title: Development of a novel liquid bead array human papillomavirus genotyping assay (PGMY-LX) and comparison with linear array for continuity in longitudinal cohort studies.
abstract: Studies of the natural history of human papillomavirus (HPV) infection require reproducible, type-specific testing of the viral types that infect cervical tissue; Linear Array (LA) is one method that has been widely used. We sought to develop a cost-effective, high-throughput alternative using the same PGMY09/11 primer/probe system and offering sensitivity and specificity comparable to those with LA to ensure continuity in longitudinal studies. We report here on a Luminex-based approach, PGMY-LX, that offers type-specific detection of 33 oncogenic and nononcogenic types. Detection of HPV type-specific plasmid DNA was highly specific, with high signal-to-noise ratios for all types except nononcogenic type 40 and no cross-reactivity between types. Cohen's unweighted κ values for 378 clinical samples tested by both LA and PGMY-LX were ≥0.8 (range, 0.80 to 1.0) for 25 types, including oncogenic HPV types 16, 31, 33, 39, 45, 58, and 59 and possibly oncogenic types 53, 66, 73, and 82) and >0.7 (range, 0.74 to 0.79) for oncogenic types 18, 35, 51, and 56 and probable oncogenic type 68b, indicating substantial or better type-specific agreement between the two methods. The reproducibility by PGMY-LX of the types detected by LA varied from 94% when a single HPV type was present to 66% when multiple types were present. The interrun reproducibility for PGMY-LX varied from 98% for single-type infections to 85% for multiple-type infections. The high reproducibility of PGMY-LX and the type-specific agreement with LA allows PGMY-LX to be incorporated into longitudinal, cohort studies that have historically relied on LA.
authors: Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, USA nozzaris@peds.ucsf.edu.
authors: Sepideh
authors: S
authors: Farhat
authors: Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, USA.
authors: Mark E
authors: ME
authors: Scott
authors: Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, USA.
authors: Yifei
authors: Y
authors: Ma
authors: Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, USA.
authors: Anna-Barbara
authors: AB
authors: Moscicki
mesh_terms: D000328:Adult; D005260:Female; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D008137:Longitudinal Studies; D027383:Papillomaviridae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D030361:Papillomavirus Infections / Q000821:virology*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D055815:Young Adult
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