Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing-the FRAGMENT approach

Chang Sun, Thomas McAndrew, Benjamin C. Smith, Zigui Chen, Marina Frimer, Robert D. Burk

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Invasive cervix cancer (ICC) is the third most common malignant tumor in women and human papillomavirus 16 (HPV16) causes more than 50% of ICC. DNA methylation is a covalent modification predominantly occurring at CpG dinucleotides and increased methylation across the HPV16 genome is strongly associated with ICC development. Next generation (Next Gen) sequencing has been proposed as a novel approach to determine DNA methylation. However, utilization of this method to survey CpG methylation in the HPV16 genome is not well described. Moreover, it provides additional information on methylation "haplotypes." In the current study, we chose 12 random samples, amplified multiple segments in the HPV16 bisulfite treated genome with specific barcodes, inspected the methylation ratio at 31 CpG sites for all samples using Illumina sequencing, and compared the results with quantitative pyrosequencing. Most of the CpG sites were highly consistent between the two approaches (overall correlation, r =0.92), thus verifying that Next Gen sequencing is an accurate and convenient method to survey HPV16 methylation and thus can be used in clinical samples for risk assessment. Moreover, the CpG methylation patterns (methylation haplotypes) in single molecules identified an excess of complete-and non-methylated molecules and a substantial amount of partial-methylated ones, thus indicating a complex dynamic for the mechanisms of HPV16 CpG methylation. In summary, the advantages of Next Gen sequencing compared to pyrosequencing for HPV genome methylation analyses include higher throughput, increased resolution, and improved efficiency of time and resources.

Original languageEnglish (US)
Article numberArticle 150
JournalFrontiers in Genetics
Volume5
Issue numberJUN
DOIs
StatePublished - 2014

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High-Throughput Nucleotide Sequencing
DNA Methylation
Methylation
Human papillomavirus 16
Uterine Cervical Neoplasms
Genome
Therapeutics
Haplotypes
hydrogen sulfite

Keywords

  • CpG methylation
  • Human papillomavirus
  • Methylation
  • Methylation haplotypes
  • Next generation sequencing

ASJC Scopus subject areas

  • Genetics
  • Molecular Medicine
  • Genetics(clinical)

Cite this

Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing-the FRAGMENT approach. / Sun, Chang; McAndrew, Thomas; Smith, Benjamin C.; Chen, Zigui; Frimer, Marina; Burk, Robert D.

In: Frontiers in Genetics, Vol. 5, No. JUN, Article 150, 2014.

Research output: Contribution to journalArticle

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