Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-1 (of 1 Records) |
Query Trace: Rajeeven MS[original query] |
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Universal Human Papillomavirus Typing Assay: Whole Genome Sequencing Following Target Enrichment.
Li T , Unger ER , Batra D , Sheth M , Steinau M , Jasinski J , Jones J , Rajeeven MS . J Clin Microbiol 2016 55 (3) 811-823 We designed a universal HPV typing assay based on target enrichment and whole genome sequencing (eWGS). The RNA bait included 23,941 probes targeting 191 HPV types and 12 targeting beta-globin as control. We used Agilent SureSelect XT2 protocol for library preparation, Illumina HiSeq 2500 for sequencing and CLC genomics workbench for sequence analysis. Mapping stringency for type assignment was determined based on 8 (6 HPV-positive and 2 HPV negative) control samples. Using the optimal mapping conditions, types were assigned to 24 blinded samples. eWGS results were 100% concordant with Linear Array (LA) genotyping results for 9 plasmid samples and fully or partially concordant for 9 of the 15 cervical-vaginal samples, with 95.83% overall-type specific concordance for LA genotyping. eWGS identified 7 HPV types not included in the LA genotyping. Since this method does not involve degenerate primers targeting HPV genomic regions, PCR bias in genotype detection is minimized. With further refinements aimed at reducing cost and increasing throughput, this first application of eWGS for universal HPV typing could be a useful method to elucidate HPV epidemiology. |
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