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Am J Clin Pathol. 2014 Jun;141(6):796-804. doi: 10.1309/AJCP9P2KJSXEKCJB.

Development and validation of a new HPV genotyping assay based on next-generation sequencing.

Author information

1
From BGI Shenzhen, Shenzhen, China; BGI Tianjin, Tianjin, China;
2
From BGI Shenzhen, Shenzhen, China;
3
BGI Tianjin, Tianjin, China;
4
Peking University Shenzhen Hospital, Shenzhen, China;
5
Shenzhen Second People's Hospital, Shenzhen, China; and.
6
Department of Anatomic Pathology, and.
7
Preventive Oncology International and Women's Health Institute, Cleveland Clinic, Cleveland, OH. jlb@poiinc.org.

Abstract

OBJECTIVES:

We developed a new human papillomavirus (HPV) genotyping assay based on multiplex polymerase chain reaction and next-generation sequencing (NGS) methods for large-scale cervical cancer screening.

METHODS:

We first trained the assay on 1,170 self-collected samples, balancing the cutoff points for high-risk types. Then using 4,262 separate self-collected specimens, we compared concordance, sensitivity, and specificity for cervical intraepithelial neoplasia type 2 (CIN2) or higher and CIN type 3 (CIN3) or higher of the HPV sequencing assay with that of Hybrid Capture 2 (HC2) direct samples and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assay self-samples.

RESULTS:

All assays had a good agreement. The sensitivity for CIN2 or higher and CIN3 or higher of the self-sampling specimens tested with the sequencing assay run on both MiSeq and Ion Torrent Personal Genome Machine sequencer was similar to that of direct-sampling specimens tested with HC2 (P > .05), but the specificity of the sequencing assay for CIN2 or higher and CIN3 or higher was significantly higher than that of HC2 (P < .01).

CONCLUSIONS:

This population-based study has demonstrated the applicability of a new NGS high-risk HPV assay for primary cervical cancer screening based on self-collection.

KEYWORDS:

Cervical cancer screening; HPV genotyping test; Ion Torrent PGM; MiSeq; Next-generation sequencing (NGS); Self-sampling

PMID:
24838323
DOI:
10.1309/AJCP9P2KJSXEKCJB
[Indexed for MEDLINE]

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