Abstract for presentation at 11th International Congress of Human Genetics

Design of Multiplexed Oligionucleotide Ligation Assays for High Throughput Insertion-Deletion Polymorphism Genotyping

  • Ryan Koehler, Applied Biosystems, Foster City, CA, USA, United States
  • Zheng Zhang, Applied Biosystems, Foster City, CA, USA, United States
  • Sabine Short, Applied Biosystems, Foster City, CA, USA, United States
  • Andreas Tobler, Applied Biosystems, Foster City, CA, USA, United States
  • Michael Wenz, Applied Biosystems, Foster City, CA, USA, United States
  • Francisco De La Vega, Applied Biosystems, Foster City, CA, USA, United States

    • Insertion and deletions are important mediators of inherited disease susceptibility and somatic cell changes that might be a prelude to cancer. We made improvements to the SNPlex(TM) Genotyping System, a multiplexed assay based on oligonucleotide ligation, to determine genotypes of insertion/deletions (indel) polymorphisms as well as single-nucleotide polymorphisms (SNP). The improved assay design algorithms ensure that target-specific probe-sets meet the thermodynamic and genome specificity requirements of the assay format. To validate the design pipeline, we genotyped a set of candidate indel polymorphism from public SNP databases in human DNA samples and compared with the results of a set of SNPs selected as a QC control set for the HapMap project. Overall design and assay performance rates are comparable for both SNP and indels. A key advantage of this format is that important SNP and indel polymorphisms may be genotyped together within a single multiplex assay in a mix-and-match fashion. Additional work to improve the design pipeline to develop assays targeting longer inserts, multi-base polymorphisms, and copy number variation is underway.

    Conference Organiser - ICMS Pty Ltd