinct. TP53 mutations were more frequent in T-MN (29.5% versus 7%), while spliceosomal complex mutations were more common in P-MDS (56.5% versus 25.6%).In contrast to P-MDS, the ring sideroblasts (RS) phenotype was not associated with better survival in T-MN, most probably due to genetic association with TP53 mutations. SF3B1 was mutated in 96% of P-MDS with ≥15% RS, but in only 32% T-MN. TP53 mutations were detected in 92% T-MN with ≥15% RS and SF3B1 wild-type cases. Interestingly, T-MN and P-MDS patients with “Very low” or “Low” Revised International Prognostic Scoring System (IPSS-R) showed similar biological and clinical characteristics. In a Cox-regression analysis, TP53 mutation was a poor prognostic factor in T-MN, independent of IPSS-R cytogenetic, disease-modifying therapy and NRAS mutation.Our data have direct implications for T-MN management and provide evidence that, in addition to conventional disease parameters, mutational analysis should be incorporated in T-MN risk stratification.

  Study EGAS00001003547

• WGS of Newly Diagnosed and Refractory/Relapsed Multiple Myeloma

  This dataset includes paired tumor and non-tumor WGS data from patients diagnosed with newly diagnosed (n = 6), refractory/relapsed multiple myeloma (n = 3) or plasma cell leukemia (n = 1). These samples presented >95% tumor PCs in bone marrow aspirates. Plasma cells and T cells (non-tumor cells) were isolated from bone marrow aspirates using a magnetic approach.

  Dataset EGAD50000001177

• RNAseq Data Cyr61-MAC and HUVEC

  Gene expression of MAC enriched by adhesion to Cyr61 in comparison to HUVEC. This dataset includes RNAseq Data from myeloid angiogenic cells (MAC) enriched from peripheral blood by adhesion to Cyr61 (4 samples prepared from different donors) and of human umbilical vein endothelial cells (HUVEC) (4 samples). Illumina NextSeq500 technology was used. FASTQ data are provided.

  Dataset EGAD50000000758

• RNAseq counts

  RNA-seq data from ILC samples. This dataset includes raw, unnormalized counts per gene, per sample.

  Dataset EGAD50000000826

• Whole genome sequencing of HSPC and SI clones of disomy- and trisomy 21 fetuses samples (HiSeq X Ten samples)

  Whole genome sequencing of HSPC and SI clones of 2 disomy- and 1 trisomy 21 fetuses samples (HiSeq X Ten samples). 5 disomy clones and 5 trisomy clones were included in this experiment. Three bulk samples were also included.

  Dataset EGAD00001005459

• Single-cell RNA-seq of AML blasts pre and post culture

  This dataset contains 6 Fastq files from 3 samples (pre-culture (n=1), post culture in standard (n=1) or niche-llike (n=1) conditions) from 1 AML patient. They correspond to single-cell RNA sequencing on Illumina plateform of 3 libraries prepared with 10X Genomics gene expression V3.1 chemistry.

  Dataset EGAD00001008772

• Blood and skin fibroblasts PSA study

  This dataset contains RNA-sequencing of blood samples from Healthy Controls (n=7), PSA patients (n=27) and RA patients (n=9). It also contains RNA-sequencing data of skin fibroblasts from healthy controls (n=3) and PSA patients (n=3).

  Dataset EGAD00001009069

• Genome-wide array data Algeria

  This dataset contains genome-wide array data from Amazigh (Chaoui and Mozabite) and non-Amazigh Algerian individuals. Chaoui were sampled in Oum El Bouaghi (n=47), Batna (n=46), and Khenchela (n=37). Mozabite were sampled in Ghardaïa (n=14). Non-Imazighen were sampled in Algiers (n=34).

  Dataset EGAD00001010900

• Low-coverage whole-genome sequencing of cancer and healthy plasma circulating DNA

  Plasma samples from patients with melanoma (stage II/III/IV) and breast cancer (stage IV) as well as healthy individuals were subjected to low-coverage whole-genome sequencing (less than 10x average depth). This dataset contains raw fastq files from 39 breast cancer, 127 melanoma and 42 healthy control plasma samples.

  Dataset EGAD00001011817

• WGS of tumor and blood control samples of neuroblastoma

  high coverage whole genome sequencing of 38 samples was done on a patterned flowcell v.2.5 (150 bp paired end, HiSeq X Ten) with coverage of about 60x for the tumor and whole blood control samples. All tumors had a tumor cell content of ≥60%. Sequencing libraries were prepared using the Truseq DNA Nano kit (Illumina) according to the manufacturers’ instructions and size selected using SPRI beads (Beckman Coulter Genomics).

  Dataset EGAD00001009624

• Patient-derived models of primary breast cancer for preclinical development of novel neoadjuvant therapies

  Generation of the first large-scale cohort of mouse intraductal patient-derived xenograft (MIND-PDX) models of primary invasive breast cancer (IBC) and a collection of matched PDX-derived organoids (PDXO) representing all molecular subtypes of IBC, including estrogen receptor (ER-) positive breast cancer. Furthermore, we show that our IBC-MIND cohort can serve as a platform to test experimental neoadjuvant treatment options in different molecular subtypes of breast cancer.

  Study EGAS50000000398

• Cas9-targeted-based long-read sequencing for genetic screening of RPE65 locus

  In order to compare sequencing performance of different technologies in a specific locus, we sequenced blood samples of five inherited retinal dystrophies (IRD) patients harboring a monoallelic variant in RPE65 that remained uncharacterized with: 1) Clinical exome targeted sequencing (CES), 2) whole genome sequencing (WGS), and 3) Long-read sequencing on a MinION platform where CRISPR-Cas9 guide RNA probes were designed to target a 31 kb region including the entire RPE65 locus.

  Study EGAS50000000596

• EGAD00010000807

  Illumina HumanCoreExome genotyping data from the British Society for Surgery of the Hand Genetics of Dupuytren’s Disease consortium (BSSH-GODD consortium) collection

  Dataset EGAD00010000807

• WGS of T-cell and NK-cell lymphoma for ICGC (NKTL-SG)

  WGS of T-cell and NK-cell lymphoma The tumor samples were sequenced with Illumina HiSeq 2500 platform and the resulting FASTq files have been uploaded.

  Dataset EGAD00001003271

• Subclonal diversification of primary breast cancer

  Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant.

  Dataset EGAD00001000965

• Papua New Guinean Genome Diversity Project (PGDP)

  The PGDP dataset includes 58 whole genome sequences for Papua New Guinean individuals from different locations. DNA was extrated from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGDP dataset provides Fastq and BAM files.

  Dataset EGAD00001007783