Designing Primers for SNaPshot Technique

  • Greiciane Gaburro PanetoEmail author
  • Francisco de Paula Careta
Part of the Methods in Molecular Biology book series (MIMB, volume 1275)


The SNaPshot technique, also known as minisequencing, is a primer extension-based method developed for the analysis of Single Nucleotide Polymorphisms (SNPs). Using this technique, it is possible to analyze more than 50 SNPs distributed throughout the genome in a single multiplex reaction, making it an advantage when compared with traditional sequencing reaction. In this chapter, you will find a step-by-step guide to design a multiplex primer assay for SNaPshot reaction.

Key words

SNP Genotyping Multiplex SNaPshot Primer 


  1. 1.
    Sachidanandam R, Weissman D, Schmidt SC et al (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928–933CrossRefPubMedGoogle Scholar
  2. 2.
    Taillon-Miller P, Gu Z, Li Q et al (1998) Overlapping genomic sequences: a treasure trove of single nucleotide polymorphisms. Genome Res 8:748–754PubMedCentralPubMedGoogle Scholar
  3. 3.
    Smigielski E, Sirotkin K, Ward M et al (1999) dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28:352–355CrossRefGoogle Scholar
  4. 4.
    Ramos E, Doumatey A, Elkahloun AG et al (2014) Pharmacogenomics, ancestry and clinical decision making for global populations. Pharmacogenomics J 14:217–222CrossRefPubMedGoogle Scholar
  5. 5.
    Stoneking M, Hedgecock D, Higuchi RG et al (1991) Populations variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 48:370–382PubMedCentralPubMedGoogle Scholar
  6. 6.
    Chemale G, Paneto GG, Menezes MA et al (2013) Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework. Forensic Sci Int Genet 7:353–358CrossRefPubMedGoogle Scholar
  7. 7.
    Kidd KK, Speed WC, Pakstis AJ et al (2014) Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet 10:23–32CrossRefPubMedGoogle Scholar
  8. 8.
    Borsting C, Sanchez JJ, Hansen HE et al (2008) Performance of the SNPforID 52 SNP-plex assay in paternity testing. Forensic Sci Int Genet 2:292–300CrossRefPubMedGoogle Scholar
  9. 9.
    Magnin S, Viel E, Baraquin A et al (2011) A multiplex SNaPshot assay as a rapid method for detecting KRAS and BRAF mutations in advanced colorectal cancers. J Mol Diagn 13:485–492CrossRefPubMedCentralPubMedGoogle Scholar
  10. 10.
    Coutinho A, Valverde G, Fehren-Schmitz L et al (2014) AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas. PLoS One 26:e93292CrossRefGoogle Scholar
  11. 11.
    Yang L, Sun H, Chen D et al (2014) Application of multiplex SNaPshot assay in measurement of PLAC4 RNA-SNP allelic ratio for noninvasive prenatal detection of trisomy 21. Prenat Diagn 34:139–144CrossRefPubMedGoogle Scholar
  12. 12.
    Marshall OJ (2004) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 20:2471–2472CrossRefPubMedGoogle Scholar
  13. 13.
    Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37:226–231PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Greiciane Gaburro Paneto
    • 1
    Email author
  • Francisco de Paula Careta
    • 2
  1. 1.Department of Pharmacy and NutritionFederal University of Espirito SantoAlegreBrazil
  2. 2.Department of Pharmacy and NutritionFederal University of Espirito SantoAlegreBrazil

Personalised recommendations