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• CLL_cancer_Sample_Sequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from CLL cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000011

• Whole_Genome_Sequencing_of_hiPS_cells

  Human induced pluripotent stem (hiPS) cells hold great promise for regenerative medicine. Safety issues of use of hiPS cells however remain to be addressed. One of such issues is mutations derived from somatic donor cells and introduced during genome manipulation. We sequence whole genomes of hiPS cells and analyzed mutations. Our study brings hiPS cell technology one step closer to application to regenerative medicine.

  Study EGAS00001000008

• RNA-seq of STIC lesions and adjacent normal samples

  In this study, we characterize premalignant lesions of the fallopian tube (serous tubal intraepithelial carcinomas) to explore the earliest events of tumorigenesis following mutation of the TP53 tumor suppressor gene. We conduct laser capture microdissection to isolate premalignant cells from adjacent normal cells, and subject isolated tissues to RNA-seq. Our findings reveal the earliest transcriptional changes established during premalignancy within the fallopian tube.

  Study EGAS50000000200

• Base modification analysis using single molecule real-time sequencing

  Based on the kinetic characteristics of single-molecule real-time sequencing, we implement a method to directly detect DNA modifications such as 5mC. However, there are room to further improve the accuracy of whole-genome-wide DNA modifications. Therefore, this study aims to utilize deep learning methods for the comprehensive profiling of multiple DNA modifications, including 5mC, 5hmC, and 6mA, using SMRT-seq.

  Study EGAS50000000366

• De novo detection of somatic variants

  The Tumor Profiler Study is an observational trial combining a prospective diagnostic approach to assess the relevance of in-depth tumor profiling to support clinical decision-making with an exploratory approach to improve the biological understanding of the disease. This dataset contains scDNA-seq data for 3 ovarian cancer samples from the Tumor Profiler Study used to validate LongSom. LongSom is a computational workflow leveraging high-quality long-read scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy-number alterations (CNAs), and gene fusions, to reconstruct tumor clonal heterogeneity.

  Dataset EGAD50000001292

• The_Little_Princess_Knowledge_Bank_RNAseq

  The purpose of the knowledge bank is to serve as a community resource and to address the following specific questions about Wilms tumour: (1) Do genetic, epigenetic, or transcriptional features predict outcome and thus lend themselves to treatment stratification? (2) What are the genetic drivers of Wilms tumour, considering the entire histological spectrum of Wilms tumour including the most common subtypes classified as intermediate risk?

  Study EGAS00001005244

• Mixed_Leukemia_Rearrangement_Screen

  Genomic libraries will be generated from total genomic DNA derived from Mixed Leukemia and MPD samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the illumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000180

• Whole_Genome_sequencing_of_individuals_from_Carlantino__Italy

  This study includes whole-genome sequencing data (at 4x depth) of 100 individuals from an Italian genetic isolate population (Carlantino, abbreviated CARL) of the Italian Network of Genetic Isolates (INGI). The INGI-CARL_SEQ 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.

  Study EGAS00001000460

• Developing somatic copy number and mutation calling tools for a bespoke sequencing platform

  We previously developed a linked-read sequencing platform (DigiPico) for analysing whole cancer genomes from picogram quantities of tumour DNA. The aim of this study was to develop and evaluate the specialised computational approaches required to obtain clinically useful results from the raw data. To this end, we performed matched DigiPico, bulk tumour and germline WGS on samples from four patients.

  Study EGAS00001007195

• Familial_Thrombocytosis_germline_exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 3 relatives from a family with multiple affected familial thrombocytosis (FT) patients. Germline DNA from 2-4 patients affected with FT will be used to prepare libraries and sequenced in one lane of HiSeq sequencing, mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000088