- MassARRAY is a high-throughput genotyping and genetic analysis platform developed by Sequenom (now part of Agena Bioscience) that utilizes matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to detect genetic variations with high accuracy and efficiency.
- Unlike fluorescence-based microarrays or next-generation sequencing (NGS), which rely on optical or sequence readouts, MassARRAY directly measures the mass of DNA fragments to distinguish between genetic variants. This mass-based detection provides unambiguous results, making the platform especially valuable for targeted genotyping, mutation detection, copy number variation analysis, and methylation studies.
- The principle of MassARRAY revolves around the precise discrimination of DNA fragments generated through a primer extension reaction. The workflow begins with PCR amplification of the DNA region containing the variant of interest. Following amplification, a single-base primer extension (SBE) reaction is performed using mass-modified nucleotides, generating extended DNA fragments whose lengths and masses depend on the incorporated nucleotide. These products are then transferred onto a silicon chip with an energy-absorbing matrix, and analyzed by MALDI-TOF MS. The time-of-flight measurements are converted into mass spectra, allowing clear identification of the alleles based on their unique molecular weights.
- One of the defining features of the MassARRAY system is its flexibility and multiplexing capacity. It can simultaneously analyze dozens of genetic loci across many samples in a single run, making it particularly suitable for medium-scale genotyping projects where full genome sequencing would be unnecessary or cost-prohibitive. The platform provides accurate allele calling, low error rates, and the ability to genotype single nucleotide polymorphisms (SNPs), small insertions and deletions, somatic mutations, and quantitative differences such as copy number variations (CNVs).
- Applications of MassARRAY span across biomedical research, clinical diagnostics, pharmacogenomics, oncology, infectious disease, and agriculture. In pharmacogenomics, it is used to genotype SNPs associated with drug metabolism and response, supporting precision medicine initiatives. In oncology, the platform enables detection of cancer-related somatic mutations and copy number alterations, aiding in tumor classification and treatment planning. It has also been applied to DNA methylation analysis using the EpiTYPER assay, which measures epigenetic modifications with high resolution. In population genetics and agriculture, MassARRAY supports trait mapping, marker-assisted breeding, and genetic diversity studies.
- Compared to sequencing-based methods, MassARRAY offers distinct advantages: it is cost-effective for targeted genotyping, requires less data analysis, and provides high specificity without the background noise typical of fluorescence-based arrays. However, it does have limitations: it is restricted to known variants, lacks the discovery potential of NGS, and has lower throughput compared to large-scale sequencing platforms. Despite these limitations, it fills an important niche between traditional genotyping arrays and whole-genome sequencing, offering a balanced solution for accuracy, scalability, and cost-effectiveness.
