Wei Tiffany Ding

US Patent:

20080154567, Jun 26, 2008

Filed:

Dec 19, 2007

Appl. No.:

11/959536

Inventors:

Ping Qiu - Edison NJ, US
Jonathan Richard Greene - South Orange NJ, US
Wei Ding - Scotch Plains NJ, US
Qing Zhang - Short Hills NJ, US

International Classification:

G06G 7/58

US Classification:

703 11

Abstract:

The present invention relates to a method for developing algorithms that are capable of discriminating among different genotypes and subtypes of a virus of interest. The method includes aligning a set of viral nucleotide sequences having known genotypes and analyzing the aligned sequences to identify nucleotide positions at which the nucleotide is conserved within genotypes, but diversified across the different known genotypes. These positions, referred to herein as genotyping positions, are employed as predictive variables to compile a variable input table for analysis by a statistical classification algorithm. The variable input table also includes the nucleotide present at each genotyping position as a value and the genotype for each of the aligned sequences as a response variable. The algorithm analyzes the sequences of nucleotides at the genotyping positions across the aligned viral sequences, and uses the results of this analysis to specify parameters for each genotyping position that when combined across the genotyping positions will discriminate among the genotypes represented in the input sequences. The algorithm generated by this method is useful in a method of predicting the genotype of a viral isolate of interest, such as a virus present in a biological sample obtained from an individual.