We selected SNPs (rs8051542, rs12443621, rs3803662, rs4784227 and rs3112612) in the TOX3/LOC643714 locus at 16q12.1 from the confirmatory results from GWAS or meta-analysis in multiple populations [6 (link),7 (link),11 (link),20 (link)].
The five SNPs were genotyped using the SEQUENOM MassARRAY matrix-assisted laser desorption ionization-time of flight mass spectrometry platform (Sequenom, San Diego, CA, USA). Primers for multiplex PCR and extended reactions were designed using proprietary software (Assay Designer, version 3.1) provided by Sequenom Inc (San Diego, CA, USA). In accordance with the manufacturer’s instructions, SNPs were genotyped using Sequenom MassARRAY genotyping technology (Sequenom, San Diego, CA, USA) and amplified in multiplex PCR by a standard PCR protocol. The genomic amplification product was cleaned using shrimp alkaline phosphatase (Sequenom, San Diego, CA, USA) to neutralize any unincorporated dNTPs, followed by a single-base extension reaction using the iPLEX enzyme (Sequenom, San Diego, CA, USA) and mass-modified terminators (Sequenom, San Diego, CA, USA). The products of the iPLEX reaction were desalted and transferred onto a SpectroCHIP (Sequenom, San Diego, CA, USA) by the MassARRAY nanodispenser (Sequenom, San Diego, CA, USA), which was then analyzed by the MassARRAY analyzer by combining base calling with the clustering algorithm.
The five SNPs were genotyped using the SEQUENOM MassARRAY matrix-assisted laser desorption ionization-time of flight mass spectrometry platform (Sequenom, San Diego, CA, USA). Primers for multiplex PCR and extended reactions were designed using proprietary software (Assay Designer, version 3.1) provided by Sequenom Inc (San Diego, CA, USA). In accordance with the manufacturer’s instructions, SNPs were genotyped using Sequenom MassARRAY genotyping technology (Sequenom, San Diego, CA, USA) and amplified in multiplex PCR by a standard PCR protocol. The genomic amplification product was cleaned using shrimp alkaline phosphatase (Sequenom, San Diego, CA, USA) to neutralize any unincorporated dNTPs, followed by a single-base extension reaction using the iPLEX enzyme (Sequenom, San Diego, CA, USA) and mass-modified terminators (Sequenom, San Diego, CA, USA). The products of the iPLEX reaction were desalted and transferred onto a SpectroCHIP (Sequenom, San Diego, CA, USA) by the MassARRAY nanodispenser (Sequenom, San Diego, CA, USA), which was then analyzed by the MassARRAY analyzer by combining base calling with the clustering algorithm.
Free full text: Click here
