APR 24, 2018 8:00 AM PDT

KASP genotyping - better by design

Sponsored by: LGC Seracare
Speaker
  • Senior Scientist - Scientific Support, LGC
    Biography
      Jonathan studied Molecular Biology at Birkbeck College while working at G.R. Micro Ltd, a contract research company focused on both surveillance and development of antimicrobial/anti-infective compounds. He worked from laboratory aide to scientist whilst completing his degree at night. Incidentally, the company was later acquired by Quotient Bioresearch Ltd which is now the LGC Groups' Fordham facility. He carried on to study for a PhD in microbiology at UCL, looking at beta-lactamases from the soil bacterium Citrobacter freundii focusing on the role of plasmids and other mobile genetic elements in their mobilisation in to human enteric pathogens. Jonathan was lucky enough to utilise a wide variety of molecular biology techniques and sequencing, gaining a fond appreciation for bioinformatics. He was offered a position with KBioscience / LGC Genomics in 2013 to help build a technical support team, better understand our customers, how they use our chemistries and how we can help them get the best results possible. One of his first roles was to implement sequence analysis in to LGC's assay design software, called Magic Box, for automated whole genome primer analysis for any species.

    Abstract

    In this talk we will cover basic principles of KASP® genotyping chemistry and designing assays that are specific to desired targets. We will go over commonly encountered challenges such as targeting highly conserved regions of genomes to polyploidy and distinguishing targets on chromosomes that are part of a collective of similar organisms, e.g. wheat. We will start with the basics of BLAST for highlighting regions to avoid and move on to the annotation of these regions for submission to LGC for design. From simple diploids such as human and tomato to more complex genome structures such as potato and wheat, we will show real examples before and after analysis.

    Learning Objectives:

    • Become familiar with how KASP works and how different design strategies can be used to answer a multitude of research questions.
    • Apply publicly available sequence analysis tools to solve common problem faced when designing primers and translating this for sequence submission with worked examples.
    • Show how these simple design principles can be used to answer more complex genetic questions such as differentiating and selectively target loci in polyploid genomes or targeting large insertions / deletions / rearrangements using worked examples.

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