HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer

Lisa Mirabello, Marina Frimer, Ariana Harari, Thomas McAndrew, Benjamin Smith, Zigui Chen, Nicolas Wentzensen, Sholom Wacholder, Philip E. Castle, Tina Raine-Bennett, Mark Schiffman, Robert D. Burk

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

We have developed and evaluated a next-generation bisulfite sequencing (NGS) assay to distinguish HPV16 cervical precancer (CIN2-3; N 559) from HPV16-positive transient infections (N540). Cervical DNA was isolated and treated with bisulfite and HPV16 methylation was quantified by (i) amplification with barcoded primers and massively parallel single molecule sequencing and (ii) site-specific pyrosequencing. Assays were evaluated for agreement using intraclass correlation coefficients (ICC). Odds ratios (OR) for high methylation vs. low methylation were calculated. Single site pyrosequencing and NGS data were correlated (ICC50.61) and both indicated hypermethylation was associated with precancer (ORs of 2-37). Concordant NGS and pyrosequencing results yieled ORs that were stronger when compared with using either assay separately. Within the L1 region, the ORs for CIN2-3 were 14.3 and 22.4 using pyrosequencing and NGS assays, respectively; when both methods agreed the OR was 153. NGS assays provide methylation haplotypes, termed methyl-haplotypes from single molecule reads: cases had increased methylhaplotypes with≥1 methylated CpG site(s) per fragment compared with controls, particularly in L1 (p53.0 3 10-8). The maximum discrimination of cases from controls for a L1 methyl-haplotype had an AUC of 0.89 corresponding to a sensitivity of 92.5% and a specificity of 73.1%. The strengthening of the OR when the two assays were concordant suggests the true association of CpG methylation with precancer is stronger than with either assay. As cervical cancer prevention moves to DNA testing methods, DNA based biomarkers, such as HPV methylation could serve as a reflex strategy to identify women at high risk for cervix cancer.

Original languageEnglish (US)
Pages (from-to)E146-E153
JournalInternational Journal of Cancer
Volume136
Issue number4
DOIs
StatePublished - Feb 15 2015

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Haplotypes
Methylation
Odds Ratio
Uterine Cervical Neoplasms
DNA
Area Under Curve
Reflex
hydrogen sulfite
Biomarkers
Infection

Keywords

  • Cervical precancer
  • HPV16
  • Methylation
  • Next-generation sequencing
  • Pyrosequencing

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer. / Mirabello, Lisa; Frimer, Marina; Harari, Ariana; McAndrew, Thomas; Smith, Benjamin; Chen, Zigui; Wentzensen, Nicolas; Wacholder, Sholom; Castle, Philip E.; Raine-Bennett, Tina; Schiffman, Mark; Burk, Robert D.

In: International Journal of Cancer, Vol. 136, No. 4, 15.02.2015, p. E146-E153.

Research output: Contribution to journalArticle

Mirabello, L, Frimer, M, Harari, A, McAndrew, T, Smith, B, Chen, Z, Wentzensen, N, Wacholder, S, Castle, PE, Raine-Bennett, T, Schiffman, M & Burk, RD 2015, 'HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer', International Journal of Cancer, vol. 136, no. 4, pp. E146-E153. https://doi.org/10.1002/ijc.29119
Mirabello, Lisa ; Frimer, Marina ; Harari, Ariana ; McAndrew, Thomas ; Smith, Benjamin ; Chen, Zigui ; Wentzensen, Nicolas ; Wacholder, Sholom ; Castle, Philip E. ; Raine-Bennett, Tina ; Schiffman, Mark ; Burk, Robert D. / HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer. In: International Journal of Cancer. 2015 ; Vol. 136, No. 4. pp. E146-E153.
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abstract = "We have developed and evaluated a next-generation bisulfite sequencing (NGS) assay to distinguish HPV16 cervical precancer (CIN2-3; N 559) from HPV16-positive transient infections (N540). Cervical DNA was isolated and treated with bisulfite and HPV16 methylation was quantified by (i) amplification with barcoded primers and massively parallel single molecule sequencing and (ii) site-specific pyrosequencing. Assays were evaluated for agreement using intraclass correlation coefficients (ICC). Odds ratios (OR) for high methylation vs. low methylation were calculated. Single site pyrosequencing and NGS data were correlated (ICC50.61) and both indicated hypermethylation was associated with precancer (ORs of 2-37). Concordant NGS and pyrosequencing results yieled ORs that were stronger when compared with using either assay separately. Within the L1 region, the ORs for CIN2-3 were 14.3 and 22.4 using pyrosequencing and NGS assays, respectively; when both methods agreed the OR was 153. NGS assays provide methylation haplotypes, termed methyl-haplotypes from single molecule reads: cases had increased methylhaplotypes with≥1 methylated CpG site(s) per fragment compared with controls, particularly in L1 (p53.0 3 10-8). The maximum discrimination of cases from controls for a L1 methyl-haplotype had an AUC of 0.89 corresponding to a sensitivity of 92.5{\%} and a specificity of 73.1{\%}. The strengthening of the OR when the two assays were concordant suggests the true association of CpG methylation with precancer is stronger than with either assay. As cervical cancer prevention moves to DNA testing methods, DNA based biomarkers, such as HPV methylation could serve as a reflex strategy to identify women at high risk for cervix cancer.",
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AU - Wentzensen, Nicolas

AU - Wacholder, Sholom

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