Polymorphism ratio sequencing: a new approach for single nucleotide polymorphism discovery and genotyping.
Polymorphism ratio sequencing (PRS) combines the advantages of high-throughput DNA sequencing with new labeling and pooling schemes to produce a powerful assay for sensitive single nucleotide polymorphism (SNP) discovery, rapid genotyping, and accurate, multiplexed allele frequency determination. In the PRS method, dideoxy-terminator extension ladders generated from a sample and reference template are labeled with different energy-transfer fluorescent dyes and coinjected into a separation capillary for comparison of relative signal intensities. We demonstrate the PRS method by screening two human mitochondrial genomes for sequence variations using a microfabricated capillary array electrophoresis device. A titration of multiplexed DNA samples places the limit of minor allele frequency detection at 5%. PRS is a sensitive and robust polymorphism detection method for the analysis of individual or multiplexed samples that is compatible with any four-color fluorescence DNA sequencer.
Blazej
Robert G
RG
University of California, Berkeley/University of California, San Francisco Joint Bioengineering Graduate Group, Berkeley, California 94720, USA.
Paegel
Brian M
BM
Mathies
Richard A
RA
D003062:Codon / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D020459:Genes, rRNA / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D016678:Genome; D005838:Genotype; D006801:Humans; D008928:Mitochondria / Q000235:genetics; D024101:Mitochondrial Proteins / Q000235:genetics; D011110:Polymorphism, Genetic / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012313:RNA / Q000235:genetics; D000077278:RNA, Mitochondrial; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
D003062:Codon; D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins; D000077278:RNA, Mitochondrial; D012313:RNA; D012343:RNA, Transfer