- Chip-based genotyping by mass spectrometry is an advanced analytical approach that combines the high-throughput capabilities of microarray (chip) technology with the precision of mass spectrometry (MS) to detect and analyze genetic variations at the DNA level.
- This technique allows researchers to genotype specific single nucleotide polymorphisms (SNPs), small insertions or deletions, and other genetic markers with high sensitivity and accuracy. Unlike fluorescence-based genotyping arrays, which depend on hybridization and optical detection, mass spectrometry leverages differences in the mass-to-charge ratio (m/z) of DNA fragments to provide direct molecular readouts, thereby reducing potential cross-hybridization errors and improving specificity.
- The principle of chip-based MS genotyping begins with PCR amplification of DNA regions that contain the variant of interest. Following amplification, a primer extension reaction is performed, where nucleotides complementary to the SNP site are incorporated. The resulting extended DNA fragments differ in mass depending on the incorporated nucleotide. These products are then transferred to a specially designed chip or microarray surface for analysis by mass spectrometry, commonly using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. The MALDI-TOF instrument measures the exact mass of each DNA fragment, enabling discrimination of alleles based on subtle mass differences.
- One of the best-known platforms in this domain is Sequenom’s MassARRAY system, which uses MALDI-TOF MS to genotype hundreds to thousands of SNPs in parallel. By spotting PCR and extension products onto a chip matrix and analyzing them by MS, the system achieves a balance between high-throughput capability and precise allele determination. The use of chips not only organizes and parallelizes the reactions but also enhances reproducibility and sample handling efficiency.
- Applications of chip-based genotyping by MS are broad and impactful. In biomedical research, it is widely used for SNP discovery, genetic association studies, and pharmacogenomics research to identify genetic variants influencing drug metabolism and therapeutic response. In clinical diagnostics, this method supports the detection of mutations linked to inherited diseases, cancer biomarkers, and infectious disease genotyping, offering a powerful tool for precision medicine. In agriculture and livestock genetics, it aids in marker-assisted breeding and trait selection. The ability to simultaneously analyze many genetic markers across multiple samples makes it especially valuable in large-scale studies where cost and accuracy are equally important.
- The method offers several advantages over traditional chip-based fluorescence genotyping. Mass spectrometry provides unambiguous results based on molecular weight, avoiding problems of fluorescence overlap or signal noise. It is also highly scalable, multiplexing dozens of SNPs in a single reaction. Furthermore, it allows for cost-effective targeted genotyping in situations where sequencing would be excessive or impractical. However, limitations include the requirement for prior knowledge of the variants, moderate throughput compared to next-generation sequencing (NGS), and specialized instrumentation, which can be costly to maintain.
