Structural variants (SVs) in the form of copy-number variants (CNVs), inversions, translocations, and insertions, are responsible for the expression of disease phenotypes and have a critical role in human evolution. Despite its relevance, SVs lack basic information such as somatic and germline de novo formation rate, mutational signatures associated with DNA metabolic processes and specific contribution to the expression of human phenotypic traits. Technology limitation associated with the distinct molecular features of SV classes contribute to this large knowledge gap compared to single-nucleotide variants (SNVs).
Particular types of SVs are more affected by this knowledge gap because they escape detection by routine genome sequencing. These “hidden” DNA variants include small insertions and deletions (indels), mobile elements insertions, inversions, and complex genomic rearrangements CGRs, i.e. multiple structural variants formed in a single event. They require specialized sequencing methodologies and analytical tools for detection, alignment, and phasing.
One of the aims of the Carvalho Lab’s research program is to investigate the structure, origin, and formation mechanism of SVs, more specifically indels, inversions, and CGRs associated with genetic disorders. For that goal, the lab applies the latest DNA sequencing platforms to investigate long DNA molecules such as PacBio HiFi, Oxford Nanopore (ONT) and Bionano Genome Mapping in addition to develop bioinformatic tools for analysis. Parental DNA provides key ancestral information that allows identification of susceptible genomic structures and provide insights into how SVs are formed in the DNA.
Figure – Overview of types of structural variants investigated in rare diseases and methodologies currently applied in the lab.
a. Types of SVs causative of rare diseases1.
b. Complex genomic rearrangements (CGRs) are often constituted by inversions associated with copy-number variants2, 3, 4. These structural variants are rarely studied due to detection and clinical interpretation challenges2, 3.
c. Examples of genomic methodologies applied in the Carvalho Lab to investigate CGRs.
Legend: DUP-TRP/INV-DUP: CGR consisting of inverted triplication flanked by duplications found in ~20% of individuals with MECP2 duplication syndrome5, a neurodevelopmental disorder that affects mostly boys (https://rarediseases.org/rare-diseases/mecp2-duplication-syndrome/; https://mecp2d.org/)4, 5.
1. Carvalho CM, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet. 2016;17(4):224-38. Epub 2016/03/01. doi: 10.1038/nrg.2015.25. PubMed PMID: 26924765; PMCID: 4827625.
2. Carvalho CM, Ramocki MB, Pehlivan D, Franco LM, Gonzaga-Jauregui C, Fang P, McCall A, Pivnick EK, Hines-Dowell S, Seaver LH, Friehling L, Lee S, Smith R, Del Gaudio D, Withers M, Liu P, Cheung SW, Belmont JW, Zoghbi HY, Hastings PJ, Lupski JR. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nat Genet. 2011;43(11):1074-81. Epub 2011/10/04. doi: 10.1038/ng.944. PubMed PMID: 21964572; PMCID: 3235474.
3. Grochowski CM, Krepischi ACV, Eisfeldt J, Du H, Bertola DR, Oliveira D, Costa SS, Lupski JR, Lindstrand A, Carvalho CMB. Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome. Front Genet. 2021;12:708348. Epub 20210826. doi: 10.3389/fgene.2021.708348. PubMed PMID: 34512724; PMCID: PMC8427664.
4. Pettersson M, Grochowski CM, Wincent J, Eisfeldt J, et al., Carvalho CMB, Lindstrand A. Cytogenetically visible inversions are formed by multiple molecular mechanisms. Hum Mutat. 2020;41(11):1979-98. Epub 20201001. doi: 10.1002/humu.24106. PubMed PMID: 32906200; PMCID: PMC7702065.
5. Schuy J, Grochowski CM, Carvalho CMB, Lindstrand A. Complex genomic rearrangements: an underestimated cause of rare diseases. Trends Genet. : TIG. 2022. Epub 20220709. doi: 10.1016/j.tig.2022.06.003. PubMed PMID: 35820967.