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Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Gerton JL, Phillippy AM, Colonna V, Garrison E. Recombination between heterologous human acrocentric chromosomes. Nature 2023; 617:335-343. [PMID: 37165241 PMCID: PMC10172130 DOI: 10.1038/s41586-023-05976-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/17/2023] [Indexed: 05/12/2023]
Abstract
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembly of a human genome-the Telomere-to-Telomere Consortium's CHM13 assembly (T2T-CHM13)-provided a model of their homology3, it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination6,7. The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations8, and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago9.
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Affiliation(s)
- Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Silvia Buonaiuto
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Christian Fischer
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vincenza Colonna
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
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La Starza R, Barba G, Nofrini V, Pierini T, Pierini V, Marcomigni L, Perruccio K, Matteucci C, Storlazzi CT, Daniele G, Crescenzi B, Giansanti M, Giovenali P, Dal Cin P, Mecucci C. Multiple EWSR1-WT1 and WT1-EWSR1 copies in two cases of desmoplastic round cell tumor. Cancer Genet 2013; 206:387-92. [PMID: 24388397 DOI: 10.1016/j.cancergen.2013.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/23/2013] [Accepted: 10/30/2013] [Indexed: 02/05/2023]
Abstract
To provide new insights into the genomic profile of desmoplastic round cell tumors (DSRCT), we applied fluorescence in situ hybridization (FISH) and metaphase comparative genomic hybridization (M-CGH) to two newly diagnosed cases. FISH detected multiple subclones bearing one to three copies of der(11)t(11;22)(p13;q12) and/or der(22)t(11;22)(p13;q12) in both patients. This peculiar genomic imbalance might result from derivative chromosome duplication due to non-disjunction and/or mitotic recombination between normal and derivative chromosomes 11 and 22. Concomitant loss of normal chromosomes (i.e., 11 in patient 1 and 22 in patient 2) caused loss of the WT1 or EWSR1 wild-type allele. M-CGH identified other genomic imbalances: gain at chromosome 3 in both cases and chromosome 5 polysomy in patient 1. Common genomic events (i.e., trisomy 3 and extra EWSR1-WT1 and WT1-EWSR1 copies) probably contributed to disease pathogenesis and/or evolution of DSRCT. Our study demonstrated that an integrated molecular cytogenetic approach identified EWSR1-WT1 cooperating molecular events and genetic markers for prognosis. Thus, FISH and M-CGH might well be applied in a large series of patients to elucidate the genomic background of DSRCT.
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Affiliation(s)
- Roberta La Starza
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | - Gianluca Barba
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | - Valeria Nofrini
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | - Tiziana Pierini
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | - Valentina Pierini
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | | | | | - Caterina Matteucci
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | | | - Giulia Daniele
- Department of Genetics and Microbiology, University of Bari, Bari, Italy
| | - Barbara Crescenzi
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | | | - Paolo Giovenali
- Diagnostic Cytology and Histology, Perugia General Hospital, Perugia, Italy
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Cristina Mecucci
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy.
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Abstract
The karyotypes of 14 patients with Paget's disease of bone were studied. The patients were recruited from our bone metabolism clinic where they received specific therapy for their skeletal disease. Eight of the 14 patients had chromosomal translocations localized to the D and G groups. None of the patients were related to one another, nor had any had the same lifelong environment. Thus, 57% of a sample of active patients with Paget's disease had Robertsonian translocations. By comparison, an age and sex-matched group of eight controls and 13 patients with osteoporosis who had been treated with bisphosphonates demonstrated no Robertsonian translocations. The prevalence of Robertsonian translocations in 14,000 newborns was reported to be 0.1%. These data suggest that a factor from the environment introduced during the lifetime of the patient could be present and could, in addition to genetic factors, affect gene replication during the development of Paget's disease.
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Affiliation(s)
- B G Mills
- University of Southern California School of Dentistry, Los Angeles, California, USA
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