title: Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads.
abstract: 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.
authors.affiliation: Department of Gene Technology, Royal Institute of Technology (Kungliga Tekniska Högskolan, KTH), AlbaNova University Center, Stockholm, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Pettersson
authors.forename: Pawel
authors.initials: P
authors.lastname: Zajac
authors.forename: Patrik L
authors.initials: PL
authors.lastname: Ståhl
authors.forename: Josefin A
authors.initials: JA
authors.lastname: Jacobsson
authors.forename: Robert
authors.initials: R
authors.lastname: Fredriksson
authors.forename: Claude
authors.initials: C
authors.lastname: Marcus
authors.forename: Helgi B
authors.initials: HB
authors.lastname: Schiöth
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
authors.forename: Afshin
authors.initials: A
authors.lastname: Ahmadian
mesh_terms: D000483:Alleles; D005787:Gene Frequency; D006801:Humans; D009711:Nucleotides / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D009711:Nucleotides