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• Genetics of Fuchs Corneal Dystrophy

  This grant proposal continues to expand our understanding of the clinical presentation of Fuchs corneal dystrophy, and its underlying genetic basis, which will lead to the development of better therapeutic models and treatment for a common corneal dystrophy that affects 4% of the US population over age 40.

  Study phs001834

• Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

  In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

  Study EGAS50000000141

• BELLINI clinical trial bulk RNA-Seq data: cohorts A, B & С

  RNA-Seq data of 78 breast cancer primary tumors obtained from 45 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (15 patients, 25 samples) received nivolumab for 4 weeks, patients in cohort B (15 patients, 28 samples) received nivolumab + ipilimumab for 4 weeks, and patients in cohort C (15 patients, 25 samples) received nivolumab + ipilimumab for 6 weeks. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000808

• Variables of mass cytometry (CyTOF) innate immune cell counts

  For 61 COVID-19 patients we performed a CyTOF analysis to characterize the innate immune landscape associated with disesase severity. For this study, 37 analyzed populations have been included, speccialy focused in monocyte-macrophague subpopulations. For more information, please consult DOI: 10.3389/fimmu.2022.1094644

  Study EGAS50000000588

• Genotype variables of the 61 COVID-19 patient cohort used in the main project of data integration

  We selected SNPs with a minor allele frequency (MAF) higher than 10% in the Caucasian population from the Ensembl database. Specifically, we selected ACE2 (rs2285666), MX1 (rs469390), and TMPRSS2 (rs2070788) for the present analysis. For more information, please refer to:

  Study EGAS50000000589

• Long Read sequencing data from 4 tumor/germline samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). Additionally, tumor/germline samples from 4 patients were sequenced using Oxford Nanopore technology. This dataset contains 8 BAM files corresponding to the Long read sequencing data.

  Dataset EGAD50000000731

• RnaSeq data from 414 tumor samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 414 BAM files corresponding to the full total RNA-sequencing dataset.

  Dataset EGAD50000000733

• Multi-omics analysis of CUD in the VS

  The aim was to molecularly characterize the human ventral striatum in CUD. For this, we generated epigenomic, transcriptomic, and proteomic datasets at the bulk-level, performed integrative multi-omics analyses and further analyzed CUD-associated transcriptomic changes at a cell type-specific level using snRNA-seq.

  Study EGAS50000000623

• Non-invasive prediction of immunotherapy response (NIPIT) project

  This project aims to find transcriptomic biomarkers for immunotherapy response prediction in several cancer types. So far, we have performed poly-A RNA-seq using whloe blood and peripheral blood mononuclear cells from 33 non-small cell lung cancer patients, collected before and after the start of immunotherapy.

  Study EGAS50000000266

• Base modification analysis using single molecule real-time sequencing

  This dataset was generated using single-molecule real-time sequencing for both training and testing purposes. The DNA samples isolated from human buffy coats or placenta of healthy individuals (n=4,) were prepared in a way that four types of base modifications were incorporated, including unmodified controls, 5mC, 5hmC, and 6mA. The sequence data for each sample consists of subreads produced by single-molecule real-time sequencing and stored in a bam format. Details of the specific experiments conducted in this study are outlined in our manuscript.

  Dataset EGAD50000000541