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• Whole exome sequencing of Zimbabwean patients with suspected Mendelian disorders

  This study presents whole exome sequencing data from Zimbabwean individuals with suspected Mendelian disorders, including sickle cell disease, Fanconi anemia, haemophilia, and muscular dystrophy. The dataset includes both affected individuals and family members to support inheritance-based analyses. Variant calling was performed using the Illumina DRAGEN pipeline, with downstream variant prioritisation and interpretation conducted using the Zi-Mendelian bioinformatics pipeline. This study supports rare disease genomics and precision medicine efforts in African populations.

  Study EGAS50000001708

• Autozygosity pilot - QMUL

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing British-Pakistani cohort samples will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consists of low coverage whole exome sequencing on these samples.

  Dataset EGAD00001001027

• Human four week embryo head as reference for generating an enhancer compendium for neuronal and neural crest development using neural tube organoids.

  This study has the aim of generating an enhancer code compendium of early human neuronal and neural crest development. For this purpose, we generated human neural tube organoids from single cells from two induced pluripotent stem cell lines. The organoids were subject to combined single cell multiomics at four time points of differentiation. To evaluate the biological relevance of the cell types and states obtained from the organoids, we compared with data obtained from 10XGenomics single cell multiomics on the head of a single four weeks post conception human embryo.

  Study EGAS50000001031

• B cell activation

  To investigate the gene programs involved in B cell activation and antibody switching, we profiled the gene expression at the single cell level as well as the antibody repertoire of human naive and memory B cells at resting and following three time points of activation. Through CRISPR perturbations, we defined IRF4 as a central regulator of both GC and plasma cell fates, acting independently of PRDM1 in GC commitment. Finally, leveraging machine learning classification methods trained solely on transcriptomic profiles, we accurately predicted sister cell relationships, revealing that plasma cell gene expression programs are heritable and tightly conserved within a clone.

  Study EGAS50000001468

• Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies

  To identify early driver mutations in ovarian cancer cells, we used dense whole genome sequencing of micrometastases and microscopic residual disease collected at three time points from a single patient during treatment for high-grade serous ovarian cancer (HGSOC). Laser capture microdissection of tumour islets was performed on samples prior to chemotherapy, after three cycles of chemotherapy and at recurrence. Long frament read whole genome sequencing was performed and mutations were identified. To our knowledge, this is the first longitudinal study that attempts to investigate spatial and temporal micro-heterogeneity in cancer.

  Study EGAS00001001909

• Microbiome

  16S-sequencing: All stool samples were processed according to the standards of the Flemish Gut Flora Project (Falony et al., 2016). All samples were processed together and sequenced in as a single batch (dual index run DI23R22) which included positive controls (PC, identical stool sample), negative controls (PCR-mix) and ‘blanks’ or negative controls of the extraction (no sample). In addition, a Runella strain (RS) was included to check for potential cross-contamination, as this strain is not present in human samples. The V4 region of the 16S rRNA gene was amplified with the primer pair 515F and 806R (GTGYCAGCMGCCGCGGTAA and GGACTACNVGGGTWTCTAAT, resp.), modified to contain a barcode sequence between each primer and the Illumina adaptor sequences to produce dual- barcoded libraries (Tito et al., 2019). Sequencing was performed on the Illumina MiSeq. Sequences were processed using the LotuS (Hildebrand et al., 2014) and DADA2 pipeline (Callahan et al., 2016) using RDP 16 as the reference taxonomy.

  Dataset EGAD50000002027

• Fecal metagenomics and plasma metabolomics

  This dataset contains all fecal shotgun metagenomics and metabolomics of the study which investigated the effects of the probiotic strain Anaerobutyricum soehngenii. Shotgun data is from three different time points, baseline and two follow up. Metabolomics sets are pre and post intervention, both fasted and post prandially. Data on randomization and metformin use can be found in the analysis.

  Dataset EGAD50000000608

• WES of der(1;7)(q10;p10)

  This dataset contains the BAM files of WES of 26 myeloid neoplasm patients with der(1;7)(q10;p10)(+) cases. The dataset was used to identify key driver genes in patients with der(1;7)(q10;p10). Already known drivers along with novel driver genes were identified through the use of this WES.

  Dataset EGAD50000000986

• Short-read (RNA-seq)

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Dataset EGAD00001006596

• Cancerous Adaptive Dosing Melanoma WGS Dataset

  Illumina NovaSeq 6000 30x WGS of 26 samples, each with up to 5 matched timepoints. Timepoints A,B,C,D,and E correspond to Pretreatment, Week 3, Week 6, Week 9, and Week 12 after treatment, respectively. Additional sample metadata (sample recurrence, treatment course, age, sex, comorbidities, etc.) are present in sample description.

  Dataset EGAD00001010926