Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity.bioRxiv : the preprint server for biology ⢠January 27, 2025
Matt Danzi, Isaac R Xu, Sarah Fazal, Egor Dolzhenko, David Pellerin, Ben Weisburd, Chloe Reuter, Jacinda Sampson, Chiara Folland, Matthew Wheeler, Anne O'donnell Luria, Stefan Wuchty, Gianina Ravenscroft, Michael Eberle
Tandem repeats are a highly polymorphic class of genomic variation that play causal roles in rare diseases but are notoriously difficult to sequence using short-read techniques1,2. Most previous studies profiling tandem repeats genome-wide have reduced the description of each locus to the singular value of the length of the entire repetitive locus3,4. Here we introduce a comprehensive database of 3.6 billion tandem repeat allele sequences from over one thousand individuals using HiFi long-read sequencing. We show that the previously identified pathogenic loci are among the most variable tandem repeat loci in the genome, when incorporating nucleotide resolution sequence content to measure the longest pure motif segment. More broadly, we introduce a novel measure, 'tandem repeat constraint', that assists in distinguishing potentially pathogenic from benign loci. Our approach of measuring variation as 'the length of the longest pure segment' successfully prioritizes pathogenic repeats within their previously published linkage regions. We also present evidence for two novel pathogenic repeat expansion candidates. In summary, this analysis significantly clarifies the potential for short tandem repeat pathogenicity at over 1.7 million tandem repeat loci and will aid the identification of disease-causing repeat expansions.
Current understanding of skeletal muscle repeat expansion disorders.Current Opinion In Neurology ⢠June 09, 2025
Manon Boivin, Gianina Ravenscroft
Objective: Here, we summarize the current knowledge about the genetics and proposed mechanisms of disease underlying skeletal muscle short tandem repeat (STR) expansion disorders.
Results: The human genome contains up to 2 million STRs (also known as microsatellites), which are highly variable repetitions of two to six nucleotide-long DNA motifs. These elements, present in both coding and noncoding sequences, are highly instable, and their polymorphic variations have important roles in genes regulation and human phenotypic trait diversity. Importantly, expansion over a threshold size of a subset of these STR is the cause of approximately 60 neurological diseases, including some major muscle disorders such as myotonic dystrophy, oculopharyngodistal myopathy (OPDM) and oculopharyngeal muscular dystrophy. The discovery and characterisation of a number of these STR expansion disorders, in particular for OPDM, has been enabled in recent years by advanced genomic technologies.
Conclusions: Many recently described STR expansion disorders are now recognized and genetic testing of patients is possible on a research basis, clinical testing for these newly described repeat loci is not yet readily available and is complicated by the reduced penetrance seen in some families, rendering clinical interpretation more difficult. The phenotypic spectrums associated with these STR expansion disorders are also evolving as unbiased sequencing approaches identified expansions at known loci in individuals with phenotypes that are quite different to those in which the STR expansions were first characterized. The pathomechanisms associated with these newer STR expansion disorders is still poorly understood, however there is evidence of both RNA toxicity and polyGly toxicity. Additional STR expansions underlying skeletal muscle diseases are likely to be identified in coming years and may shed further light onto the complex genetics, epigenetics and disease mechanisms underlying these disorders.
The evolving genetic landscape of neuromuscular fetal akinesias.Journal Of Neuromuscular Diseases ⢠May 13, 2025
GĂśknur HaliloÄlu, Gianina Ravenscroft
Fetal akinesia is a broad term used to describe absent (or reduced, fetal hypokinesia) fetal movements, and it can be detected as early as the first trimester. Depending on the developmental age of onset, anything that interferes or limits the normal in utero movement results in a range of deformations affecting multiple organs and organ systems. Arthrogryposis, also termed arthrogryposis multiplex congenita (AMC), is a definitive terminology for multiple congenital contractures, with two major subgroups; amyoplasia and distal arthrogryposis (DA). The spectrum includes fetal akinesia deformation sequence (FADS), lethal congenital contracture syndrome (LCCS), and multiple pterygium syndrome (MPS). Variants in more than >400 genes are known to cause AMC, and it is increasingly recognized that variants in genes encoding critical components (including ventral horn cell, peripheral nerve, neuromuscular junction, skeletal muscle) of the extended motor unit underlie âź40% of presentations. With unbiased screening approaches, including sequencing of comprehensive disease gene panels, exomes and genomes, novel genes and phenotypic expansions associated with known human disease genes have been uncovered in the setting of fetal akinesia. Autosomal-recessive titinopathy is the most frequent genetic cause of AMC. Accurate genetic diagnosis is critical to genetic counseling and informing family planning. Around 50% remain undiagnosed following comprehensive prenatal, diagnostic or research screening. Comprehensive phenotyping and periodic reanalysis with appropriate genomic tools are valuable strategies when faced with initial inconclusive results. There are likely many novel causative genes still to identify, which will inform our understanding of the molecular pathways underlying early human development and in utero movement.
Long-read sequencing for diagnosis of genetic myopathies.BMJ Neurology Open ⢠November 25, 2024
Dennis Yeow, Laura Rudaks, Ryan Davis, Karl Ng, Roula Ghaoui, Pak Cheong, Gianina Ravenscroft, Marina Kennerson, Ira Deveson, Kishore Kumar
Genetic myopathies are caused by pathogenic variants in >300 genes across the nuclear and mitochondrial genomes. Although short-read next-generation sequencing (NGS) has revolutionised the diagnosis of genetic disorders, large and/or complex genetic variants, which are over-represented in the genetic myopathies, are not well characterised using this approach. Long-read sequencing (LRS) is a newer genetic testing technology that overcomes many of the limitations of NGS. In particular, LRS provides improved detection of challenging variant types, including short tandem repeat (STR) expansions, copy number variants and structural variants, as well as improved variant phasing and concurrent assessment of epigenetic changes, including DNA methylation. The ability to concurrently detect multiple STR expansions is particularly relevant given the growing number of recently described genetic myopathies associated with STR expansions. LRS will also aid in the identification of new myopathy genes and molecular mechanisms. However, use of LRS technology is currently limited by high cost, low accessibility, the need for specialised DNA extraction procedures, limited availability of LRS bioinformatic tools and pipelines, and the relative lack of healthy control LRS variant databases. Once these barriers are addressed, the implementation of LRS into clinical diagnostic pipelines will undoubtedly streamline the diagnostic algorithm and increase the diagnostic rate for genetic myopathies. In this review, we discuss the utility and critical impact of LRS in this field.
Somatic instability of the FGF14-SCA27B GAAâ˘TTC repeat reveals a marked expansion bias in the cerebellumMedRxiv : The Preprint Server For Health Sciences ⢠July 15, 2024
David Pellerin, Jean-loup MĂŠreaux, Susana Boluda, Matt Danzi, Marie-josĂŠe Dicaire, Claire-sophie Davoine, David Genis, Guinevere Spurdens, Catherine Ashton, Jillian Hammond, Brandon Gerhart, Viorica Chelban, Phuong Le, Maryam Safisamghabadi, Christopher Yanick, Hamin Lee, Sathiji Nageshwaran, Gabriel Matos Rodrigues, Zane Jaunmuktane, Kevin Petrecca, Schahram Akbarian, AndrĂŠ Nussenzweig, Karen Usdin, Mathilde Renaud, CĂŠline Bonnet, Gianina Ravenscroft, Mario Saporta, Jill Napierala, Henry Houlden, Ira Deveson, Marek Napierala, Alexis Brice, Laura Molina Porcel, Danielle Seilhean, Stephan Zuchner, Alexandra Durr, Bernard Brais
Spinocerebellar ataxia 27B (SCA27B) is a common autosomal dominant ataxia caused by an intronic GAAâ˘TTC repeat expansion in FGF14 . Neuropathological studies have shown that neuronal loss is largely restricted to the cerebellum. Although the repeat locus is highly unstable during intergenerational transmission, it remains unknown whether it exhibits cerebral mosaicism and progressive instability throughout life. We conducted an analysis of the FGF14 GAAâ˘TTC repeat somatic instability across 156 serial blood samples from 69 individuals, fibroblasts, induced pluripotent stem cells, and post-mortem brain tissues from six controls and six patients with SCA27B, alongside methylation profiling using targeted long-read sequencing. Peripheral tissues exhibited minimal somatic instability, which did not significantly change over periods of more than 20 years. In post-mortem brains, the GAAâ˘TTC repeat was remarkably stable across all regions, except in the cerebellar hemispheres and vermis. The levels of somatic expansion in the cerebellar hemispheres and vermis were, on average, 3.15 and 2.72 times greater relative to other examined brain regions, respectively. Additionally, levels of somatic expansion in the brain increased with repeat length and tissue expression of FGF14 . We found no significant difference in methylation of wild-type and expanded FGF14 alleles in post-mortem cerebellar hemispheres between patients and controls. In conclusion, our study revealed that the FGF14 GAAâ˘TTC repeat exhibits a cerebellar-specific expansion bias, which may explain the pure and late-onset cerebellar involvement in SCA27B.
