A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform

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.

been characterized using a resequencing array approach (5, 9) . Most recently, resequencing of 14 smallpox virus genomes has been reported using a set of seven 30 K GeneChip arrays and a classical PCR-based approach (10) . These studies have shown the promise of the technology and the limitations associated with no-calls and mis-called bases. PCR amplification of long targets (>10 kb) generally used in resequencing is non-trivial and limits sample processing throughput. Zwick et al. (20) have sequenced 0.5% of the B. anthracis genome from 56 strains using resequencing arrays and recognized a need for resequencing of a larger percentage of the genome from multiple isolates to detect rare recombination events. Whole-genome resequencing of multiple strains will provide an enhanced genomic overview and a higher-resolution genotyping of an organism.