Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration
Michael Talkowski and colleagues examine karyotypically balanced genomic rearrangement landscapes in the germline at single-nucleotide resolution. They find predominant roles for complex reorganization and non-homologous repair in such 'chromothripsis' processes, suggesting a mechanism of...
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| Published in | Nature genetics Vol. 44; no. 4; pp. 390 - 397 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.04.2012
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Michael Talkowski and colleagues examine karyotypically balanced genomic rearrangement landscapes in the germline at single-nucleotide resolution. They find predominant roles for complex reorganization and non-homologous repair in such 'chromothripsis' processes, suggesting a mechanism of template switching and blunt-end ligation.
We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations. |
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| AbstractList | We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically-interpreted translocations and inversions. We confirm that the recently described phenomenon of “chromothripsis” (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline where it can resolve to a karyotypically balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign CNVs. We compared these results to experimentally-generated DNA breakage-repair by sequencing seven transgenic animals, and revealed extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion is the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations. We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations. [PUBLICATION ABSTRACT] We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31 %) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations. We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations. Michael Talkowski and colleagues examine karyotypically balanced genomic rearrangement landscapes in the germline at single-nucleotide resolution. They find predominant roles for complex reorganization and non-homologous repair in such 'chromothripsis' processes, suggesting a mechanism of template switching and blunt-end ligation. We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations. We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints |
| Audience | Academic |
| Author | Chiang, Colby MacDonald, Marcy E Blumenthal, Ian Shen, Yiping Gusella, James F Talkowski, Michael E Hanscom, Carrie Hall, Ira M Borowsky, Mark L Lee, Charles Mills, Ryan E Morton, Cynthia C McLaughlan, Clive J Ohsumi, Toshiro K Snell, Russell G Jacobsen, Jessie C Reid, Suzanne J Bawden, C Simon Faull, Richard L M Daly, Mark J Rudiger, Skye R Lindgren, Amelia M Ernst, Carl Kirby, Andrew Heilbut, Adrian |
| AuthorAffiliation | 9 Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA 2 Departments of Genetics and Neurology, Harvard Medical School, Boston, MA, USA 3 Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA 5 Molecular Biology and Reproductive Technology Laboratories, Livestock and Farming Systems Division, South Australian Research and Development Institute, Roseworthy, SA, Australia 6 The Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand 1 Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA 4 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA 11 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA 7 School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, New Zealand 12 Department of Obstetrics, Gynecology, and Repr |
| AuthorAffiliation_xml | – name: 2 Departments of Genetics and Neurology, Harvard Medical School, Boston, MA, USA – name: 4 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA – name: 8 Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand – name: 12 Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, USA – name: 6 The Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand – name: 5 Molecular Biology and Reproductive Technology Laboratories, Livestock and Farming Systems Division, South Australian Research and Development Institute, Roseworthy, SA, Australia – name: 7 School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, New Zealand – name: 10 Department of Laboratory Medicine, Children’s Hospital Boston, Boston, MA, USA – name: 11 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA – name: 3 Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA – name: 1 Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA – name: 9 Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA |
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Center for Human Genetic Research, Massachusetts General Hospital – sequence: 6 givenname: Ian surname: Blumenthal fullname: Blumenthal, Ian organization: Center for Human Genetic Research, Massachusetts General Hospital – sequence: 7 givenname: Ryan E surname: Mills fullname: Mills, Ryan E organization: Department of Pathology, Brigham and Women's Hospital and Harvard Medical School – sequence: 8 givenname: Andrew surname: Kirby fullname: Kirby, Andrew organization: Center for Human Genetic Research, Massachusetts General Hospital, Program in Medical and Population Genetics, Broad Institute – sequence: 9 givenname: Amelia M surname: Lindgren fullname: Lindgren, Amelia M organization: Department of Pathology, Brigham and Women's Hospital and Harvard Medical School – sequence: 10 givenname: Skye R surname: Rudiger fullname: Rudiger, Skye R organization: Livestock and Farming Systems Division, Molecular Biology Laboratory, South Australian Research and Development Institute, Livestock and Farming Systems Division, Reproductive Technology Laboratory, South Australian Research and Development Institute – sequence: 11 givenname: Clive J surname: McLaughlan fullname: McLaughlan, Clive J organization: Livestock and Farming Systems Division, Molecular Biology Laboratory, South Australian Research and Development Institute, Livestock and Farming Systems Division, Reproductive Technology Laboratory, South Australian Research and Development Institute – sequence: 12 givenname: C Simon surname: Bawden fullname: Bawden, C Simon organization: Livestock and Farming Systems Division, Molecular Biology Laboratory, South Australian Research and Development Institute, Livestock and Farming Systems Division, Reproductive Technology Laboratory, South Australian Research and Development Institute – sequence: 13 givenname: Suzanne J surname: Reid fullname: Reid, Suzanne J organization: The Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, School of Biological Sciences, Faculty of Science, The University of Auckland – sequence: 14 givenname: Richard L M surname: Faull fullname: Faull, Richard L M organization: The Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, The University of Auckland – sequence: 15 givenname: Russell G surname: Snell fullname: Snell, Russell G organization: The Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, School of Biological Sciences, Faculty of Science, The University of Auckland – sequence: 16 givenname: Ira M surname: Hall fullname: Hall, Ira M organization: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine – sequence: 17 givenname: Yiping surname: Shen fullname: Shen, Yiping organization: Center for Human Genetic Research, Massachusetts General Hospital, Department of Laboratory Medicine, Children's Hospital Boston – sequence: 18 givenname: Toshiro K surname: Ohsumi fullname: Ohsumi, Toshiro K organization: Department of Molecular Biology, Massachusetts General Hospital – sequence: 19 givenname: Mark L surname: Borowsky fullname: Borowsky, Mark L organization: Department of Molecular Biology, Massachusetts General Hospital – sequence: 20 givenname: Mark J surname: Daly fullname: Daly, Mark J organization: Center for Human Genetic Research, Massachusetts General Hospital, Program in Medical and Population Genetics, Broad Institute – sequence: 21 givenname: Charles surname: Lee fullname: Lee, Charles organization: Department of Pathology, Brigham and Women's Hospital and Harvard Medical School – sequence: 22 givenname: Cynthia C surname: Morton fullname: Morton, Cynthia C organization: Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Program in Medical and Population Genetics, Broad Institute, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital – sequence: 23 givenname: Marcy E surname: MacDonald fullname: MacDonald, Marcy E organization: Center for Human Genetic Research, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Department of Neurology, Harvard Medical School, Program in Medical and Population Genetics, Broad Institute – sequence: 24 givenname: James F surname: Gusella fullname: Gusella, James F organization: Center for Human Genetic Research, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Department of Neurology, Harvard Medical School, Program in Medical and Population Genetics, Broad Institute – sequence: 25 givenname: Michael E surname: Talkowski fullname: Talkowski, Michael E email: talkowski@chgr.mgh.harvard.edu organization: Center for Human Genetic Research, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Department of Neurology, Harvard Medical School, Program in Medical and Population Genetics, Broad Institute |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=25767237$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/22388000$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | Springer Nature America, Inc. 2012 2015 INIST-CNRS COPYRIGHT 2012 Nature Publishing Group Copyright Nature Publishing Group Apr 2012 |
| Copyright_xml | – notice: Springer Nature America, Inc. 2012 – notice: 2015 INIST-CNRS – notice: COPYRIGHT 2012 Nature Publishing Group – notice: Copyright Nature Publishing Group Apr 2012 |
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| DOI | 10.1038/ng.2202 |
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| Keywords | Repair Germ line |
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| Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 Current affiliation: Department of Psychiatry, McGill University, Montreal, QC equally contributing authors |
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| Snippet | Michael Talkowski and colleagues examine karyotypically balanced genomic rearrangement landscapes in the germline at single-nucleotide resolution. They find... We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted... We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically-interpreted... |
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| SubjectTerms | 631/208/2489/144 631/208/69 Agriculture Animal genetic engineering Animal Genetics and Genomics Animals Animals, Genetically Modified Autism Biological and medical sciences Biomedical and Life Sciences Biomedicine Cancer Cancer Research Chromosome Breakage Chromosome Inversion Chromosomes DNA DNA End-Joining Repair - genetics Experiments Fundamental and applied biological sciences. Psychology Gene Function Gene Rearrangement Genetic research Genetically modified animals Genetics of eukaryotes. Biological and molecular evolution Genomes Genomics Germ-Line Mutation Hospitals Human Genetics Humans Medical research Molecular and cellular biology Molecular genetics Molecular Sequence Data Mutagenesis. Repair Neoplasms - genetics Oligonucleotide Array Sequence Analysis Physiological aspects Sequence Analysis, DNA Translocation, Genetic |
| Title | Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration |
| URI | https://link.springer.com/article/10.1038/ng.2202 https://www.ncbi.nlm.nih.gov/pubmed/22388000 https://www.proquest.com/docview/1011784443 https://www.proquest.com/docview/1034818966 https://www.proquest.com/docview/963489964 https://pubmed.ncbi.nlm.nih.gov/PMC3340016 |
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