APR 12, 2018 9:00 AM PDT

QIAseq Digital Sequencing and Biomedical Genomics Workbench: Application to Liquid Biopsy in Bladder Cancer Research

Speaker
  • Senior Scientist, Biomedical Genomics, QIAGEN
    Biography
      Dr. Francesco Lescai graduated in Medical Biotechnology at the University of Bologna and was a awarded a Ph.D. in experimental pathology, with studies in genetics of human ageing and Alzheimer Disease. He then pioneered the analysis of human exomes at University College London, first at UCL Genomics and then at the Centre for Translational Genomics, Institute of Child Health and Great Ormond Street Hospital. Francesco then took on the position of Associate Professor of Human Genomics and Bioinformatics at the Department of Biomedicine of Aarhus University, where his main research focus was the use of genome sequencing in the area of precision medicine, and in particular the genetic causes of psychiatric disorders such as schizophrenia and autism. He joined QIAGEN in November 2017 as a Senior Scientist for Biomedical Genomics, in the Global Product Management team for CLC Workbenches.
      Francesco has been a member of the Executive Board of the European Federation of Biotechnology, is in the Editorial Board of several journals and has been in different Expert Groups at the European Commission. He also coordinates a Horizon2020 project on responsible industrial innovation.

    Abstract

    This presentation illustrates the features of QIAGEN sample to insight approach, and how it combines a powerful chemistry based on unique molecular indexes (UMIs) and a UMI-aware bioinformatics workflow in the Biomedical Genomics Workbench with QIAseq Panel Analysis Plugin. This approach reaches impressive performances in detecting low allele-fraction variants, and the integration with other QIAGEN solutions such as Ingenuity Variant Analysis (IVA) and QCI Interpret allows to further explore the results for their biological and pathological relevance.

    The use of DNA panels is a cost-effective approach to reach the high coverage needed for research  applications like liquid biopsy. In such scenarios, the capability to distinguish between sequencing or amplification errors and real findings is crucial, in order to detect clinically relevant mutations at low allele-fraction levels. UMIs address this challenge, if combined with bioinformatics capable of exploiting their added value. 

    Liquid biopsy is emerging as a new and non-invasive approach to characterize cancer mutation profiles. However, some tumours like urothelial cancer are particularly challenging, due to their location and biology. In this work we explore the performance of our workflow and its insights on bladder cancer. 

    We compared the results from tissue and plasma libraries extracted with QIAGEN QIAamp MinElute ccfDNA and QIAamp Circulating Nucleic Acid kits from individuals with bladder cancer, and show that the recovery of variants (i.e. variants identified in the tissue also called in the plasma) ranges above 70% for SNVs. A very good achievement, in the biological context of urothelial cancer. We further explore the results from a pathological perspective, and show the success in capturing biologically relevant mutations, classified by their pathogenicity and actionability according to existing guidelines.


    Show Resources
    You May Also Like
    JAN 23, 2020 9:00 AM PST
    C.E. CREDITS
    JAN 23, 2020 9:00 AM PST
    DATE: January 23, 2020 TIME: 9:00am PST, 12:00pm EST...
    APR 07, 2020 8:00 AM PDT
    C.E. CREDITS
    APR 07, 2020 8:00 AM PDT
    DATE: April 7, 2020 TIME: 8:00am PT, 11:00am ET This webinar sets out to establish why quality control is key to robust, reliable, reproducible science. We will look at best practice criteri...
    MAY 08, 2020 10:00 AM PDT
    C.E. CREDITS
    MAY 08, 2020 10:00 AM PDT
    DATE: May 8, 2020 TIME: 10:00am PT, 11:00am MT, 1:00pm ET The application of next generation sequencing to interrogate immune repertoires and methods in which these highly complex dataset...
    MAR 03, 2020 9:00 AM JST
    C.E. CREDITS
    MAR 03, 2020 9:00 AM JST
    DATE: March 3, 2020 TIME: 9:00am JST A major limitation in the ex vivo expansion of harvested human hematopoietic stem-progenitor cells (HSPCs) is the rapid differentiation of HSPCs at the e...
    FEB 25, 2020 9:00 AM PST
    C.E. CREDITS
    FEB 25, 2020 9:00 AM PST
    Learn about how to generate a small scale CAR-T workflow using ThermoFisher products See detailed characterization tools that can be utilized and applied in a CAR-T workflow...
    DEC 10, 2019 9:00 AM PST
    C.E. CREDITS
    DEC 10, 2019 9:00 AM PST
    DATE: December 10, 2019TIME: 9:00am PST, 12:00pm EST A major limitation in the ex vivo expansion of harvested human hematopoietic stem-progenitor cells (HSPCs) is the rapid dif...
    Loading Comments...
    Show Resources