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.

In order to determine the base-calling frequency and accuracy of the Affymetrix platform, we performed a series of hybridizations using the LVS reference genomic DNA represented on the resequencing chips and the standard Affymetrix data processing methods. These data are summarized in Table 1 and excludes data from the SCHU S4 and plasmid-specific portions of the resequencing chips. The resequencing results from two experiments on the LVS query sample yielded a call rate !98.178% and 167 and 177 base calls, respectively, that differed from the chip reference sequence. ABI sequencing of PCR amplicons confirmed that only three of these candidate SNPs were actual differences between the reference genome sequence and our LVS genomic DNA. These three expected SNP locations correspond to sequencing errors in the LVS reference sequence that have since been corrected in the published sequence for LVS (GenBank Accession: AM 233362). These results represent the approximate upper limit of the technology's performance in our hands. It was anticipated that less than optimal results would occur when utilizing the GeneChips Õ to sequence a non-identical query genome. To assess this assumption, we performed hybridizations using another strain (SCHU S4) for which complete DNA sequence information was available.