Characterization of structural chromosomal variants by massively parallel sequencing

Chromosomal Structural Variation (SV) such as translocations, inversions, deletions, and duplications are rearrangements of one or several DNA molecules. SVs are widespread across the human genome, and each individual carries thousands of SVs of different types and sizes. SV are known to contribute both to phenotypic diversity and disease traits, and are therefore of interest in multiple fields, including rare diseases research, and clinical diagnostics.

Herein, we present five studies, focused on the analysis of SV using whole genome sequencing (WGS). The project has increased our knowledge regarding the frequency, structure and mechanisms of formation of structural variants in the human genome. In Paper I, II, and IV, we develop and evaluate software for detection and analysis of SV using WGS data. In Paper II, III and IV, we utilize WGS data to delineate the structure and determine the mechanism of formation of several complex SVs. In Paper II, we compare multiple sequencing technologies, and apply these technologies to solve the structure of three complex chromosomal rearrangements. Lastly, in Paper V, we validate the use of SV calling from WGS as a routine test in rare disease diagnostics.

Through these studies, we developed and tested tools suitable for WGS SV analysis in a clinical setting. These tools are now part of the routine clinical pipeline; and many of the tools are used by researchers and clinics around the world.

List of scientific papers

I. Jesper Eisfeldt*, Francesco Vezzi*, Pall Olason, Daniel Nilsson, Anna Lindstrand. (2017). TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Research. 6:664. *Equal contribution.
https://doi.org/10.12688/f1000research.11168.2

II. Jesper Eisfeldt*, Maria Pettersson*, Francesco Vezzi, Josephine Wincent, Max Käller, Joel Gruselius, Daniel Nilsson, Elisabeth Syk Lundberg, Claudia M. B. Carvalho, Anna Lindstrand. (2019). Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements. PLOS Genetics. 15(2):e1007858. *Equal contribution.
https://doi.org/10.1371/journal.pgen.1007858

III. Lusine Nazaryan-Petersen*, Jesper Eisfeldt*, Maria Pettersson, Johanna Lundin, Daniel Nilsson, Josephine Wincent, Agne Lieden, Lovisa Lovmar, Jesper Ottosson, Jelena Gacic, Outi Mäkitie, Ann Nordgren, Francesco Vezzi, Valtteri Wirta, Max Käller, Tina Duelund Hjortshøj, Cathrine Jespersgaard, Rayan Houssari, Laura Pignata, Mads Bak, Niels Tommerup, Elisabeth Syk Lundberg, Zeynep Tümer*, Anna Lindstrand*. (2018). Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization. PLOS Genetics. 14(11):e1007780. *Equal contribution.
https://doi.org/10.1371/journal.pgen.1007780

IV. Jesper Eisfeldt. Adam Ameur, Daniel Nilsson, Anna Lindstrand. (2019). Discovery of Novel Sequences in 1,000 Swedish Genomes. Molecular Biology and Evolution. Msz176.
https://doi.org/10.1093/molbev/msz176

V. Anna Lindstrand, Jesper Eisfeldt, Maria Pettersson, Claudia M. B. Carvalho, Malin Kvarnung, Giedre Grigelioniene, Britt-Marie Anderlid, Olof Bjerin, Peter Gustavsson, Anna Hammarsjö, Patrik Georgii Hemming, Erik Iwarsson, Maria Johansson Soller, Kristina Lagerstedt-Robinson, Agne Lieden, Måns Magnusson, Marcel Martin, Helena Malmgren, Magnus Nordenskjöld, Ameli Norling, Ellika Sahlin, Henrik Stranneheim, Emma Tham, Josephine Wincent, Sofia Ygberg, Anna Wedell, Valtteri Wirta, Ann Nordgren, Johanna Lundin, Daniel Nilsson. From cytogenetics to cytogenomics: WGS as a first line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. [Manuscript]