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Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD)

By Yi Dai, Pidong Li, Zhiqiang Wang, Fan Liang, Fan Yang, Li Fang, Yu Huang, Shangzhi Huang, Jiapeng Zhou, Depeng Wang, Liying Cui, Kai Wang

Posted 21 Mar 2018
bioRxiv DOI: 10.1101/286104

Purpose: Facioscapulohumeral Muscular Dystrophy (FSHD) is a common adult muscular dystrophy. Over 95% of FSHD cases are associated with contraction of the D4Z4 tandem repeat (~3.3kb per unit) at 4q35 with a specific genomic configuration (haplotype) called 4qA. Molecular diagnosis of FSHD typically requires pulsed-field gel electrophoresis with Southern blotting. We aim to develop novel genomic and computational methods for characterizing D4Z4 repeat numbers in FSHD. Methods: We leveraged a single-molecule optical mapping platform that maps locations of restriction enzyme sites on high molecular weight (>150kb) DNA molecules. We developed bioinformatics methods to address several challenges, including the differentiation of 4qA with 4qB alleles, the differentiation of 4q35 and 10q26 segmental duplications, the quantification of repeat numbers with different enzymes that may or may not have recognition sites within D4Z4 repeats. We evaluated the method on 25 human subjects (13 patients, 3 individual control subjects, 9 control subjects from 3 families) labeled by the Nb.BssSI and/or Nt.BspQI enzymes. Results: We demonstrated that the method gave a direct quantitative measurement of repeat numbers on D4Z4 repeats with 4qA allelic configuration and the levels of post-zygotic mosaicism. Our method had high concordance with Southern blots from several cohorts on two platforms (Bionano Saphyr and Bionano Irys), but with improved quantification of repeat numbers. Conclusion: While the study is limited by small sample size, our results demonstrated that single-molecule optical mapping is a viable approach for more refined analysis on genotype-phenotype relationships in FSHD, especially when post-zygotic mosaicism is present.

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