Allelotypling by massively parallel pyrosequencling of SNP-carrying trinucleotide threads

作者：Pettersson Erik; Zajac Pawel; Stahl Patrik L; Jacobsson Josefin A; Fredriksson Robert; Marcus Claude; Schioth Helgi B; Lundeberg Joakim; Ahmadian Afshin^*

来源：Human Mutation, 2008, 29(2): 323-329.

DOI：10.1002/humu.20655

• trinucleotide threading
• pooled genomic DNA
• association studies
• multiplexing
• SNP
• allelotyping
• cancer
• obesity

Here we present an approach for allelotyping combining the multiplexing features of the trinucleotide threading (TnT) method with pooling of genomic DNA and massively parallel pyrosequencing, enabling reliable allele frequency estimation in large cohorts. The approach offers several benefits as compared to array,based methods and allows undertaking highly complex studies without compromising accuracy, while keeping the workload to a minimum. This proof-of-concept study involves formation of trinucleotide threads, targeting a total of 147 single-nucleotide polymorphisms (SNPs) related to obesity and cancer, for multiplex amplification and allele extraction from a pool of 462 genomes, followed by massively parallel pyrosequencing. Approximately 177k reads were approved, identified, and assigned to SNP-carrying threads rendering representative allele frequencies in the cohort.

• 出版日期2008-2