title: Quantification of single nucleotide polymorphisms by automated DNA sequencing.
abstract: Single nucleotide polymorphisms (SNPs) are linked to phenotypes associated with diseases and drug responses. Many techniques are now available to identify and quantify such SNPs in DNA or RNA pools, although the information on the latter is limited. The majority of these methodologies require prior knowledge of target sequences, normally obtained through DNA sequencing. Direct quantitation of SNPs from DNA sequencing raw data will save time and money for large amount sample analysis. A high throughput DNA sequencing assay, in combination with a SNP quantitative algorithm, was developed for the quantitation of a SNP present in HCV RNA sequences. For a side-by-side comparison, a Pyrosequencing assay was also developed. Quantitation performance was evaluated for both methods. The direct DNA sequencing quantitation method was shown to be more linear, accurate, sensitive, and reproducible than the Pyrosequencing method for the quantitation of the SNP present in HCV RNA molecules.
authors.affiliation: Bioinformatics Group and Discovery Technology Department, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Qiu
authors.forename: George J
authors.initials: GJ
authors.lastname: Soder
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Sanfiorenzo
authors.forename: Luquan
authors.initials: L
authors.lastname: Wang
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Greene
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Fritz
authors.forename: Xiao-Yan
authors.initials: XY
authors.lastname: Cai
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D004279:DNA, Viral / Q000235:genetics; D016174:Hepacivirus / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012313:RNA / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004279:DNA, Viral; D012313:RNA