title: Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.
abstract: Whole-genome microarrays with large-insert clones designed to determine DNA copy number often show variation in hybridization intensity that is related to the genomic position of the clones. We found these 'genomic waves' to be present in Illumina and Affymetrix SNP genotyping arrays, confirming that they are not platform-specific. The causes of genomic waves are not well-understood, and they may prevent accurate inference of copy number variations (CNVs). By measuring DNA concentration for 1444 samples and by genotyping the same sample multiple times with varying DNA quantity, we demonstrated that DNA quantity correlates with the magnitude of waves. We further showed that wavy signal patterns correlate best with GC content, among multiple genomic features considered. To measure the magnitude of waves, we proposed a GC-wave factor (GCWF) measure, which is a reliable predictor of DNA quantity (correlation coefficient = 0.994 based on samples with serial dilution). Finally, we developed a computational approach by fitting regression models with GC content included as a predictor variable, and we show that this approach improves the accuracy of CNV detection. With the wide application of whole-genome SNP genotyping techniques, our wave adjustment method will be important for taking full advantage of genotyped samples for CNV analysis.
authors.affiliation: Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Diskin
authors.forename: Mingyao
authors.initials: M
authors.lastname: Li
authors.forename: Cuiping
authors.initials: C
authors.lastname: Hou
authors.forename: Shuzhang
authors.initials: S
authors.lastname: Yang
authors.forename: Joseph
authors.initials: J
authors.lastname: Glessner
authors.forename: Hakon
authors.initials: H
authors.lastname: Hakonarson
authors.forename: Maja
authors.initials: M
authors.lastname: Bucan
authors.forename: John M
authors.initials: JM
authors.lastname: Maris
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
mesh_terms: D016477:Artifacts; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000032:analysis; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide
chemical_list: D004247:DNA
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