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.

One outcome that initially seemed puzzling was the much larger number of false-positive SNPs in the SCHU S4 data that remained after the data were treated with the filters. This outcome was directly related to the nature of the SCHU S4 sample. A mapping of the SCHU S4 genome onto the LVS reference sequence, produced with the MUMer software, reveals many rearrangements in SCHU S4 relative to LVS. A feature probe on the resequencing chip that spans one of these rearrangement boundaries would be expected to hybridize poorly with the SCHU S4 sample, and this increased the likelihood that alternate sequences would hybridize more strongly, increasing the false-positive calls. This outcome suggests that the resequencing platform could be used to identify The results shown are for the LVS sample, using the Affymetrix-recommended batch analysis parameters, including a quality score threshold of 12 and a call rate cutoff of 0.5. Those portions of chip F that represent the SCHU S4 reference and the plasmids were excluded from this analysis. Therefore, this represents the performance of the system under ideal circumstances: the chips are challenged with a sample that is essentially identical to the chip reference.