Multiplexed SNP genotyping using primer single-base extension (SBE) and microsphere arrays

Abstract

Single-nucleotide polymorphisms (SNPs), genome sites with single-base sequence differences between individual chromosomes, are the most common type of genetic variation. Single-base changes can result in disease phenotypes, confer susceptibility or resistance to toxins or pathogens, or serve as markers for distinct allelic segments of DNA, making SNPs an important emerging tool in both basic and clinical research. This unit presents detailed protocols for multiplexed SNP genotyping using primer single-base extension (SBE) adapted to microspheres and flow cytometry. The methods described are best suited for typing a modest number of SNPs in a large number of samples. The Basic Protocol describes extension of the genotyping primers by one nucleotide, a labeled dideoxyribonucleotide that reveals the nucleotide base at that position on the template strand. The extended primers are then captured onto microspheres bearing an oligonucleotide "address" that is the reverse complement of a sequence on the 5' end of the genotyping primers and subsequently measured using flow cytometry.