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Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscape

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Abstract

We present a comprehensive clinically oriented workflow for large-insert genome sequencing (liGS)-based nucleotide level resolution and interpretation of de novo (dn) apparently balanced chromosomal abnormalities (BCA) in prenatal diagnosis (PND). Retrospective or concomitant with conventional PND and liGS, molecular and newly developed clinically inspired bioinformatic tools (TAD-GConTool and CNV-ConTool) are applied to analyze and assess the functional and phenotypic outcome of dn structural variants (dnSVs). Retrospective analysis of four phenotype-associated dnSVs identified during conventional PND precisely reveal the genomic elements disrupted by the translocation breakpoints. Identification of autosomal dominant disease due to the disruption of ANKS1B and WDR26 by t(12;17)(q23.1;q21.33)dn and t(1;3)(q24.11;p25.3)dn breakpoints, respectively, substantiated the proposed workflow. We then applied this workflow to two ongoing prenatal cases with apparently balanced dnBCAs: 46,XX,t(16;17)(q24;q21.3)dn referred for increased risk on combined first trimester screening and 46,XY,t(2;19)(p13;q13.1)dn referred due to a previous trisomy 21 pregnancy. Translocation breakpoints in the t(16;17) involve ANKRD11 and WNT3 and disruption of ANKRD11 resulted in KBG syndrome confirmed in postnatal follow-up. Breakpoints in the t(2;19) are within ATP6V1B1 and the 3′ UTR of CEP89, and are not interpreted to cause disease. Genotype–phenotype correlation confirms the causative role of WDR26 in the Skraban-Deardorff and 1q41q42 microdeletion phenocopy syndromes, and that disruption of ANKS1B causes ANKS1B haploinsufficiency syndrome. In sum, we show that an liGS-based approach can be realized in PND care providing additional information concerning clinical outcomes of dnBCAs in patients with such rearrangements.

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available at https://decipher.sanger.ac.uk/ and their LoF intolerance, expressed as oe-ratio of LoF variants stated below the genes (http://gnomad.broadinstitute.org/). ANKRD11 causing KBGS is marked with a hash mark (#). Data for IMR90 fibroblasts, hESCs and LCL GM12878 are according to Dixon et al. (2012) and Moore et al. (2015), respectively

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Acknowledgements

We dedicate this article to Maria Guida Boavida who founded the Human Genetics Laboratory as the precursor of the current Department of Human Genetics at the National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal. She and her colleagues performed the first chromosomal prenatal diagnosis from cultured amniocytes in Portugal in July 1977 (no. 77180). However, the first translocation in PND, a paternally inherited Robertsonian t(13;14) (no. 80321), was only identified in June 1980. Almost 40 years later, we report application of an liGS-based approach for the identification of dnBCAs breakpoints in PND. First, we are grateful to the family members for their involvement in this study. We thank Dr. Michael Talkowski and members of his lab for library preparation and sequencing data generation. We thank Jader Cruz for echographic diagnosis of fetal heart defects, to Hildeberto Correia, Ana Cristina Alves and Bárbara Marques for conventional prenatal diagnosis, and to Márcia Rodrigues, Sofia Nunes, Teresa Kay, and Rui Gonçalves for their contribution to the project. C.C.M. is supported (GM061354) by the National Institutes of Health (USA) and the NIHR Manchester Biomedical Research Centre, UK. This research was supported by national funds through FCT—Fundação para a Ciência e a Tecnologia, Research Grant HMSP-ICT/0016/2013 of the Harvard Medical School—Portugal Program in Translational Research and Information.

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Author notes

  1. João P. Freixo and Joana Fino contributed equally to the work.

Authors and Affiliations

  1. Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal

    Dezső David, Joana Fino, Mariana Marques & Manuela Cardoso

  2. Department of Medical Genetics, Central Lisbon Hospital Center (CHLC), Lisbon, Portugal

    João P. Freixo & Inês Carvalho

  3. Harvard Medical School, Boston, MA, USA

    Raul E. Piña-Aguilar & Cynthia C. Morton

  4. Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA, USA

    Raul E. Piña-Aguilar & Cynthia C. Morton

  5. Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA

    Cynthia C. Morton

  6. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Cynthia C. Morton

  7. Manchester Academic Health Science Center, University of Manchester, Manchester, UK

    Cynthia C. Morton

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  1. Dezső David
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Correspondence to Dezső David.

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This study was approved by the Ethics Committee of the National Institute of Health Doutor Ricardo Jorge and was carried out according to the Principles of the Declaration of Helsinki of the World Medical Association. Samples were obtained after written informed consent of the participants or their legal representatives. Additional informed consent was obtained from all individual participants for whom identifying information is included in this article.

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David, D., Freixo, J.P., Fino, J. et al. Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscape. Hum Genet 139, 531–543 (2020). https://doi.org/10.1007/s00439-020-02121-x

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