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MassARRAY SNP Genotyping

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CD Genomics offers a rapid and accurate custom SNP validation on the Sequenom MassARRAY MALDI–TOF instrument. Our MassARRAY system combines mass spectrometry, sensitive and robust chemistry, and advanced data analysis software to meet your SNP genotyping needs. As a Sequenom service provider, we aim to provide the highest level of service, confidentiality and customer support.

MassARRAY SNP Genotyping

The MassARRAY System is a non-fluorescent detection platform utilizing mass spectrometry to accurately and sensitively measure PCR-derived amplicons. For projects that require genotyping tens to hundreds of SNPs with hundreds samples, mass spectrometry-based platforms provide cost-effective, simplified designing and accurate methods for SNP genotyping. Sequenom genotyping technology is based upon primer extension using allele-specific mixtures of dNTPs and ddNTPs with mass spectrometric analysis of the products. The iPLEX Gold platform on the Sequenom is designed to genotype multiplex pools up to 32 SNPs per well, but we typically achieve between 25 and 30 loci. 

Workflow

To initial the service, a custom assay is designed for each pool of SNPs to be genotyped in a single multiplex reaction. Three primers are utilized per SNP, two for amplification and one for the extension reaction. Primers are unlabeled and usually 15-25 bp in length. Multiplex PCR assays target ~100 bp amplicons containing SNPs of interest. After multiplex PCR amplification, unused nucleotides are eliminated by digestion with shrimp alkaline phosphatase. The extension primers are then added, annealed and extended with an optimized mixture of modified nucleotides. Depending upon the alleles present, the primer extension products will have different masses, and the mixture of primer extension products is analyzed by mass spectrometry. Genotyping software calls each SNP genotype based upon the measured mass of each primer extension product present compared to the calculated mass of all possible extension products for that pool of SNPs. The procedures for our MassARRAY SNP Genotyping is illustrated in Figure 1.

Workflow of MassARRAY SNP Genotyping Figure 1. Workflow of MassARRAY SNP Genotyping.

Sample and Submission Requirement

We require 2 µL of DNA at a concentration of 5-10 ng/µL of genomic DNA per multiplex pool to initiate the SNP genotyping process. To begin a project, users need to provide a list of variants or SNP ID (rs#) with 100-200 bps up and downstream sequence. The reference alleles and variants should be denoted in brackets (for example [G/A] or [G/-] where the dash denotes a deletion). Samples can be submitted in either 384- or 96-well plates with at least 2 open wells for negative controls, the DNA samples should be eluted in water.

Data Analysis

Genotypes are determined through ratio analysis of the MALDI-TOF mass spectrometer.

Key Features and Advantages:

  • Accurate and Automated. Nucleic acid detection by mass spectrometry enables readout by molecular mass, and using state-of-the-art technologies for automated, non-contact dispensing of reagents
  • Scalable and Flexible. We offer a variety of options for sample and assay throughput.
  • Cost Effective. Multiplex analysis reduces per sample cost, and scalable throughput optimizes batch and resource requirements.
  • High Multiplex Capability. Multiplex up to 30 SNP loci in a single cell.
  • Fast Assay Design. A new assay can be designed within a few hours. In addition, a semi-automated workflow and unmodified oligos provide rapid turnaround times
  • Achieve high quality results with reduced and simplified sample handling.

Our MassARRAY System offers a unique solution for SNP genotyping with low input material and provides precise, rapid, and cost-effective analysis for your project. Our service includes customized SNP panels 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.

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CONTACT CD GENOMICS

45-1 Ramsey Road, Shirley, NY 11967, USA
Tel: 1-631-275-3058
Fax: 1-631-614-7828
Email: info@cd-genomics.com