Titel: Optical genome mapping for repeat expansion disorder testing
ID: W8-006
Art: Invited talk
Redezeit: 15 min
Session: Workshop 8
(Epi-)Genomics and Cancer

Referent: Kornelia Neveling (Nijmegen/NL)

Abstract - Text


Short tandem repeat (STR) expansions are often unstable and can be associated with genetic disorders, with the size of expansions correlating with the severity and age of onset. Therefore, being able to accurately detect the total length of expansion and any somatic expansions is important. Current diagnostic assays include laborious repeat-primed PCR-based tests as well as Southern blotting, which are unable to precisely determine long repeat expansions and/or require set-up for each locus separately. Sequencing based assays have not yet replaced these diagnostics assays.

Here we show that using intact high molecular weight optical genome mapping (OGM) molecules, the length of repeat expansions across the genome can be revealed efficiently. We performed OGM for 60 samples with known clinically relevant repeat expansions for 4 loci (FMR1, DMPK, CNBP, RFC1) all involved in various movement disorders or developmental disease. Using OGM, we can select within the reference genome the two labels flanking the repeats of interest, measure the interval lengths of the aligned molecules, and estimate the mean and variance of the repeat sizes. Using the label distances in the optical mapping molecules, a histogram of repeat sizes and a Gaussian mixture model can be used to identify the zygosity of the repeat expansion region. Moreover, with the standard deviations of the clusters, a mosaic expansion of various repeat sizes is observed.

All known disease causing repeat expansions were detected, and allelic differences were obvious – either between wildtype and expanded alleles, or two expanded alleles for recessive cases. An apparent strength of OGM was the more accurate length measurement for very long repeat expansion alleles. In addition we now have evidence for somatic repeat instability for several repeat expansions, such as DMPK, leveraging the analysis of intact, native DNA molecules. Whether absolute repeat size or somatic (in)stability have prognostic value is currently investigated.

In conclusion, for tandem repeat expansions, above ~500 bp, optical genome mapping provides an efficient method to identity repeat lengths across multiple loci simultaneously. With long intact molecules spanning repeats even kilobases in size, absolute repeat lengths and somatic instability can be detected with high confidence.