title: Practical interpretation of CYP2D6 haplotypes: Comparison and integration of automated and expert calling.
abstract: We describe a population genetic approach to compare samples interpreted with expert calling (EC) versus automated calling (AC) for CYP2D6 haplotyping. The analysis represents 4812 haplotype calls based on signal data generated by the Luminex xMap analyzers from 2406 patients referred to a high-complexity molecular diagnostics laboratory for CYP450 testing. DNA was extracted from buccal swabs. We compared the results of expert calls (EC) and automated calls (AC) with regard to haplotype number and frequency. The ratio of EC to AC was 1:3. Haplotype frequencies from EC and AC samples were convergent across haplotypes, and their distribution was not statistically different between the groups. Most duplications required EC, as only expansions with homozygous or hemizygous haplotypes could be automatedly called. High-complexity laboratories can offer equivalent interpretation to automated calling for non-expanded CYP2D6 loci, and superior interpretation for duplications. We have validated scientific expert calling specified by scoring rules as standard operating procedure integrated with an automated calling algorithm. The integration of EC with AC is a practical strategy for CYP2D6 clinical haplotyping.
authors.affiliation: Laboratory of Personalized Health, Genomas Inc, United States. Electronic address: g.ruano@genomas.net.
authors.forename: Gualberto
authors.initials: G
authors.lastname: Ruaño
authors.affiliation: Laboratory of Personalized Health, Genomas Inc, United States.
authors.forename: Mohan
authors.initials: M
authors.lastname: Kocherla
authors.affiliation: Laboratory of Personalized Health, Genomas Inc, United States.
authors.forename: James S
authors.initials: JS
authors.lastname: Graydon
authors.affiliation: Yale University School of Public Health, United States.
authors.forename: Theodore R
authors.initials: TR
authors.lastname: Holford
authors.affiliation: Clinical Laboratory Partners, Hartford Hospital, United States.
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Makowski
authors.affiliation: Institute of Living, Hartford Hospital, United States.
authors.forename: John W
authors.initials: JW
authors.lastname: Goethe
mesh_terms: D001185:Artificial Intelligence; D001331:Automation; D019389:Cytochrome P-450 CYP2D6 / Q000235:genetics*; D003627:Data Interpretation, Statistical; D005260:Female; D020440:Gene Duplication; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D008297:Male; D015203:Reproducibility of Results; D012984:Software
chemical_list: D019389:Cytochrome P-450 CYP2D6
keywords: Buccal swab; CYP2D6 haplotyping; Gene duplications; Genotyping software; Laboratory Information System; Molecular diagnostics interpretation