July 7, 2019  |  

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

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

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.

Journal: Molecular genetics and genomics
DOI: 10.1007/s00438-016-1167-2
Year: 2016

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