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Open Access Technical Note

Three multiplex snapshot assays for SNP genotyping in candidate innate immune genes

Lisa M Esteves1, Sara M Bulhões1, Maria J Brilhante1 and Luisa Mota-Vieira123*

Author Affiliations

1 Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE, São Miguel Island, Azores, Portugal

2 Instituto Gulbenkian de Ciência, Oeiras, Portugal

3 Center for Biodiversity, Functional & Integrative Genomics (BIOFIG), Lisbon, Portugal

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BMC Research Notes 2013, 6:54  doi:10.1186/1756-0500-6-54

Published: 7 February 2013

Abstract

Background

Innate immune system is the first line of research when studying immune response to diverse infections and autoimmune/inflammatory diseases. This immune response has been reported to be genetically diverse, due to polymorphisms coded by different genes. For this reason, our purpose was to develop a multiplex assay that allows the genotyping of candidate single nucleotide polymorphisms (SNPs) in innate immune genes.

Findings

We developed three multiplex PCR panels coupled with the minisequencing (SNaPshot) technique (multiplex PCR, multiplex primer extension, and capillary electrophoresis). The panels were tested in a sample set composed of 100 anonymous DNAs from healthy blood donors living in São Miguel Island (Azores, Portugal). Sixteen relevant SNPs among nine genes of the innate immune system – IL1α, IL1β, IL6, IL10, IL12RB1, TLR2, TLR4, TLR9 and CD14 – were genotyped and validated by direct sequencing, with the exception of one that was undetected by minisequencing. We suggest that these panels can be used in future studies for detection of risk gene variants in several populations and/or diseases.

Conclusions

In summary, we propose a multiplex assay that is able to identify the most frequent candidate SNPs in innate immune genes, using a medium scale genotyping platform. The assays can be used to evaluate the risk gene variants in populations of various geographic origins.

Keywords:
Innate immune genes; Polymorphisms; SNaPshot multiplex PCR