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Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. (Funktionell Farmakologi)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. (Funktionell Farmakologi)
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2008 (English)In: Human Mutation, ISSN 1059-7794, E-ISSN 1098-1004, Vol. 29, no 2, 323-329 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2008. Vol. 29, no 2, 323-329 p.
Keyword [en]
trinucleotide threading, pooled genomic DNA, association studies, multiplexing, SNP, allelotyping, cancer, obesity
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-99150DOI: 10.1002/humu.20655ISI: 000253033000016PubMedID: 17994569OAI: oai:DiVA.org:uu-99150DiVA: diva2:202286
Available from: 2009-03-09 Created: 2009-03-09 Last updated: 2017-12-13Bibliographically approved

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