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_30
Snippet: Most array-based resequencing studies use purified PCR products rather than whole-genome DNA as described here. We wished to test whether, despite their additional complexity, genomic DNA samples could be reliably resequenced and what specific impediments might be encountered. Hybridization of a whole-genome sample on an Affymetrix Õ resequencing array platform can lead to incorrect base calls due to a number of systematic effects. Most of these.....
Document: Most array-based resequencing studies use purified PCR products rather than whole-genome DNA as described here. We wished to test whether, despite their additional complexity, genomic DNA samples could be reliably resequenced and what specific impediments might be encountered. Hybridization of a whole-genome sample on an Affymetrix Õ resequencing array platform can lead to incorrect base calls due to a number of systematic effects. Most of these adverse effects were predictable and therefore could be accounted for through application of specific bioinformatic data processing. These effects, and the bioinformatic filters, are described in Materials and Methods section.
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