title: Genotyping performance between saliva and blood-derived genomic DNAs on the DMET array: a comparison.
abstract: The Affymetrix Drug Metabolism Enzymes and Transporters (DMET) microarray is the first assay to offer a large representation of SNPs conferring genetic diversity across known pharmacokinetic markers. As a convenient and painless alternative to blood, saliva samples have been reported to work well for genotyping on the high density SNP arrays, but no reports to date have examined this application for saliva-derived DNA on the DMET platform. Genomic DNA extractions from saliva samples produced an ample quantity of genomic DNA for DMET arrays, however when human amplifiable DNA was measured, it was determined that a large percentage of this DNA was from bacteria or fungi. A mean of 37.3% human amplifiable DNA was determined for saliva-derived DNAs, which results in a significant decrease in the genotyping call rate (88.8%) when compared with blood-derived DNAs (99.1%). More interestingly, the percentage of human amplifiable DNA correlated with a higher genotyping call rate, and almost all samples with more than 31.3% human DNA produced a genotyping call rate of at least 96%. SNP genotyping results for saliva derived DNA (n = 39) illustrated a 98.7% concordance when compared with blood DNA. In conclusion, when compared with blood DNA and tested on the DMET array, saliva-derived DNA provided adequate genotyping quality with a significant lower number of SNP calls. Saliva-derived DNA does perform very well if it contains greater than 31.3% human amplifiable DNA.
authors.affiliation: Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America.
authors.forename: Yueshan
authors.initials: Y
authors.lastname: Hu
authors.forename: Erik A
authors.initials: EA
authors.lastname: Ehli
authors.forename: Kelly
authors.initials: K
authors.lastname: Nelson
authors.forename: Krista
authors.initials: K
authors.lastname: Bohlen
authors.forename: Christophina
authors.initials: C
authors.lastname: Lynch
authors.forename: Patty
authors.initials: P
authors.lastname: Huizenga
authors.forename: Julie
authors.initials: J
authors.lastname: Kittlelsrud
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Soundy
authors.forename: Gareth E
authors.initials: GE
authors.lastname: Davies
mesh_terms: D015415:Biomarkers / Q000032:analysis*; D004247:DNA / Q000097:blood / Q000235:genetics* / Q000302:isolation & purification; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D001523:Mental Disorders / Q000097:blood / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012463:Saliva / Q000378:metabolism*
chemical_list: D015415:Biomarkers; D004247:DNA