Abstract
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis underlying rare diseases. The aim of this study was to resolve a 9p24 rearrangement segregating in a family through five generations with a congenital heart defect (congenital pulmonary and aortic valvular stenosis and pulmonary artery stenosis), by applying a combined genomic analysis. The analysis involved multiple techniques, including karyotype, chromosomal microarray analysis (CMA), FISH, genome sequencing (GS), RNA-seq, and optical genome mapping (OGM). A complex 9p24 SV was hinted at by CMA results, showing three interspersed duplicated segments. Combined GS and OGM analyses revealed that the 9p24 duplications constitute a complex SV, on which a set of breakpoints matches the boundaries of the CMA duplicated sequences. The proposed structure for this complex rearrangement implies three duplications associated with an inversion of ~ 2 Mb region on chromosome 9 and a SINE element insertion at the more distal breakpoint. Interestingly, this genomic structure of rearrangement forms a chimeric transcript of the KANK1/DMRT1 loci, which was confirmed by both RNA-seq and Sanger sequencing on blood samples from 9p24 rearrangement carriers. Altogether with breakpoint amplification and FISH analysis, this combined approach allowed a deep characterization of this complex rearrangement. Although the genotype–phenotype correlation remains elusive from the molecular mechanism point of view, this study identified a large genomic rearrangement at 9p24 segregating with a familial congenital heart defect, revealing a genetic biomarker that was successfully applied for embryo selection, changing the reproductive perspective of affected individuals.
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Acknowledgements
Our sincere thanks are due to the individuals of the family here described for providing consent to participate in this study. We would like to thank Mrs. Ligia Sumi VIeira and Ms. Galina Koksharova for the technical support.
Funding
The researchers from the Institute of Bioscience (University of São Paulo) have financial support of Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP 2013/08028–1) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq 305806/2019–0). CMBC is supported by the National Institute of General Medical Sciences (NIGMS R01 GM132589). V.F. was partially supported by the budget project of Institute of Cytology and Genetics SB RAS (state project FWNR-2022–0019) and FAPESP fellowship (2022/11064–9).
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CR and ACVK conceived and designed the study. Material preparation and data collection were performed by SSC, VF, MP, AR, MTS, and PZ. SSC, VF, CMBC, CR, and ACVK analyzed data. The first draft of the manuscript was written by VF and ACVK, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
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da Costa, S.S., Fishman, V., Pinheiro, M. et al. A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations. Chromosome Res 32, 6 (2024). https://doi.org/10.1007/s10577-024-09750-2
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DOI: https://doi.org/10.1007/s10577-024-09750-2