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_36
Snippet: We did not expect to find any genuine SNP calls in the results from the LVS experiments, as the design of the resequencing chips was primarily based on this genome sequence. ABI sequence validation of 290 SNP calls from the unfiltered data sets confirmed three of these LVS base calls as true SNPs. ABI sequence validation of a subset of 562 possible SNP locations from the SCHU S4 strain (versus the LVS reference strain) are shown in Table 4 . Sequ.....
Document: We did not expect to find any genuine SNP calls in the results from the LVS experiments, as the design of the resequencing chips was primarily based on this genome sequence. ABI sequence validation of 290 SNP calls from the unfiltered data sets confirmed three of these LVS base calls as true SNPs. ABI sequence validation of a subset of 562 possible SNP locations from the SCHU S4 strain (versus the LVS reference strain) are shown in Table 4 . Sequence results were obtained for 484 ($86.1%) of the 562 selected locations, of which 320 and 164 were believed to be false positives and false negatives, respectively, based on previously published sequences. Only 5 out of the 320 suspected false positives were true SNPs. Similarly, six of the suspected false negatives were found to be true negatives in our validation results. It is not clear whether these differences are due to errors in the published SCHU S4 genomic sequence or they represent genuine point mutations in our sample DNA as compared to the SCHU S4 strain DNA used to obtain the published genomic sequence. The complete lists of validated SNP locations and the results are shown in Supplementary Tables 2 and 3.
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