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 language | English (US) |
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Pages (from-to) | 1-14 |
Number of pages | 14 |
Journal | Molecular Genetics and Genomics |
DOIs | |
State | Accepted/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