RT Journal
A1 Sharim, Hila
A1 Grunwald, Assaf
A1 Gabrieli, Tslil
A1 Michaeli, Yael
A1 Margalit, Sapir
A1 Torchinsky, Dmitry
A1 Arielly, Rani
A1 Nifker, Gil
A1 Juhasz, Matyas
A1 Gularek, Felix
A1 Almalvez, Miguel
A1 Dufault, Brandon
A1 Chandra, Sreetama Sen
A1 Liu, Alexander
A1 Bhattacharya, Surajit
A1 Chen, Yi-Wen
A1 Vilain, Eric
A1 Wagner, Kathryn R.
A1 Pevsner, Jonathan
A1 Reifenberger, Jeff
A1 Lam, Ernest T.
A1 Hastie, Alex R.
A1 Cao, Han
A1 Barseghyan, Hayk
A1 Weinhold, Elmar
A1 Ebenstein, Yuval
T1 Long-read single-molecule maps of the functional methylome
JF Genome Research 
JO Genome Research 
YR 2019 
FD April 01 
VO 29 
IS 4 
SP 646 
OP 656 
DO 10.1101/gr.240739.118 
UL http://genome.cshlp.org/content/29/4/646.abstract 
AB We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs. The method provides kilobase pair–scale genomic methylation patterns comparable to whole-genome bisulfite sequencing (WGBS) along genes and regulatory elements. These long single-molecule reads allow for methylation variation calling and analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell second-generation sequencing. The method is applied here to study facioscapulohumeral muscular dystrophy (FSHD), simultaneously recording the haplotype, copy number, and methylation status of the disease-associated, highly repetitive locus on Chromosome 4q.