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• Spatial Profiling Reveals Resistance in HER2+ Gastric Cancer

  HER2-positive gastric cancer (HER2+ GC) exhibits significant intra-tumoral heterogeneity and frequent development of resistance to HER2-targeted therapies. This study aimed to characterize the spatial tumor microenvironment (TME) and identify mechanisms of resistance to HER2 blockade including trastuzumab and trastuzumab deruxtecan (T-DXd) in HER2+ GC, with the goal of informing novel therapeutic strategies. We performed spatial transcriptomics on pre- and post-treatment samples from patients with HER2+ metastatic GC who received trastuzumab-based therapy.

  Dataset EGAD50000000898

• RNA sequencing of untreated and treated KRAS-mutated metastatic colorectal cancer PDX-derived organoids.

  RNA sequencing was performed on patient-derived xenograft (PDX)-derived organoid models of metastatic colorectal cancer (mCRC). The aim of this study was to characterize the transcriptional landscape of KRAS-mutant mCRC cells in response to therapeutic strategies targeting the EGFR and KRAS signaling pathways. Transcriptomic profiling was conducted following drug treatments to investigate molecular changes associated with single and combination therapies. A total of 24 samples were analyzed.

  Dataset EGAD50000002443

• Whole genome sequencing of metastatic melanomas from a patient with primary resistance to BRAF inhibition

  Here, we investigated the underlying cause of treatment failure in a patient with BRAF mutant melanoma who presented primary resistance. We used whole-genome sequencing (WGS) to characterise five metastatic tumours from a BRAF mutant melanoma patient who presented intrinsic resistance.

  Study EGAS00001000580

• Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness

  In this work, using exome sequencing, we identified biallelic PNLPA6 mutations in patients with childhood blindness due to severe photoreceptor death and clinical features of Leber congenital amaurosis (LCA) and, interestingly, also of the rare Oliver McFarlane Syndrome

  Study EGAS00001001013

• RNA-seq on bronchial brushings collected in controlled human exposure to diesel exhaust

  COPA study examined the impact of short-term exposure on airway epithelium transcriptome. It was a randomized, double-blind, controlled human exposure study to diesel exhaust with a crossover design. This human study was registered on clinicaltrials.gov with the identifier NCT02236039.

  Study EGAS00001006966

• MCL NGS data

  We have performed a comprehensive and integrative genomic study of mantle cell lymphoma (MCL) to elucidate the features that may determine the different clinical and biological behavior of the two molecular subtypes of this lymphoma, conventional (cMCL) and leukemic non-nodal MCL (nnMCL). This data integrated with epigenomics and transcriptomics has allowed to uncover novel molecular mechanisms in the origin and development of these tumors and provide relevant information to stratify patients in different risk groups.

  Dataset EGAD00001006025

• RA-Map Early Rheumatoid Arthritis patient genotyping (InfiniumCoreExome-24-v1)

  Genotyping of 244 early RA patients and 44 vaccine recipient controls was performed using the Illumina InfiniumCoreExome-24-v1-1 according to the manufacturer’s SOP. Raw idats from the Illumina iScan instrument were imported into GenomeStudio (v2011.1). Samples < 90 % call rate were excluded. Data was exported to PLINK PED/MAP format on the forward strand. Data was converted from PED/MAP to BED/BIM/FAM using PLINK v1.07.

  Dataset EGAD00001006736

• Trimmed bam-files from whole genome sequencing data from plasma DNA

  Single-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002254

• VRK3 depletion in Pontine Diffuse Midline Glioma DMG-K27 altered cells

  In order to investigate possible mechanisms underlying the phenotype of cell fitness decline observed following decrease of VRK3 in pontine DMG-K27 altered cells 7, we examined differences in global gene expression. RNA-seq was performed 44h and 60h post-transduction with two distinct shRNAs targeting VRK3 to be able to evaluate the early impact of VRK3 knock-down (KD) in four independent in vitro models of DMG

  Dataset EGAD00001010097

• Whole Genome sequencing of individuals from Val Borbera, Italy

  This study includes Phase 2 whole-genome sequencing data (at 4x depth)of 100 individuals from an Italian genetic isolate population (Val Borbera, abbreviated VBI) of the Italian Network of Genetic Isolates (INGI). The INGI-VBI_SEQ2 project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.

  Dataset EGAD00001000731