Testing for Facioscapulohumeral Muscular Dystrophy with Optical Genome Mapping

Abstract

The introduction of optical genome mapping has improved time constraints and a lack of specificity from previous methodologies when performing genome‐wide analyses of samples. Optical genome mapping allows for the detection of structural variations, aberrations, and functionality traits from a single stained molecule of DNA. Though the preparation time is increased compared to previously utilized visualization techniques, optical genome mapping significantly reduces the time needed for analysis. Specifically, individual disease pipelines have been developed to rapidly analyze prepared samples. One of these diseases, Facioscapulohumeral Muscular Dystrophy (FSHD), is detected through quantification of the D4Z4 repeat array on chromosome 4q35. Optical genome mapping, with the ability to enumerate the repeats of the D4Z4 array, has demonstrated the capability to precisely diagnose FSHD. In this protocol, the preparation of samples and subsequent loading and analysis in an optical genome mapping system is discussed for the detection and analysis of FSHD. These methods should prove highly useful in FSHD analyses and beyond with the development of further disease analysis pipelines within the instrument. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Genomic DNA isolation, labeling, and staining Basic Protocol 2: Mapping and analysis with the Bionano Saphyr® system

Optical Genome Mapping for Oncology Applications

“…For detailed loading instructions, refer to the Saphyr System User Guide or refer to the Current Protocols article by Koppikar et al (2023).…”

The FSHD jigsaw: are we placing the tiles in the right position?

“…In itself, the D4Z4 array structure impedes direct testing in preimplantation genetic diagnosis [50], and the highly recombinogenic nature of the 4q and 10q subtelomeres obstacles the use of alternative markers for PGD [51]. More recently, molecular combing [52–54] and optical mapping techniques (OGM) [55,56] have emerged to estimate the size of the array. In particular (OGM) has been applied to FSHD [55] for its ability to enumerate the repeats of the D4Z4 array on single long molecules of DNA.…”

“…More recently, molecular combing [52–54] and optical mapping techniques (OGM) [55,56] have emerged to estimate the size of the array. In particular (OGM) has been applied to FSHD [55] for its ability to enumerate the repeats of the D4Z4 array on single long molecules of DNA. These methods have the potential to investigate structural variation associated with D4Z4 repeats throughout the entire genome, adding new capacity for interpreting uncommon molecular findings and phenotypes, even though they are technically and cost-effectively demanding, and none of them provides detailed information about the methylation status of the D4Z4 locus, a hallmark of FSHD.…”

Case report: Identification of facioscapulohumeral muscular dystrophy 1 in two siblings with normal phenotypic parents using optical genome mapping

“…The most commonly used technique for diagnosing FSHD1 is Southern blotting, which is time-consuming (because it involves multiple enzymatic reactions) and only results in an estimate of the number of D4Z4 repeat units based on the band size. In recent years, OGM has emerged as an effective method for a precise determination of the number of repeat units and differentiating DNA fragments from 4q35 and 10q26 ( 11 , 18 ).…”

“…A simple and uniform method of diagnosis that enables easy interpretation replication by laboratories worldwide would be beneficial. Optical genome mapping (OGM) offers an accurate and highly reproducible method for identifying FSHD-associated chromosomal abnormalities ( 11 ). This method overcomes some of the important problems encountered in conventional analytical techniques, such as distinguishing 4q35-D4Z4 repeats from the highly homologous 10q26 array, measuring the number of repeats at 4q35, and differentiating between the 4qA and 4qB alleles ( 12 ).…”