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_20
Snippet: In general, the DNA sequence of query strains is not known. Therefore, it is not possible to identify locations that are subject to alternate homology effects with total confidence. However, an underlying assumption of the resequencing method is that the query DNA is similar to the reference sequence represented on the chip. Our approach to the problem of the alternate homology effect exploits this assumption. For each SNP observed in the raw res.....
Document: In general, the DNA sequence of query strains is not known. Therefore, it is not possible to identify locations that are subject to alternate homology effects with total confidence. However, an underlying assumption of the resequencing method is that the query DNA is similar to the reference sequence represented on the chip. Our approach to the problem of the alternate homology effect exploits this assumption. For each SNP observed in the raw results, we search for any alternate sequences within the reference sequence that could account for the SNP call. The difference in binding energy between the alternate (SNP) sequence and the reference sequence is used to differentiate between likely artifacts and genuine SNPs. (Calculated binding energy is a much more sensitive predictor of actual binding potential than Tm.)
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