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The Pap Smear Challenge: Comparing Clinical Performance of a Novel "Molecular Pap" Based on Next-Generation Sequencing to Traditional Cervical Cancer Screening

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Technical Report,01 Apr 2018,31 Mar 2019

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US Army Brooke Army Medical Center FORT SAM HOUSTON United States

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The Molecular Pap is an integrated panel of biomarkers based on Human Papillomavirus HPV deep sequencing and quantitative DNA methylation of 3 human genes by pyrosequencing. To validate our biomarker panel and predictive model for Pap smear classification, we proposed to collect 700 Pap smear samples from each of 6 diagnostic categories for HPV genotyping and methylation quantification for direct comparison to traditional cervical cancer screening cytology - cobasregistered trademarkHPV. Methods This prospective, cross-sectional study uses residual liquid-based cytology samples for HPV genotyping and epigenetic analysis by pyrosequencing. A total of 3,037 Pap samples have been collected to date and have undergone various stages of DNA extraction, HPV DNA amplification, Sanger and deep sequencing, and bioinformatics analysis. Results NA. Study is on-going. Accomplishments Year 2 Pap sample collection has reached 80 percent of target accrual and molecular analyses are in-progress. Six contracts for supplies, software, cloud-based bioinformatics, and taxonomic profiling have been awarded. The development of a real-world, automated, data science pipeline for multiple types of genomics data has been initiated.

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  • Medicine and Medical Research

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