MassARRAY® SNP Genotyping Services

N2Jenomics Lab Pvt. Ltd. provides fast, accurate, and customizable MassARRAY® SNP Genotyping services using the Agena Bioscience MassARRAY® MALDI-TOF platform. By integrating matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry with advanced assay chemistry and powerful data analysis software, we deliver highly reliable SNP genotyping solutions for research, breeding, and clinical applications. Our scalable workflow supports both small and large projects, ensuring high-quality results with rapid turnaround times.

Introduction to MassARRAY® SNP Genotyping

MassARRAY® SNP Genotyping is a high-throughput technology that accurately identifies single nucleotide polymorphisms (SNPs) through a combination of PCR amplification, single-base primer extension, and MALDI-TOF mass spectrometry. Following amplification of the target DNA region, a primer extension reaction incorporates a single nucleotide at the SNP position. The resulting extension products are analyzed according to their molecular mass, allowing precise discrimination between different alleles.

This technology supports simultaneous analysis of multiple SNPs within a single reaction, making it an efficient and economical solution for medium- and high-throughput genotyping projects. In addition to SNP detection, the versatile MassARRAY® platform can be applied to copy number variation (CNV) analysis, DNA methylation studies, mutation screening, gene expression research, pathogen identification, and other targeted genomic applications. Its flexibility and high analytical performance have made it a widely adopted platform across life sciences, agriculture, biomedical research, and precision medicine.

Advantages of MassARRAY® SNP Genotyping

• High Accuracy and Automation

The MassARRAY® platform utilizes MALDI-TOF mass spectrometry to distinguish genetic variants based on molecular mass, delivering highly accurate and reproducible results. Automated sample processing minimizes manual intervention, improving consistency and laboratory efficiency.

• Flexible and Scalable Workflow

Our genotyping solutions are designed to accommodate a wide range of project sizes, from a limited number of SNPs to large validation studies involving thousands of samples. The workflow can be tailored to match your specific research objectives.

• High Multiplexing Capability

MassARRAY® technology enables simultaneous analysis of up to 30 SNPs in a single multiplex assay, significantly increasing throughput while reducing reagent consumption and processing time.

• Rapid Assay Development

Custom SNP assays can be designed and optimized quickly using streamlined workflows and standardized oligonucleotides, enabling faster project initiation and shorter turnaround times.

• Cost-Effective Genotyping

Multiplex analysis reduces the cost per sample by allowing multiple SNPs to be analyzed in a single reaction. Combined with scalable throughput, this makes MassARRAY® an economical solution for large-scale SNP validation studies.

Applications of MassARRAY® SNP Genotyping

MassARRAY® SNP Genotyping is widely used across diverse areas of genomics research, including:

• • SNP genotyping and targeted mutation detection
• • Rare variant and ultra-sensitive mutation analysis
• • DNA methylation profiling
• • Copy number variation (CNV) analysis
• • Plant and animal variety identification
• • Custom functional gene panel development
• • Pharmacogenomics and precision medicine research
• • Biomarker discovery and validation
• • Agricultural genomics and molecular breeding
• • Clinical and translational genomics research

MassARRAY SNP Genotyping Workflow

The procedures for our MassARRAY SNP Genotyping is illustrated below.

Service Specifications

	Sample requirements Sample type: genomic DNA DNA concentration: 20-50 ng/µL, DNA volume: ≥ 15 µL, OD260/280 = 1.7~2.0 without degradation or RNA contamination
	Chip Printing Sequenom MassARRAY iPLEX Gold Platform
	Data Analysis Genotypes are determined through ratio analysis of the MALDI-TOF mass spectrometer Quality control and detection of oligonucleotides SNP typing and SNP allele frequency calculation Detection and analysis of somatic mutation Methylation quantitative analysis …and more

Analysis Pipeline

Deliverables

•  
• • The original sequencing data
• • Experimental results
• • Data analysis report

Our service includes customized SNP panel design, oligo manufacture and pool balancing, iPLEX chemistry running, analysis of genotyping, and delivery of genotype report in Excel format. Our workflows can be designed to accommodate both small and large assay requirements. If you have additional requirements or questions, please feel free to contact us.

1. How many samples can be analyzed using the MassARRAY® System?

The sample throughput depends on the assay configuration and the type of SpectroCHIP® Array selected. The MassARRAY® System processes two SpectroCHIPs per run and supports both 96-well and 384-well formats. For single-well assays, a single run can accommodate up to 192 samples using the 96-well format or up to 768 samples with the 384-well format. Actual throughput may vary depending on assay multiplexing and project requirements.

2. What level of accuracy does MassARRAY® SNP genotyping provide?

MassARRAY® technology is recognized for its exceptional analytical performance. When optimized protocols and high-quality samples are used, SNP genotyping accuracy and reproducibility can exceed 99%, making it a trusted platform for both research and validation studies.

3. Is MassARRAY® a reliable platform for SNP genotyping?

Yes. MassARRAY® is a well-established genotyping platform widely adopted in genetics, molecular diagnostics, agricultural genomics, precision medicine, and biomedical research. Its high sensitivity, reproducibility, and multiplexing capability have contributed to its use in numerous peer-reviewed studies published in leading international scientific journals. The platform is trusted by researchers worldwide for accurate SNP detection and genetic variant analysis.

4. What is the working principle of the MassARRAY® System?

MassARRAY® technology combines Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) with primer extension chemistry to detect genetic variants. Following PCR amplification and primer extension, DNA fragments are analyzed based on their molecular mass. Since each nucleotide has a unique molecular weight, the system accurately differentiates alleles by measuring mass differences, enabling rapid and highly precise SNP genotyping. This label-free detection method provides excellent specificity while supporting medium- and high-throughput genetic analysis.