Resolution of ring chromosomes, Robertsonian translocations, and complex structural variants from long-read sequencing and telomere-to-telomere assembly

Yulia Mostovoy; Philip M Boone; Yongqing Huang; Kiran V Garimella; Kar-Tong Tan; Bianca E Russell; Monica Salani; Celine E F de Esch; John Lemanski; Benjamin Curall; Jen Hauenstein; Diane Lucente; Tera Bowers; Tim DeSmet; Stacey Gabriel; Cynthia C Morton; Matthew Meyerson; Alex R Hastie; James Gusella; Fabiola Quintero-Rivera; Harrison Brand; Michael E Talkowski

doi:10.1016/j.ajhg.2024.10.006

Resolution of ring chromosomes, Robertsonian translocations, and complex structural variants from long-read sequencing and telomere-to-telomere assembly

Am J Hum Genet. 2024 Nov 5:S0002-9297(24)00375-6. doi: 10.1016/j.ajhg.2024.10.006. Online ahead of print.

Authors

Yulia Mostovoy¹, Philip M Boone², Yongqing Huang³, Kiran V Garimella³, Kar-Tong Tan⁴, Bianca E Russell⁵, Monica Salani⁶, Celine E F de Esch¹, John Lemanski⁶, Benjamin Curall¹, Jen Hauenstein⁷, Diane Lucente⁶, Tera Bowers⁸, Tim DeSmet⁸, Stacey Gabriel⁸, Cynthia C Morton⁹, Matthew Meyerson⁴, Alex R Hastie⁷, James Gusella¹⁰, Fabiola Quintero-Rivera¹¹, Harrison Brand¹², Michael E Talkowski¹³

Affiliations

¹ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA.
² Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA.
³ Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁴ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁵ Division of Genetics, Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁶ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
⁷ Bionano Genomics, Inc, San Diego, CA 92121, USA.
⁸ Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁹ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Manchester Center for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester M13 9PL, UK.
¹⁰ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
¹¹ Departments of Pathology, Laboratory Medicine, and Pediatrics, Division of Genetic and Genomic Medicine, University of California, Irvine, Irvine, CA 92697, USA.
¹² Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; Pediatric Surgery Research Laboratory, Department of Pediatrics, Boston, MA 02114, USA.
¹³ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: mtalkowski@mgh.harvard.edu.

PMID: 39520989
DOI: 10.1016/j.ajhg.2024.10.006

Abstract

Delineation of structural variants (SVs) at sequence resolution in highly repetitive genomic regions has long been intractable. The sequence properties, origins, and functional effects of classes of genomic rearrangements such as ring chromosomes and Robertsonian translocations thus remain unknown. To resolve these complex structures, we leveraged several recent milestones in the field, including (1) the emergence of long-read sequencing, (2) the gapless telomere-to-telomere (T2T) assembly, and (3) a tool (BigClipper) to discover chromosomal rearrangements from long reads. We applied these technologies across 13 cases with ring chromosomes, Robertsonian translocations, and complex SVs that were unresolved by short reads, followed by validation using optical genome mapping (OGM). Our analyses resolved 10 of 13 cases, including a Robertsonian translocation and all ring chromosomes. Multiple breakpoints were localized to genomic regions previously recalcitrant to sequencing such as acrocentric p-arms, ribosomal DNA arrays, and telomeric repeats, and involved complex structures such as a deletion-inversion and interchromosomal dispersed duplications. We further performed methylation profiling from long-read data to discover phased differential methylation in a gene promoter proximal to a ring fusion, suggesting a long-range position effect (LRPE) with heterochromatin spreading. Breakpoint sequences suggested mechanisms of SV formation such as microhomology-mediated and non-homologous end-joining, as well as non-allelic homologous recombination. These methods provide some of the first glimpses into the sequence resolution of Robertsonian translocations and illuminate the structural diversity of ring chromosomes and complex chromosomal rearrangements with implications for genome biology, prediction of LRPEs from integrated multi-omics technologies, and molecular diagnostics in rare disease cases.

Keywords: Robertsonian translocation; acrocentric p-arm; inversion; long-read sequencing; optical genome mapping; ring chromosome; telomere-to-telomere.