Structural genomic variation in human disease

Structural variants (SVs) are physical changes in the structure of chromosomes and include both unbalanced copy number variants (CNVs) and balanced events (translocations, inversions and insertions). Many SVs constitute benign background variation and are found frequently in healthy individuals. Others may cause disease through gene disruption, deletion or duplication of dosage sensitive genes, or by disrupting the 3D structure of the genome. In this thesis, we have delineated the exact structure of rearranged chromosomes and performed breakpoint junction analysis to study mutational signatures and underlying mechanisms of formation.

In paper I, we characterized and analyzed breakpoint junction sequences of 23 cytogenetically balanced translocations with mate-pair whole genome sequencing (WGS) and 17% of the translocations had microhomology and/or templated insertions in the breakpoint junctions, indicative of replication-based repair mechanisms. Genes were disrupted in 48% of breakpoints, highlighting a number of novel candidate genes and providing a molecular diagnosis in three cases. In paper II, we used targeted array comparative genomic hybridization and WGS to show that intragenic exonic duplications, formed through Alu-Alu fusion events, within MATN3 and IFT81 cause monogenic skeletal dysplasia disorders. Follow-up studies in primary cells and in zebrafish embryos showed that expression of a shorter IFT81 transcript alone is compatible with life. In paper III, we used WGS to investigate a benign complex chromosome rearrangement on chromosome 5p, detected in a healthy woman, which through unequal crossing-over during meiosis evolved into a pathogenic rearrangement including a duplication of the NIPBL gene in her daughter. In paper IV, we characterized the breakpoint junctions in 16 cytogenetically detected inversions. Contrary to what was expected, the vast majority of the resolved inversions were not mediated by inverted repeats through non-allelic homologous recombination. The mutational signatures in all the resolved inversions (11/16) indicate other mechanisms than ectopic recombination including replicative mechanisms in 2 cases. In paper V, we utilized WGS to perform a detailed characterization of 21 cases harboring multiple CNVs clustering on the same chromosome. The analysis revealed that multiple cellular mechanisms are involved in the formation of such SVs.

In conclusion, the results of this thesis show that WGS is a powerful way to delineate the structure of balanced, unbalanced and complex SVs. These studies have identified diseasecausing aberrations, new candidate genes for further studies of neurodevelopmental disorders, and contributed to the understanding of how, when and why SVs arise.

List of scientific papers

I. Nilsson D, Pettersson M, Gustavsson P, Forster A, Hofmeister W, Wincent J, Zachariadis V, Anderlid BM, Nordgren A, Makitie O, Wirta V, Kaller M, Vezzi F, Lupski JR, Nordenskjold M, Syk Lundberg E, Carvalho CM, Lindstrand A. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. Human mutation. (2017) 38(2):180-192.
https://doi.org/10.1002/humu.23146

II. Pettersson M, Vaz R, Hammarsjo A, Eisfeldt J, Carvalho CMB, Hofmeister W, Tham E, Horemuzova E, Voss U, Nishimura G, Klintberg B, Nordgren A, Nilsson D, Grigelioniene G, Lindstrand A. Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias. Human mutation. (2018) 39(10):1456-1467.
https://doi.org/10.1002/humu.23605

III. Pettersson M, Eisfeldt J, Syk Lundberg E, Lundin J, Lindstrand A. Flanking complex copy number variants in the same family formed through unequal crossing-over during meiosis. Mutation Research. (2018) 812:1-4.
https://doi.org/10.1016/j.mrfmmm.2018.10.001

IV. Pettersson M, Grochowski CM, Wincent J, Eisfeldt J, Cheung SW, Krepischi ACV, Rosenberg C, Lupski JR, Ottosson J, Lovmar L, Gacic J, Syk Lundberg E, Nilsson D, Carvalho CMB, Lindstrand A. Cytogenetically detected inversions are rarely formed by ectopic recombination between inverted repeats. [Manuscript]

V. Nazaryan-Petersen L, Eisfeldt J, Pettersson M, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, Makitie O, Nordgren N, Vezzi F, Wirta V, Kaller M, Duelund Hjortshøj T, Jespersgaard C, Houssari R, Pignata L, Bak M, Tommerup N, Syk Lundberg E, Tümer Z, Lindstrand A. Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization. PLoS Genetics. (2018) 14(11):e1007780.
https://doi.org/10.1371/journal.pgen.1007780