Exploration of Neurodegenerative Diseases Using Long-Read Sequencing and Optical Genome Mapping Technologies

Abstract

Genetic factors play a central role in neurodegenerative disorders. Over the past few decades, significant progress has been made in identifying the causative genes of numerous monogenic disorders, largely due to the widespread adoption of next-generation sequencing (NGS) technologies in both research and clinical settings. However, many likely monogenic disorders still lack an accurate molecular diagnosis, primarily because conventional NGS methods are not effective at detecting structural variants and repeat expansions, both of which are crucial in many neurogenetic diseases. Recently, long-read sequencing (LRS) and optical genome mapping technologies have emerged as powerful tools, offering the ability to capture more complex genetic variations. These technologies have already led to the discovery of novel genes responsible for well-characterized neurodegenerative diseases (ND), enhancing the understanding of the biological underpinning of these conditions. Although currently LRS is mostly used in a research setting, we anticipate broader implementation of these methods in clinical laboratories in the near future. In this review, we explore the contributions of these technologies to ND research and highlight the remaining challenges for future advancements. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Keywords: long‐read sequencing; neurodegenerative diseases; optical genome mapping.

FIG. 1

Schematic overview of the advantages of long‐read sequencing in complex variant detection. (A) Representation of an average short read and long read at scale (150 bp and 30 kbp). (B) Short reads cannot fully encompass the inverted segment (red segment), therefore likely missing the inversion in contrast with long reads. Furthermore, short reads within the rearrangement do not provide any information on the inversion, whereas most of the long reads encompass at least either the abnormal “AC” or “BD” sequences, facilitating the identification of the inversion. For copy number variations, most of the long reads identify either (C) two copies of exon 2 in a row for the duplication or (D) the absence of exon 2 (junction of exons 1 and 3) for the deletion, whereas any of the short reads would capture the rearrangement. (E) The red segment is expanded compared to the reference. If >150 bp, “in‐repeat” short reads would not be able to map within the expansion (gray reads), whereas long reads are either able to go through the full expansion or capture most of it. In addition, the interruption motif (the red A) is captured by long reads and not by short reads. For the phase of the variant (F and G), if the distance is longer than the length of short reads (150 bases usually), long reads can solve the phase because they encompass both variants, either showing one of the two if they are in trans († and *) or the two (‡) or any ($) if they are in cis. (H) The sequences of genes and pseudogenes are very similar, hampering the ability of short reads to correctly map either one (in gray), unlike long reads. The consequence is that, if a variant occurs either in the gene or the pseudogene (the purple trait in the scheme), short reads are unable to accurately assign it to the correct DNA location (% and £). Because a single long read can capture both and surrounding sequences, they accurately map the variant (¶ and §). Of note, reads shown in the schemes are not at scale. A1, allele 1; A2, allele 2; SRS, short‐read sequencing; LRS, long‐read sequencing. [Color figure can be viewed at wileyonlinelibrary.com]

FIG. 2

Advantages of long‐read sequencing over short‐read sequencing for transcript identification. Three artificial transcripts and their frequencies of a given tissue are exhibited along with the mapping of short‐ and long reads. The number of reads decreases by the frequency of the transcript. Colors represent exons. The yellow cryptic exon (present in minor transcripts 2 and 3 only) may not be captured by short reads, whereas long reads would identify it. Therefore, the reconstruction step required for short‐read RNA sequencing misses the full transcript landscape unlike long‐read calling, which does not require a reconstruction step. [Color figure can be viewed at wileyonlinelibrary.com]