Studies of structural variation in rare disease

<p dir="ltr">As clinical genetics transitions towards clinical genomics an increasing number of variants are detected requiring clinical interpretation. This is particularly relevant for structural variants (SVs), where improved resolution methods continue to reveal novel variants as well as increasing levels of variant complexity. This thesis explores how short-read and long-read genome sequencing (GS) can detect and characterize SVs, both helping to diagnose individual patients and moving toward more comprehensive precision diagnostics for all.</p><p dir="ltr">In Studies I and II, two clinical short-read GS cohorts were compiled and analyzed: 229 individuals with neurodevelopmental disorders (NDD) and 860 individuals with neuromuscular disorders (NMD). We show that short-read GS with comprehensive variant calling captures the broad spectrum of pathogenic variants with SVs and short tandem repeats (STRs) accounting for 13% and 15%, respectively. In Study III, the pathogenicity of an inversion disrupting MEIS2, initially detected in the NMD cohort, was confirmed using targeted long-read sequencing and RNA sequencing.</p><p dir="ltr">In Study IV, 100 individuals with neurological disorders (79 NDD, 21 NMD) newly referred for short-read GS were investigated in parallel with long-read GS. Added diagnostic value was identified in 13 cases, including phasing of pseudogenes and biallelic variants in autosomal recessive genes, precise STR genotyping capturing both sequence and methylation patterns at these loci, as well as methylation profiling of imprinting regions. However, the superior ability to detect and resolve SVs proved particularly important, enabling improved assessment of pathogenicity and recurrence risk in nine cases.</p><p dir="ltr">In Study V, we examined X-chromosome inactivation in 21 individuals with balanced X-autosome translocations, complemented by data from 80 cases from the literature. Using short-read and long-read GS and the human androgen receptor assay (HUMARA), we further refined the minimal regions of the X chromosome compatible with a viable functional disomy.</p><p dir="ltr">Through these studies, we demonstrate that GS, particularly long-read GS, is a superior first-line test for individuals with neurological disorders, enabling improved SV detection, clinical interpretation, and the resolution of complex genetic variation.</p><h3>List of scientific papers</h3><p dir="ltr">I. Lindstrand A, <b>Ek M,</b> Kvarnung M, Anderlid BM, Björck E, Carlsten J, Eisfeldt J, Grigelioniene G, Gustavsson P, Hammarsjö A, Helgadóttir HT, Hellström-Pigg M, Kuchinskaya E, Lagerstedt-Robinson K, Levin L-Å, Lieden A, Lindelöf H, Malmgren H, Nilsson D, Svensson E, Paucar M, Sahlin E, Tesi B, Tham E, Winberg J, Winerdal M, Wincent J, Johansson Soller M, Pettersson M, Nordgren A. Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability. Genet Med. 2022;24(11):2296-307.<br><a href="https://doi.org/10.1016/j.gim.2022.07.022" rel="noreferrer" target="_blank">https://doi.org/10.1016/j.gim.2022.07.022</a><br><br></p><p dir="ltr">II. <b>Ek M,</b> Nilsson D, Engvall M, Malmgren H, Thonberg H, Pettersson M, Anderlid BM, Hammarsjö A, Helgadottir HT, Arnardottir S, Naess K, Nennesmo I, Paucar M, Hjartarson HT, Press R, Solders G, Sejersen T, Lindstrand A, Kvarnung M. Genome sequencing with comprehensive variant calling identifies structural variants and repeat expansions in a large fraction of individuals with ataxia and/or neuromuscular disorders. Frontiers in Neurology. 2023;14.<br><a href="https://doi.org/10.3389/fneur.2023.1170005" rel="noreferrer" target="_blank">https://doi.org/10.3389/fneur.2023.1170005</a><br><br></p><p dir="ltr">III. <b>Ek M,</b> Kvarnung M, Pettersson M, Soller M J, Anderlid B-M, Thonberg H, Eisfeldt J, Lindstrand A. Multi-omics analysis detail a submicroscopic inv(15)(q14q15) generating fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency. Sci Rep. 2024;14(1):30343<br><a href="https://doi.org/10.1038/s41598-024-81507-7" rel="noreferrer" target="_blank">https://doi.org/10.1038/s41598-024-81507-7</a><br><br></p><p dir="ltr">IV. <b>Ek M,</b> Kvarnung M, Ten Berk de Boer E, La Fleur L, Ljöstad L, Lyander A, Lejsted Færgeman S, Opstrup Drue S, Thonberg H, Nordgren A, Johansson Soller M, Wirta V, Eisfeldt J, Lindstrand A. Long-read genome sequencing enhances diagnostics of pediatric neurological disorders.<br><a href="https://doi.org/10.21203/rs.3.rs-6863124/v1" rel="noreferrer" target="_blank">https://doi.org/10.21203/rs.3.rs-6863124/v1</a><br><br></p><p dir="ltr">V. Zeib Khan S, <b>Ek M,</b> Lowther C, ten Berk de Boer E, Mehrjouy MM, Rasmussen MB, Nazaryan-Petersen L, Bache I, Bak M, Nordgren A, Ottosson J, Lovmar L, Collins RL, Morton CC, Bybjerg-Grauholm J, Sønderby Pedersen J, Midyan S, Chatron N, Pons L, Harzallah I, Januel L, Fannemel M, Misceo D, Varilo T, Kokalj Vokač N, Sheth FJ, Schinzel A, Sismani C, Vermeesch JR, Angelova L, Kalscheuer VM, Lauridsen M, del Rey G, Guitart M, Terada Abe K, Daumer-Haas C, Õunap K, Roht L, Mekkawy M, Moreno Igoa M, Schluth Bolard C, Eisfeldt J, Lindstrand A, Talkowski ME, Tommerup N. Minimal regions for functional disomy in balanced X-autosome translocations.</p>