Author: Pandya, Gagan A.; Holmes, Michael H.; Sunkara, Sirisha; Sparks, Andrew; Bai, Yun; Verratti, Kathleen; Saeed, Kelly; Venepally, Pratap; Jarrahi, Behnam; Fleischmann, Robert D.; Peterson, Scott N.
Title: A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform Document date: 2007_11_15
ID: 16tii0ha_42
Snippet: Resequencing for point mutations using microarrays was demonstrated in 1996 (21) and has become an established methodology (3). Only one high-quality reference genome sequence is required for sequencing multiple strains of the same organism. High-density resequencing microarrays offer a unique opportunity to genotype microorganisms at a nucleotide resolution, providing reliable and accurate information for identifying, typing and tracking infecti.....
Document: Resequencing for point mutations using microarrays was demonstrated in 1996 (21) and has become an established methodology (3). Only one high-quality reference genome sequence is required for sequencing multiple strains of the same organism. High-density resequencing microarrays offer a unique opportunity to genotype microorganisms at a nucleotide resolution, providing reliable and accurate information for identifying, typing and tracking infectious and bio-threat agents. Read and co-workers have demonstrated the power of comparative full-genome sequencing and identification of genetic polymorphisms in two related strains of Bacillus anthracis (22) . Resequencing arrays have also been used to detect group A streptococci and their associated antibiotic resistance markers (8) . Whole genomes of severe acute respiratory syndrome (SARS) virus have The true positive retention and false positive rejection rates are calculated relative to the number of true and false positive results in the raw, unfiltered data. The accuracy is calculated relative to the number of base calls remaining after the specified filtering step, where reference calls and true positive SNP calls are considered correct, and no-calls ('N') are not considered. A total of six false-positive SNPs were found to be both within 12 bases of a rearrangement boundary and within 12 bases of a predicted SNP.
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