Typing single nucleotide polymorphism using a gel-based sequencer: an improved efficience protocol and a new data analysis

B.J. Jungerius, A. Veenendaal, B.A. van Oost, M.F.W. te Pas, M.A.M. Groenen

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

Abstract

Single-nucleotide polymorphisms (SNPs) are increasingly used as genetic markers. Although a high number of SNP-genotyping techniques have been described, most techniques still have low throughput or require major investments. For laboratories that have access to an automated sequencer, a single-base extension (SBE) assay can be implemented using the ABI SNaPshot™ kit. Here we present a modified protocol comprising multiplex template generation, multiplex SBE reaction, and multiplex sample analysis on a gel-based sequencer such as the ABI 377. These sequencers run on a Macintosh platform, but on this platform the software available for analysis of data from the ABI 377 has limitations. First, analysis of the size standard included with the kit is not facilitated. Therefore a new size standard was designed. Second, using Genotype (ABI), the analysis of the data is very tedious and time consuming. To enable automated batch analysis of 96 samples, with 10 SNPs each, we developed SNPtyper. This is a spreadsheet-based tool that uses the data from Genotyper and offers the user a convenient interface to set parameters required for correct allele calling. In conclusion, the method described will enable any lab having access to an ABI sequencer to genotype up to 1000 SNPs per day for a single experimenter, without investing in new equipment.
Original languageEnglish
Pages (from-to)283-287
JournalMolecular Biotechnology
Volume25
Issue number3
DOIs
Publication statusPublished - 2003

Keywords

  • oligonucleotide arrays
  • genetic-variation
  • primer extension
  • hybridization
  • probes
  • dna
  • mutations
  • assay
  • pcr

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