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• Developing therapeutics for ovarian cancer using ovarian cancer organoids

  To identify effective drugs for clear cell ovarian cancer (CCC) and high-grade serous ovarian cancer (HGSC) through high-throughput drug screening using ovarian cancer organoids and to identify novel therapeutic targets based on the biological characteristics of CCC and HGSC through omics analysis.

  Study JGAS000764

• Shallow Whole Genome Sequencing (sWGS) from REPEAT trial

  Samples associated to: "A phase Ib/II study of regorafenib and paclitaxel in patients with beyond first-line advanced esophagogastric carcinoma (REPEAT)". sWGS from 97 Esophagogastric Carcinoma samples. sWGS was done to carry out Copy Number Analysis. Dataset includes: .fastq, .bam and .bai files.

  Dataset EGAD50000001161

• Exploring Genomic Mutations in Gastric Cancer among Japanese Populations

  We conducted a comprehensive analysis of whole-genome and RNA sequences obtained from biopsy samples of 65 patients with advanced gastric cancer prior to chemotherapy treatment.

  Study JGAS000754

• Enhancer profiling to identify identifies epigenetic markers of endocrine resistance in metastatic castration resistant prostate cancer patients

  ChIP-seq and matched input data of AR, FOXA1 and H3K27ac for mCRPC patient samples taken prior to and after treatment with AR targeted therapy

  Dataset EGAD00001008688

• WGS paired B-Cell lymphoma cells sorted according to CD48

  paired WGS data of one tumor of one patient with nodal B-cell lymphoma. Tumor cells were sorted according to CD48 expression in a high and low fraction. Library preparation with TruSeq Nano and sequencing on Hiseq XTen.

  Dataset EGAD00001006058

• Genome-wide array data from Eivissan and Menorcan Individuals

  VCF file with autosomal genotypes from 22 and 20 Eivissan and Menorcan samples. Affymetrix Human Origins array was used to genotype the samples and the variants were lifted over to the hg38 human genome reference.

  Dataset EGAD50000000614

• Kidney Single Cell Study (2018-08-20)

  We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney. . This dataset contains all the data available for this study on 2018-08-20.

  Dataset EGAD00001004304

• Insular Celtic population structure and genomic footprints of migration

  Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits.

  Study EGAS00001002769

• Meisal temporal lobe epilepsy sequencing study

  Our understanding of mesial temporal lobe epilepsy (MTLE) is one of the most common forms of drug-resistant epilepsy in humans. Using RNA- and small RNA-sequencing in parallel, we explored differentially expressed genes in the hippocampus and cortex of MTLE patients who had undergone surgical resection and non-epileptic controls. We found significant enrichment for astrocytic and microglial genes amongst up-regulated genes and down-regulation of neuron-specific genes in the hippocampus of MTLE patients. The transcriptome profile of the small RNAs reflected disease state more robustly than mRNAs, even across brain regions which show very little pathology.

  Study EGAS00001003922

• Pancreatic islets PISA RNA-seq samples

  GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.

  Study EGAS00001005535