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Related Experiment Videos

Robust SNP genotyping by multiplex PCR and arrayed primer extension.

Mohua Podder1, Jian Ruan, Ben W Tripp

  • 1The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St, Paul's Hospital, University of British Columbia, Vancouver, BC, V6Z 1Y6, Canada. mpodder@mrl.ubc.ca

BMC Medical Genomics
|February 2, 2008
PubMed
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Arrayed primer extension (APEX) offers a robust method for multiplex single nucleotide polymorphism (SNP) genotyping. This advanced technique achieves high accuracy and call rates, making it suitable for personalized medicine and clinical diagnostics.

Area of Science:

  • Genomics
  • Molecular Biology
  • Biotechnology

Background:

  • Arrayed primer extension (APEX) is a microarray-based minisequencing method for genetic diagnostics.
  • Its utility in personalized medicine for single nucleotide polymorphism (SNP) genotyping requires objective evaluation of assay performance.
  • Previous reports lacked comprehensive data on APEX assay completion rate, call rate, and accuracy.

Purpose of the Study:

  • To develop and validate robust APEX methodologies for SNP genotyping.
  • To compare the effectiveness of optimized APEX against established gold-standard genotyping platforms.
  • To assess the performance of APEX in terms of assay completion, call rate, and accuracy.

Main Methods:

  • Developed advanced assay design, chemistry, and analysis for APEX.

Related Experiment Videos

  • Conducted two blinded experiments using Coriell DNA samples and International HapMap Project SNP data.
  • Utilized multiplex PCR for DNA amplification, initially with 7 reactions, later optimized to a single 50-plex reaction.

    • Main Results:

    • First experiment: 41 of 50 SNPs genotyped with 99.8% concordance and 94.9% call rate across 270 samples.
    • Second experiment (optimized 50-plex PCR): Achieved 100% assay completion, 100% call rate, and >99.9% accuracy with as little as 5 ng DNA.
    • Demonstrated robust 50-plex genotyping capability with minimal DNA input.

    Conclusions:

    • Optimized APEX methodology provides robust multiplex SNP genotyping with 100% call rate and >99.9% accuracy.
    • The developed APEX methods are effective and comparable to leading genotyping platforms.
    • This methodology holds significant potential for future point-of-care clinical diagnostic applications requiring high accuracy and call rates.