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| Genomics
Fine Mapping
Sequenom, Inc.
3595 John Hopkins Ct.
San Diego, CA 92121
aloria@sequenom.com
www.sequenom.com
858-202-9194
iPLEX Gold Assay for SNP Genotyping
The iPLEX assay for SNP Genotyping is the leading application to remaining nucleotides in the reaction. Following a brief incubation,
follow up on Genome Wide association studies and perform targeted the primer extension mixture is added and conducted using a
genotyping. standardized cycling program. Finally, CleanResin is added to the
mixture to prepare it for deposition on a 384-well SpectroChip
®
.
Recently, a new protocol has been developed on the basis of the SpectropChips enable an automated readout and data analysis by a
iPLEX assay to improve the multiplexing capabilities of the assay up Compact TM MALDI-TOF mass-spectrometer.
to a level of 40-plexing. This new protocol is named iPLEX Gold.
Data analysis is performed on the Typer Software Module; a screen
The iPLEX assay is based on a simple single-base primer extension shot of the graphical interface is provided in Figure 2.
assay. A protocol overview is provided in Figure 1.
Figure 2
References:
1. Ragoussis, J., et al. Matrix Asssited Laser Desorption/Ionixation Time-
of-Flight Mass Spectrometry in Genomics Research. PLoS Genetics, 2007
Figure 1
(7) 920-29.
2. Volkman, S., et al. A Genome-wide Map of Diversity in Plasmodium
The iPLEX assay is truly homogeneous, in the sense that after falciparum. Nature Genetics, 2007, 10.1038/ng1930.
PCR, reagents are added to the reaction cocktail in a three step
3. Sladek, R., et al. A Genome-wide Association Study Identifies Novel Risk
protocol. No transfer or pipeting into different reaction containers
Loci for Type 2 Diabetes, 2007, 10.1038/nature05616.
is required.
PCR primers are designed in a region of approximately 100 base
pairs around the SNP of interest and an extension primer is designed
immediately adjacent to the SNP. The assay design is performed in a
highly automated fashion by the AssayDesigner software module.
The starting point of the iPLEX assay is PCR amplifi cation, followed
by the addition of Shrimp Alkaline Phosphatase (SAP) to inactivate
Protocol Guide ı 2008 View entire protocol online at www.biotechniques.com/protocol ı BioTechniques ı 37
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