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• Emirati Haploid Single-Sample-Assemblies (30 Individuals, 60 Assemblies)

  This dataset provides 27 phased diploid genome assemblies for Emirati trios, delivered in FASTA format. Assemblies were built with hifiasm (trio mode) from PacBio HiFi reads at ≥25× coverage for each parent and offspring, then scaffolded with NTLink and reference-guided merging using RagTag against CHM13v2. As part of the same program, a complementary set of single-sample diploid assemblies for 30 individuals (yielding 60 haplotypes) is being generated from deep PacBio HiFi data to expand a population-matched pangenome reference. Together, these resources capture Emirati genomic diversity and support downstream variant discovery and annotation.

  Dataset EGAD50000001753

• Impact of allogeneic umbilical-cord derived mesenchymal stromal cells on B-cell scRNAseq in patients with systemic lupus erythematosus

  The impact of MSC(UC) on peripheral B cells from Systemic Lupus Erythematosus (SLE) patients was studied by 10X scRNAseq. This scRNAseq study encompassed 3 SLE patients at 3 time points: before or after (1 month, and 3 months) MSC injection in order to analyze B cell subsets and their DEG. The aim of this study was to observe the potential changes of B cell subsets after MSC(UC) injection in SLE patients.

  Study EGAS50000000325

• The genomic landscape of relapsed infant and childhood KMT2A-rearranged acute leukemia

  To study the mechanisms of relapse in KMT2A-rearranged (KMT2A-r) acute lymphoblastic (ALL) and acute myeloid leukemia (AML), we performed whole-genome and exome sequencing of infants and children with relapsed ALL/AML (n=36), and longitudinal deep-sequencing of 257 samples in 30 patients. Somatic alterations in drug-response genes, most commonly in TP53 and IKZF1 (64%), were highly enriched in early relapse ALL (79%, 9-36 months after diagnosis), but rare in very early relapse ALL (<9 months, 9%). A marked chemotherapy-exposure signature was detected for mutations in early relapse ALL but not in very early ALL or AML relapse, in line with different mechanisms of relapse. Longitudinal analyses could track residual leukemia cells, clonal drug responses, and the upcoming relapse. These results highlight that KMT2A-r ALL and AML evade therapy differently and provide new insights into the mechanisms of relapse in this highly lethal form of pediatric acute leukemia.

  Study EGAS00001008197

• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy fibroblasts

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of fibroblasts derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and a patient carrying a pathogenic variant in EHMT2 (P2). Ribosomal RNA was removed using an RNase H–based depletion method, and strand-specific libraries were prepared for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002343

• oncogenic gene fusions in primary colon cancers

  This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total).

  Dataset EGAD00001003291

• Immune signature of malignant melanoma in pregnancy

  Melanoma is a highly immunogenic malignancy and there is a deep-rooted notion among clinicians that a probable systemic immunosuppressed state during pregnancy would negatively influence melanoma related prognosis. To test this hypothesis on a more fundamental level, we collected a unique set of melanoma tumor samples and performed RNAseq to draw comparisons between the immune cell infiltrate of pregnant patients and non-pregnant matched controls. We found that there is indeed no differential expression of any immune cell subset. This underscores the notion that the supposed immunosuppressive state of pregnancy does not hamper the anti-tumor immune response.

  Study EGAS50000000492

• CosMX spatial transcriptomics

  This study consists of the spatial transcriptomics analyis data generated by : CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex); NanoString, USA for n=4 SLD-HCC and n=4 non-SLD-HCC. The goal of this data is to compare SLD-HCC vs non-SLD-HCC as well as response to immunotherapy

  Dataset EGAD50000001507

• RNA sequencing

  For RNA sequencing: All sample numbers starting with 6717 are tumor samples which has been sequenced using transcriptomics (see BAM files). It concerns biopsies of metastatic lesions from patients with BRAFV600 mutated melanoma, obtained before, during and after the study treatment (see samples metadata). RNA sequencing is performed using the Illumina Novaseq 6000 system.

  Dataset EGAD50000000383

• SG10K_Pilot Dataset: Whole genome sequencing data of 4810 individuals from Singapore

  Genomic data obtained from the joint processing and variant calling of 4,810 individuals from Singapore. VCF files are by Chromosome (chr. 1-22 plus X) for all 4,810 individuals. Self-reported ethnicity is found in the "Region" column of metadata file.

  Dataset EGAD00001005337

• Egypt Genome Project - low 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 low-coverage sequencing data for 100 Egyptian samples.

  Dataset EGAD00001001372