Single-locus enrichment without amplification for sequencing and direct detection of epigenetic modifications

Thang T. Pham, Jun Yin, John S. Eid, Evan Adams, Regina Lam, Stephen W. Turner, Erick W. Loomis, Jun Yi Wang, Paul J Hagerman, Jeremiah W. Hanes

Research output: Contribution to journalArticle

14 Scopus citations

Abstract

A gene-level targeted enrichment method for direct detection of epigenetic modifications is described. The approach is demonstrated on the CGG-repeat region of the FMR1 gene, for which large repeat expansions, hitherto refractory to sequencing, are known to cause fragile X syndrome. In addition to achieving a single-locus enrichment of nearly 700,000-fold, the elimination of all amplification steps removes PCR-induced bias in the repeat count and preserves the native epigenetic modifications of the DNA. In conjunction with the single-molecule real-time sequencing approach, this enrichment method enables direct readout of the methylation status and the CGG repeat number of the FMR1 allele(s) for a clonally derived cell line. The current method avoids potential biases introduced through chemical modification and/or amplification methods for indirect detection of CpG methylation events.

Original languageEnglish (US)
Pages (from-to)1-14
Number of pages14
JournalMolecular Genetics and Genomics
DOIs
StateAccepted/In press - Jan 29 2016

Keywords

  • Epigenetic modification
  • FMR1
  • Fragile X syndrome
  • Single molecule sequencing
  • Tandem repeats
  • Targeted enrichment

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

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    Pham, T. T., Yin, J., Eid, J. S., Adams, E., Lam, R., Turner, S. W., Loomis, E. W., Wang, J. Y., Hagerman, P. J., & Hanes, J. W. (Accepted/In press). Single-locus enrichment without amplification for sequencing and direct detection of epigenetic modifications. Molecular Genetics and Genomics, 1-14. https://doi.org/10.1007/s00438-016-1167-2