Cancer Biomarkers Using Integrative Single Cell and Bulk Sequencing

  • Title: Cancer Biomarkers Using Integrative Single Cell and Bulk Sequencing
  • Presenter: Akdeş Sevim Harmancı from
  • Date: October 23, 2018
  • Language: English
  • Abstract: Cancer is a disease of genomic and epigenomic alterations. Single nucleotide changes, copy number variations (CNV), chromosomal rearrangements and modification in DNA methylation together drive the formation of a tumor. The integrative ‘omic’ approaches in cancer research have led to a deeper understanding of tumor biology and are establishing the foundation necessary to support the long-term goals of personalized medicine. In this talk, I will talk about identifying brain tumor biomarkers using integrative bulk or single-cell sequencing data. This talk will consist of two parts. The first part will cover our work where we characterized non-NF2 meningiomas through complex integrative analysis of genetic and epigenetic data. I will also explain the epigenetic and genetic mechanisms leading to atypical meningioma and malignant glioma transformation. The second part will introduce our algorithm named CaSpER, that identifies visualizes and integrates CNV events in multiscale resolution using single-cell and bulk RNA-Sequencing data.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/AkdesSerinHarmanci
  • Youtube: https://www.youtube.com/watch?v=FSL3KT8gY2s

The FoundationOne® Assay for Genomic Profiling of Solid Tumor Cancers

  • Title: The FoundationOne® Assay for Genomic Profiling of Solid Tumor Cancers
  • Presenter: Dr. Abdullah Karaman from  University Hospital Zurich
  • Date: October 5, 2018
  • Language: English
  • Abstract: Comprehensive genomic tumor profiling is the basis of precision medicine in the modern era of cancer diagnosis and treatment. The possibility to profile cancer genomes and identify driver mutations in individual tumors has changed the way how oncologists diagnose cancer, decide on therapies and identify patients for clinical trials. At the University Hospital Zurich and in in collaboration with Roche, Switzerland and Foundation Medicine Inc., Cambridge, USA, we have established the validated diagnostic FoundationOne® assay for solid tumors. The FoundationOne® assay is designed to detect various genomic alterations in 315 cancer related genes including single nucleotide variants, indels and copy number alterations. In addition, fusions and rearrangement events in 28 cancer associated genes are assessed. Besides these alterations, the microsatellite status (MSI) of 114 intronic homopolymer repeat loci and the tumor mutational burden (TMB) is determined as biomarkers for immun-checkpoint inhibitors. For its application in the clinical practice, the assay was designed to work with common FFPE blocks while guaranteeing a specificity of ≥ 99% and sensitivity of 90-99%. To reliably identify driver mutations in highly heterogeneous cancer samples, the assay includes targeted resequencing of exons with a median coverage of 500x. The FoundationOne® has already established itself as an essential element at tumor board meetings, where it supports oncologists in the diagnosis and decision making process for succeeding treatment options. Here, I will introduce the audience to the assay, give an overview of the first results obtained at the UniversityHopsital Zurich, will demonstrate its advantages and give statistics on its performance.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/AbdullahKahraman
  • Youtube: https://www.youtube.com/watch?v=zB5PjaGbrUA

RSG-Turkey is a member of The International Society for Computational Biology (ISCB) Student Council (SC) Regional Student Groups (RSG). We are a non-profit community composed of early career researchers interested in computational biology and bioinformatics.

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