Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing

We describe a method for the efficient genotyping of SNPs, involving sequencing of ordered and catenated sequence-tagged sites (OCS). In OCS, short genomic segments, each containing an SNP, are amplified by PCR using primers that carry specially designed extra nucleotides at their 5′-ends. Amplifica...

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Main Authors: Higasa, Koichiro, Hayashi, Kenshi
Formato: Artigo
Idioma:en
Publicado em: Oxford University Press 2002
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NAR Methods Online
Acesso em linha:https://ncbi.nlm.nih.gov/pmc/articles/PMC100310/
https://ncbi.nlm.nih.gov/pubmed/11809899
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spelling pubmed-1003102002-03-28 Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing Higasa, Koichiro Hayashi, Kenshi Nucleic Acids Res NAR Methods Online We describe a method for the efficient genotyping of SNPs, involving sequencing of ordered and catenated sequence-tagged sites (OCS). In OCS, short genomic segments, each containing an SNP, are amplified by PCR using primers that carry specially designed extra nucleotides at their 5′-ends. Amplification products are then combined and converted to a concatamer in a defined order by a second round of thermal cycling. The concatenation takes place because the 5′-ends of each amplicon are designed to be complementary to the ends of the presumptive neighboring amplicons. The primer sequences for OCS are chosen using newly developed dedicated software, OCS Optimizer. Using sets of SNPs, we show that at least 10 STSs can be concatenated in a predefined order and all SNPs in the STSs are accurately genotyped by one two-way sequencing reaction. Oxford University Press 2002-02-01 /pmc/articles/PMC100310/ /pubmed/11809899 Text en Copyright © 2002 Oxford University Press
institution US National Library of Medicine
collection PubMed Central
language en
format Article
topic NAR Methods Online
spellingShingle NAR Methods Online
Higasa, Koichiro
Hayashi, Kenshi
Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing
description We describe a method for the efficient genotyping of SNPs, involving sequencing of ordered and catenated sequence-tagged sites (OCS). In OCS, short genomic segments, each containing an SNP, are amplified by PCR using primers that carry specially designed extra nucleotides at their 5′-ends. Amplification products are then combined and converted to a concatamer in a defined order by a second round of thermal cycling. The concatenation takes place because the 5′-ends of each amplicon are designed to be complementary to the ends of the presumptive neighboring amplicons. The primer sequences for OCS are chosen using newly developed dedicated software, OCS Optimizer. Using sets of SNPs, we show that at least 10 STSs can be concatenated in a predefined order and all SNPs in the STSs are accurately genotyped by one two-way sequencing reaction.
author Higasa, Koichiro
Hayashi, Kenshi
author_facet Higasa, Koichiro
Hayashi, Kenshi
author_sort Higasa, Koichiro
title Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing
title_short Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing
title_full Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing
title_fullStr Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing
title_full_unstemmed Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing
title_sort ordered catenation of sequence-tagged sites and multiplexed snp genotyping by sequencing
publisher Oxford University Press
publisher_facet Oxford University Press
publishDate 2002
url https://ncbi.nlm.nih.gov/pmc/articles/PMC100310/
https://ncbi.nlm.nih.gov/pubmed/11809899
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