HPV Strain Type Diagnosis by Sequencing qPCR Amplicons via Hybridisation to Tiling Arrays

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Philip Day, Reader in Quantitative Analytical Genomics
Manchester University

Philip Day is Reader in Quantitative Analytical Genomics, Manchester University, Director of Quantitative Molecular Medicine and Principal Investigator at the Manchester Interdisciplinary Biocentre. He has developed innovative tools for precise and accurate measurement of transcripts in heterogeneous tissues and for application in cancer studies. Philip heads a group investigating the systems pathology of neuroblastoma and leukemia, and molecular biomarkers relating to prognostics. Current studies focus on assay miniaturization for single cell analyses to enable understanding of drug response activities across cell populations and cell-cell interactions. Through close collaborative studies with groups in analytical instrumentation, miniaturization, data analysis, text mining and systems biology, he is engaging biomarker integration for enabling personalized healthcare. He has over 90 peer reviewed papers and is an examiner for various research councils and journals, and RSC Editorial Board member.

Abstract
Papillomaviruses are highly diverse pathogenic viruses in humans, with some types responsible for cervical cancer.
This aetiological role for human papillomavirus has led to the development of HPV as a diagnostic test because it confers high risk in cervical screening.
We present data on the use of three techniques for HPV detection; the Roche Linear Array HPV Genotyping Test, qPCR amplicons hybridised on custom made oligonucleotide micro-arrays, and the Genome Sequencer FLX System from Roche. The results showed multiple strain type infection was evident in 6/7 samples tested when using the deep sequencing approach, which could be verified in 5/7 samples using the PCR/custom micro-array and where sufficient PCR products were available for analysis. In this study the Roche Linear Array was unable to confirm multiple infections, however in 5/7 cases this approach did show agreement with the most abundant HPV type as determined by deep sequencing. A similar comparison between the PCR/custom array and deep sequencing showed that in 6/7 samples identified the same most abundant HPV strain type. These limited studies for PCR amplicons hybridised to the tiling micro-array and employing deep sequencing as a reference revealed more multiple infections than indicated by the Roche Linear Array.