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Fisher CL, Dillon R, Anguita E, Morris-Rosendahl DJ, Awan AR. A Novel Bead-Capture Nanopore Sequencing Method for Large Structural Rearrangement Detection in Cancer. J Mol Diagn 2022; 24:1264-1278. [PMID: 36243290 DOI: 10.1016/j.jmoldx.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 08/07/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022] Open
Abstract
Rapid, cost-effective genomic stratification of structural rearrangements in cancer is often of vital importance when determining treatment; however, existing diagnostic cytogenetic and molecular testing fails to deliver the required speed when deployed at scale. Next-generation sequencing-based methods are widely used, but these can lack sensitivity and require batching of samples to be cost-effective, with long turnaround times. Here we present a novel method for rearrangement detection from genomic DNA based on third-generation long-read sequencing that overcomes these time and cost issues. The utility of this approach for the genomic stratification of patients with acute myeloid leukemia is shown based on detection of four of the most prevalent structural rearrangements. The method not only determines the precise genomic breakpoint for each expected rearrangement but also discovers and validates novel translocations in one-third of the tested samples, 80% of which involve known oncogenes. This method may prove to be a powerful tool for the diagnosis, genomic stratification, and characterization of cancers.
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Affiliation(s)
- Chloe L Fisher
- Genomics Innovation Unit, Guy's and St Thomas' NHS Trust, London, United Kingdom
| | - Richard Dillon
- Department of Medical and Molecular Genetics King's College London, London, United Kingdom; Department of Haematology, Guy's and St Thomas' NHS Trust, London, United Kingdom
| | - Eduardo Anguita
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos, Hospital Clínico San Carlos, Madrid, Spain; Department of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Deborah J Morris-Rosendahl
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy's and St Thomas' NHS Trust, London, United Kingdom; Molecular Genetics, NHLI, Imperial College London, London, United Kingdom
| | - Ali R Awan
- Genomics Innovation Unit, Guy's and St Thomas' NHS Trust, London, United Kingdom; Comprehensive Cancer Centre, King's College London, London, United Kingdom.
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2
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Sun Q, Zhang X, Zhan P, Tian W, Wang Y, Yang X. Analysis of 2 men with t(8;22)(q13;q13) and t(8;14)(q13;q22) chromosomal translocation karyotypes. Medicine (Baltimore) 2022; 101:e31091. [PMID: 36254019 PMCID: PMC9575810 DOI: 10.1097/md.0000000000031091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Male infertility is a multifactorial condition that is closely associated with chromosomal abnormalities. Reciprocal chromosomal translocation (RCT) is a significant structural genetic abnormality. The specific mechanisms of forms of RCT affecting male infertility include the product of chromosomally unbalanced gametes, thereby disrupting the structure and function of important genes responsible for spermatogenesis. RCT breakpoints have been found to disrupt gene structure and function in many medical fields However, the relationship between RCT breakpoints and male infertility remains to be determined. The purpose of this study is to describe 2 male carriers of RCTs 46,XY,t(8;22)(q13;q13) and 46,XY,t(8;14)(q13;q22). Both patients were collected from the second hospital of Jilin University. Semen parameters were detected using the computer-aided semen analysis system. Cytogenetic analysis was performed using standard operating procedure. Related genes on chromosomal breakpoints were searched using Online Mendelian Inheritance in Man. One man had semen parameters within the normal range, but the couple was infertile after 5 years of marriage. The other man showed normal semen parameters, and his wife had experienced 2 spontaneous miscarriages. Using a literature search, the association between chromosome 22q13 breakpoint and fertility were investigated. The results suggest that physicians should focus on the clinical phenotype of the patients and the breakpoints of RCT in genetic counseling. An important gene related to human male infertility is clearly located in chromosome region 22q13, and its function is worthy of further study.
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Affiliation(s)
- Qijia Sun
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Xiaoyu Zhang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Peng Zhan
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
- * Correspondence: Peng Zhan, Department of Urology, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province 130041, China (e-mail: )
| | - Wenjie Tian
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Yanli Wang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
| | - Xiao Yang
- Department of Urology, The Second Hospital of Jilin University, Changchun, China
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Luukkonen TM, Mehrjouy MM, Pöyhönen M, Anttonen A, Lahermo P, Ellonen P, Paulin L, Tommerup N, Palotie A, Varilo T. Breakpoint mapping and haplotype analysis of translocation t(1;12)(q43;q21.1) in two apparently independent families with vascular phenotypes. Mol Genet Genomic Med 2018; 6:56-68. [PMID: 29168350 PMCID: PMC5823676 DOI: 10.1002/mgg3.346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The risk of serious congenital anomaly for de novo balanced translocations is estimated to be at least 6%. We identified two apparently independent families with a balanced t(1;12)(q43;q21.1) as an outcome of a "Systematic Survey of Balanced Chromosomal Rearrangements in Finns." In the first family, carriers (n = 6) manifest with learning problems in childhood, and later with unexplained neurological symptoms (chronic headache, balance problems, tremor, fatigue) and cerebral infarctions in their 50s. In the second family, two carriers suffer from tetralogy of Fallot, one from transient ischemic attack and one from migraine. The translocation cosegregates with these vascular phenotypes and neurological symptoms. METHODS AND RESULTS We narrowed down the breakpoint regions using mate pair sequencing. We observed conserved haplotypes around the breakpoints, pointing out that this translocation has arisen only once. The chromosome 1 breakpoint truncates a CHRM3 processed transcript, and is flanked by the 5' end of CHRM3 and the 3' end of RYR2. TRHDE, KCNC2, and ATXN7L3B flank the chromosome 12 breakpoint. CONCLUSIONS This study demonstrates a balanced t(1;12)(q43;q21.1) with conserved haplotypes on the derived chromosomes. The translocation seems to result in vascular phenotype, with or without neurological symptoms, in at least two families. We suggest that the translocation influences the positional expression of CHRM3, RYR2, TRHDE, KCNC2, and/or ATXN7L3B.
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Affiliation(s)
- Tiia Maria Luukkonen
- Institute for molecular medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Department of HealthNational Institute for Health and WelfareHelsinkiFinland
| | - Mana M. Mehrjouy
- Wilhelm Johannsen Centre for Functional Genome ResearchDepartment of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Minna Pöyhönen
- Clinical GeneticsHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
- Department of Medical GeneticsUniversity of HelsinkiHelsinkiFinland
| | | | - Päivi Lahermo
- Institute for molecular medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Pekka Ellonen
- Institute for molecular medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Lars Paulin
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome ResearchDepartment of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Aarno Palotie
- Institute for molecular medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Broad Institute of Harvard and MITCambridgeMAUSA
| | - Teppo Varilo
- Department of HealthNational Institute for Health and WelfareHelsinkiFinland
- Department of Medical GeneticsUniversity of HelsinkiHelsinkiFinland
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4
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Grzesiuk JD, Pereira CS, Grangeiro CHP, Picanço-Albuquerque CG, Oliveira-Gennaro FG, Machado FB, Medina-Acosta E, Ramos ES, Yoshimoto M, Martelli L. Familial chromosomal translocation X; 22 associated with infertility and recurrent X mosaicism. Mol Cytogenet 2016; 9:45. [PMID: 27313662 PMCID: PMC4910231 DOI: 10.1186/s13039-016-0249-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/29/2016] [Indexed: 11/22/2022] Open
Abstract
Background Individuals with apparently balanced translocations, often, show no clinical findings. However, in meiosis, translocations tend to cause errors on chromosome disjunction and the ones involving sex chromosomes have particular implications for the phenotype. Male carriers of balanced X-autosome translocations are almost invariably infertile due to interruption of the spermatogenesis, but the mechanism is not fully understood. Case presentation In this case report, we performed a combination of classical cytogenetics (G-banding), molecular cytogenetics (fluorescence in situ hybridization and X-chromosome inactivation study), and cytogenomics (microarray-based comparative genomic hybridization) techniques for characterization of an inherited (X;22) translocation in a family originally referred for infertility investigation. Both proband and his sister are infertile and present the maternally inherited translocation. Interestingly, the maternal grandmother was mosaic for X chromosome monosomy suggesting that the t(X;22) in the proband’s mother arose by errors at oogenesis. The presence of the same mosaicism of the X chromosome in the proband’s aunt is consistent with this consideration. Array- CGH analysis showed no constitutional pathogenic gains or losses in the translocation carriers. The X-chromosome inactivation studies revealed that the translocated X;22 was active in 99.3% of cells in the mother and in 88% of cells in the daughter. We suggest that incomplete skewing of X inactivation (>97 %) of the daughter could justify the infertility. This study is the first description of recurrent mosaicism of the X chromosome associated with a familial X-autosome translocation. Conclusions The phenotype of infertility was probably caused by disruption of spermatogenesis due to gametogenesis specific errors resulted from meiotic pairing and segregation anomalies on the translocated chromosomes.
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Affiliation(s)
- Juliana Dourado Grzesiuk
- Genetics Department, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, 14049-900 Brazil
| | - Ciro Silveira Pereira
- Center of Biotecnology and Cellular Therapy, San Raphael Hospital, Salvador, 41253-190 Brazil
| | | | | | | | - Filipe Brum Machado
- Center of Biosciences and Biotechnology, Darcy Ribeiro State University of Northern of Rio de Janeiro, Campos dos Goytacazes, 28013-600 Brazil
| | - Enrique Medina-Acosta
- Center of Biosciences and Biotechnology, Darcy Ribeiro State University of Northern of Rio de Janeiro, Campos dos Goytacazes, 28013-600 Brazil
| | - Ester Silveira Ramos
- Genetics Department, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, 14049-900 Brazil
| | - Maisa Yoshimoto
- Department of Medical Genetics, Faculty of Medical and Dentistry, University of Alberta, Edmonton, Canada
| | - Lucia Martelli
- Genetics Department, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, 14049-900 Brazil
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5
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Unrevealed mosaicism in the next-generation sequencing era. Mol Genet Genomics 2015; 291:513-30. [PMID: 26481646 PMCID: PMC4819561 DOI: 10.1007/s00438-015-1130-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Mosaicism refers to the presence in an individual of normal and abnormal cells that are genotypically distinct and are derived from a single zygote. The incidence of mosaicism events in the human body is underestimated as the genotypes in the mosaic ratio, especially in the low-grade mosaicism, stay unrevealed. This review summarizes various research outcomes and diagnostic questions in relation to different types of mosaicism. The impact of both tested biological material and applied method on the mosaicism detection rate is especially highlighted. As next-generation sequencing technologies constitute a promising methodological solution in mosaicism detection in the coming years, revisions in current diagnostic protocols are necessary to increase the detection rate of the unrevealed mosaicism events. Since mosaicism identification is a complex process, numerous examples of multistep mosaicism investigations are presented and discussed.
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6
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Midro AT, Panasiuk B, Stasiewicz-Jarocka B, Olszewska M, Wiland E, Myśliwiec M, Kurpisz M, Shaffer LG, Gajecka M. Recurrence risks for different pregnancy outcomes and meiotic segregation analysis of spermatozoa in carriers of t(1;11)(p36.22;q12.2). J Hum Genet 2014; 59:667-74. [PMID: 25319850 DOI: 10.1038/jhg.2014.92] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 01/16/2023]
Abstract
Cumulative data obtained from two relatively large pedigrees of a unique reciprocal chromosomal translocation (RCT) t(1;11)(p36.22;q12.2) ascertained by three miscarriages (pedigree 1) and the birth of newborn with hydrocephalus and myelomeningocele (pedigree 2) were used to estimate recurrence risks for different pregnancy outcomes. Submicroscopic molecular characterization by fluorescent in situ hybridization (FISH) of RCT break points in representative carriers showed similar rearrangements in both families. Meiotic segregation patterns after sperm analysis by three-color FISH of one male carrier showed all possible outcomes resulting from 2:2 and 3:1 segregations. On the basis of empirical survival data, we suggest that only one form of chromosome imbalance resulting in monosomy 1p36.22→pter with trisomy 11q12.2→qter may be observed in progeny at birth. Segregation analysis of these pedigrees was performed by the indirect method of Stengel-Rutkowski and showed that probability rate for malformed child at birth due to an unbalanced karyotype was 3/48 (6.2±3.5%) after ascertainment correction. The risk for stillbirths/early neonatal deaths was -/48 (<1.1%) and for miscarriages was 17/48 (35.4±6.9%). However, the probability rate for children with a normal phenotype at birth was 28/48 (58.3±7.1%). The results obtained from this study may be used to determine the risks for the various pregnancy outcomes for carriers of t(1;11)(p36.22;q12.2) and can be used for genetic counseling of carriers of this rearrangement.
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Affiliation(s)
- Alina Teresa Midro
- Department of Clinical Genetics, Medical University of Bialystok, Bialystok, Poland
| | - Barbara Panasiuk
- Department of Clinical Genetics, Medical University of Bialystok, Bialystok, Poland
| | | | - Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Ewa Wiland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marta Myśliwiec
- Department of Clinical Genetics, Medical University of Bialystok, Bialystok, Poland
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA
| | - Marzena Gajecka
- 1] Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland [2] Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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7
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Bose P, Hermetz KE, Conneely KN, Rudd MK. Tandem repeats and G-rich sequences are enriched at human CNV breakpoints. PLoS One 2014; 9:e101607. [PMID: 24983241 PMCID: PMC4090240 DOI: 10.1371/journal.pone.0101607] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/09/2014] [Indexed: 11/18/2022] Open
Abstract
Chromosome breakage in germline and somatic genomes gives rise to copy number variation (CNV) responsible for genomic disorders and tumorigenesis. DNA sequence is known to play an important role in breakage at chromosome fragile sites; however, the sequences susceptible to double-strand breaks (DSBs) underlying CNV formation are largely unknown. Here we analyze 140 germline CNV breakpoints from 116 individuals to identify DNA sequences enriched at breakpoint loci compared to 2800 simulated control regions. We find that, overall, CNV breakpoints are enriched in tandem repeats and sequences predicted to form G-quadruplexes. G-rich repeats are overrepresented at terminal deletion breakpoints, which may be important for the addition of a new telomere. Interstitial deletions and duplication breakpoints are enriched in Alu repeats that in some cases mediate non-allelic homologous recombination (NAHR) between the two sides of the rearrangement. CNV breakpoints are enriched in certain classes of repeats that may play a role in DNA secondary structure, DSB susceptibility and/or DNA replication errors.
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Affiliation(s)
- Promita Bose
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Karen E. Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Karen N. Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - M. Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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8
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Robberecht C, Voet T, Zamani Esteki M, Nowakowska BA, Vermeesch JR. Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations. Genome Res 2012; 23:411-8. [PMID: 23212949 PMCID: PMC3589530 DOI: 10.1101/gr.145631.112] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Large-scale analysis of balanced chromosomal translocation breakpoints has shown nonhomologous end joining and microhomology-mediated repair to be the main drivers of interchromosomal structural aberrations. Breakpoint sequences of de novo unbalanced translocations have not yet been investigated systematically. We analyzed 12 de novo unbalanced translocations and mapped the breakpoints in nine. Surprisingly, in contrast to balanced translocations, we identify nonallelic homologous recombination (NAHR) between (retro)transposable elements and especially long interspersed elements (LINEs) as the main mutational mechanism. This finding shows yet another involvement of (retro)transposons in genomic rearrangements and exposes a profoundly different mutational mechanism compared with balanced chromosomal translocations. Furthermore, we show the existence of compound maternal/paternal derivative chromosomes, reinforcing the hypothesis that human cleavage stage embryogenesis is a cradle of chromosomal rearrangements.
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Affiliation(s)
- Caroline Robberecht
- Laboratory for Molecular Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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9
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Froyen G, Belet S, Martinez F, Santos-Rebouças C, Declercq M, Verbeeck J, Donckers L, Berland S, Mayo S, Rosello M, Pimentel M, Fintelman-Rodrigues N, Hovland R, Rodrigues dos Santos S, Raymond F, Bose T, Corbett M, Sheffield L, van Ravenswaaij-Arts C, Dijkhuizen T, Coutton C, Satre V, Siu V, Marynen P. Copy-number gains of HUWE1 due to replication- and recombination-based rearrangements. Am J Hum Genet 2012; 91:252-64. [PMID: 22840365 DOI: 10.1016/j.ajhg.2012.06.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/21/2012] [Accepted: 06/21/2012] [Indexed: 12/20/2022] Open
Abstract
We previously reported on nonrecurrent overlapping duplications at Xp11.22 in individuals with nonsyndromic intellectual disability (ID) harboring HSD17B10, HUWE1, and the microRNAs miR-98 and let-7f-2 in the smallest region of overlap. Here, we describe six additional individuals with nonsyndromic ID and overlapping microduplications that segregate in the families. High-resolution mapping of the 12 copy-number gains reduced the minimal duplicated region to the HUWE1 locus only. Consequently, increased mRNA levels were detected for HUWE1, but not HSD17B10. Marker and SNP analysis, together with identification of two de novo events, suggested a paternally derived intrachromosomal duplication event. In four independent families, we report on a polymorphic 70 kb recurrent copy-number gain, which harbors part of HUWE1 (exon 28 to 3' untranslated region), including miR-98 and let-7f-2. Our findings thus demonstrate that HUWE1 is the only remaining dosage-sensitive gene associated with the ID phenotype. Junction and in silico analysis of breakpoint regions demonstrated simple microhomology-mediated rearrangements suggestive of replication-based duplication events. Intriguingly, in a single family, the duplication was generated through nonallelic homologous recombination (NAHR) with the use of HUWE1-flanking imperfect low-copy repeats, which drive this infrequent NAHR event. The recurrent partial HUWE1 copy-number gain was also generated through NAHR, but here, the homologous sequences used were identified as TcMAR-Tigger DNA elements, a template that has not yet been reported for NAHR. In summary, we showed that an increased dosage of HUWE1 causes nonsyndromic ID and demonstrated that the Xp11.22 region is prone to recombination- and replication-based rearrangements.
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10
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Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, Duran K, Ballarati L, Vergult S, Giardino D, Hansson K, Ruivenkamp CAL, Jager M, van Haeringen A, Ippel EF, Haaf T, Passarge E, Hochstenbach R, Menten B, Larizza L, Guryev V, Poot M, Cuppen E. Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Rep 2012; 1:648-55. [PMID: 22813740 DOI: 10.1016/j.celrep.2012.05.009] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 02/09/2012] [Accepted: 05/14/2012] [Indexed: 12/20/2022] Open
Abstract
Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyze the genomes of ten patients with congenital disease who were preselected to carry complex chromosomal rearrangements with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint junctions indicates that break repair involves nonhomologous or microhomology-mediated end joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred base pairs and several megabases. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template switching. Our work provides detailed insight into the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
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11
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Hermetz KE, Surti U, Cody JD, Rudd MK. A recurrent translocation is mediated by homologous recombination between HERV-H elements. Mol Cytogenet 2012; 5:6. [PMID: 22260357 PMCID: PMC3292815 DOI: 10.1186/1755-8166-5-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 01/19/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Chromosome rearrangements are caused by many mutational mechanisms; of these, recurrent rearrangements can be particularly informative for teasing apart DNA sequence-specific factors. Some recurrent translocations are mediated by homologous recombination between large blocks of segmental duplications on different chromosomes. Here we describe a recurrent unbalanced translocation casued by recombination between shorter homologous regions on chromosomes 4 and 18 in two unrelated children with intellectual disability. RESULTS Array CGH resolved the breakpoints of the 6.97-Megabase (Mb) loss of 18q and the 7.30-Mb gain of 4q. Sequencing across the translocation breakpoints revealed that both translocations occurred between 92%-identical human endogenous retrovirus (HERV) elements in the same orientation on chromosomes 4 and 18. In addition, we find sequence variation in the chromosome 4 HERV that makes one allele more like the chromosome 18 HERV. CONCLUSIONS Homologous recombination between HERVs on the same chromosome is known to cause chromosome deletions, but this is the first report of interchromosomal HERV-HERV recombination leading to a translocation. It is possible that normal sequence variation in substrates of non-allelic homologous recombination (NAHR) affects the alignment of recombining segments and influences the propensity to chromosome rearrangement.
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Affiliation(s)
- Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
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12
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Abstract
Subtelomeres are an incredibly dynamic part of the human genome located at the ends of chromosomes just proximal to telomere repeats. Although subtelomeric variation contributes to normal polymorphism in the human genome and is a by-product of rapid evolution in these regions, rearrangements in subtelomeres can also cause intellectual disabilities and birth defects, making robust methods of detecting copy number variation in chromosome ends a must for cytogenetics labs. In recent years, methods for detecting structural variation in subtelomeres have moved from fluorescence in situ hybridization (FISH) to array technology; however, FISH is still necessary to determine the chromosomal structure of subtelomeric gains and losses identified by arrays.
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Affiliation(s)
- M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
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13
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Luo Y, Hermetz KE, Jackson JM, Mulle JG, Dodd A, Tsuchiya KD, Ballif BC, Shaffer LG, Cody JD, Ledbetter DH, Martin CL, Rudd MK. Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements. Hum Mol Genet 2011; 20:3769-78. [PMID: 21729882 DOI: 10.1093/hmg/ddr293] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromosome rearrangements are a significant cause of intellectual disability and birth defects. Subtelomeric rearrangements, including deletions, duplications and translocations of chromosome ends, were first discovered over 40 years ago and are now recognized as being responsible for several genetic syndromes. Unlike the deletions and duplications that cause some genomic disorders, subtelomeric rearrangements do not typically have recurrent breakpoints and involve many different chromosome ends. To capture the molecular mechanisms responsible for this heterogeneous class of chromosome abnormality, we coupled high-resolution array CGH with breakpoint junction sequencing of a diverse collection of subtelomeric rearrangements. We analyzed 102 breakpoints corresponding to 78 rearrangements involving 28 chromosome ends. Sequencing 21 breakpoint junctions revealed signatures of non-homologous end-joining, non-allelic homologous recombination between interspersed repeats and DNA replication processes. Thus, subtelomeric rearrangements arise from diverse mutational mechanisms. In addition, we find hotspots of subtelomeric breakage at the end of chromosomes 9q and 22q; these sites may correspond to genomic regions that are particularly susceptible to double-strand breaks. Finally, fine-mapping the smallest subtelomeric rearrangements has narrowed the critical regions for some chromosomal disorders.
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Affiliation(s)
- Yue Luo
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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14
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Pellestor F, Anahory T, Lefort G, Puechberty J, Liehr T, Hedon B, Sarda P. Complex chromosomal rearrangements: origin and meiotic behavior. Hum Reprod Update 2011; 17:476-94. [DOI: 10.1093/humupd/dmr010] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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15
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Bacolla A, Wang G, Jain A, Chuzhanova NA, Cer RZ, Collins JR, Cooper DN, Bohr VA, Vasquez KM. Non-B DNA-forming sequences and WRN deficiency independently increase the frequency of base substitution in human cells. J Biol Chem 2011; 286:10017-26. [PMID: 21285356 PMCID: PMC3060453 DOI: 10.1074/jbc.m110.176636] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 01/31/2011] [Indexed: 01/01/2023] Open
Abstract
Although alternative DNA secondary structures (non-B DNA) can induce genomic rearrangements, their associated mutational spectra remain largely unknown. The helicase activity of WRN, which is absent in the human progeroid Werner syndrome, is thought to counteract this genomic instability. We determined non-B DNA-induced mutation frequencies and spectra in human U2OS osteosarcoma cells and assessed the role of WRN in isogenic knockdown (WRN-KD) cells using a supF gene mutation reporter system flanked by triplex- or Z-DNA-forming sequences. Although both non-B DNA and WRN-KD served to increase the mutation frequency, the increase afforded by WRN-KD was independent of DNA structure despite the fact that purified WRN helicase was found to resolve these structures in vitro. In U2OS cells, ∼70% of mutations comprised single-base substitutions, mostly at G·C base-pairs, with the remaining ∼30% being microdeletions. The number of mutations at G·C base-pairs in the context of NGNN/NNCN sequences correlated well with predicted free energies of base stacking and ionization potentials, suggesting a possible origin via oxidation reactions involving electron loss and subsequent electron transfer (hole migration) between neighboring bases. A set of ∼40,000 somatic mutations at G·C base pairs identified in a lung cancer genome exhibited similar correlations, implying that hole migration may also be involved. We conclude that alternative DNA conformations, WRN deficiency and lung tumorigenesis may all serve to increase the mutation rate by promoting, through diverse pathways, oxidation reactions that perturb the electron orbitals of neighboring bases. It follows that such "hole migration" is likely to play a much more widespread role in mutagenesis than previously anticipated.
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Affiliation(s)
- Albino Bacolla
- From the Department of Molecular Carcinogenesis, Science Park-Research Division, The University of Texas, M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Guliang Wang
- From the Department of Molecular Carcinogenesis, Science Park-Research Division, The University of Texas, M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Aklank Jain
- From the Department of Molecular Carcinogenesis, Science Park-Research Division, The University of Texas, M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Nadia A. Chuzhanova
- the School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, United Kingdom
| | - Regina Z. Cer
- the Advanced Biomedical Computing Center, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Jack R. Collins
- the Advanced Biomedical Computing Center, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - David N. Cooper
- the Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, United Kingdom, and
| | - Vilhelm A. Bohr
- the Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Karen M. Vasquez
- From the Department of Molecular Carcinogenesis, Science Park-Research Division, The University of Texas, M. D. Anderson Cancer Center, Smithville, Texas 78957
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16
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Gajecka M, Saitta SC, Gentles AJ, Campbell L, Ciprero K, Geiger E, Catherwood A, Rosenfeld JA, Shaikh T, Shaffer LG. Recurrent interstitial 1p36 deletions: Evidence for germline mosaicism and complex rearrangement breakpoints. Am J Med Genet A 2011; 152A:3074-83. [PMID: 21108392 DOI: 10.1002/ajmg.a.33733] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deletions of chromosome 1p36 are one of the most frequently encountered subtelomeric alterations. Clinical features of monosomy 1p36 include neurocognitive impairment, hearing loss, seizures, cardiac defects, and characteristic facial features. The majority of cases have occurred sporadically, implying that genomic instability plays a role in the prevalence of the syndrome. Here, we report two siblings with mild phenotypic features of the deletion syndrome, including developmental delay, hearing loss, and left ventricular non-compaction (LVNC). Microarray analysis using bacterial artificial chromosome and oligonucleotide microarrays indicated the deletions were identical, suggesting germline mosaicism. Parental phenotypes were normal, and analysis by fluorescence in situ hybridization (FISH) did not show mosaicism. These small interstitial deletions were not detectable by conventional subtelomeric FISH analysis. To investigate the mechanism of deletion further, the breakpoints were cloned and sequenced, demonstrating the presence of a complex rearrangement. Sequence analysis of genes in the deletion interval did not reveal any mutations on the intact homologue that may have contributed to the LVNC seen in both children. This is the first report of apparent germline mosaicism for this disorder. Thus, our findings have important implications for diagnostic approaches and for recurrence risk counseling in families with a child with monosomy 1p36. In addition, our results further refine the minimal critical region for LVNC and hearing loss.
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Affiliation(s)
- Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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17
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Kloosterman WP, Guryev V, van Roosmalen M, Duran KJ, de Bruijn E, Bakker SCM, Letteboer T, van Nesselrooij B, Hochstenbach R, Poot M, Cuppen E. Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet 2011; 20:1916-24. [PMID: 21349919 DOI: 10.1093/hmg/ddr073] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A variety of mutational mechanisms shape the dynamic architecture of human genomes and occasionally result in congenital defects and disease. Here, we used genome-wide long mate-pair sequencing to systematically screen for inherited and de novo structural variation in a trio including a child with severe congenital abnormalities. We identified 4321 inherited structural variants and 17 de novo rearrangements. We characterized the de novo structural changes to the base-pair level revealing a complex series of balanced inter- and intra-chromosomal rearrangements consisting of 12 breakpoints involving chromosomes 1, 4 and 10. Detailed inspection of breakpoint regions indicated that a series of simultaneous double-stranded DNA breaks caused local shattering of chromosomes. Fusion of the resulting chromosomal fragments involved non-homologous end joining, since junction points displayed limited or no homology and small insertions and deletions. The pattern of random joining of chromosomal fragments that we observe here strongly resembles the somatic rearrangement patterns--termed chromothripsis--that have recently been described in deranged cancer cells. We conclude that a similar mechanism may also drive the formation of de novo structural variation in the germline.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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18
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Howarth KD, Pole JCM, Beavis JC, Batty EM, Newman S, Bignell GR, Edwards PAW. Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles. Genome Res 2011; 21:525-34. [PMID: 21252201 DOI: 10.1101/gr.114116.110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Reciprocal chromosome translocations are often not exactly reciprocal. Most familiar are deletions at the breakpoints, up to megabases in extent. We describe here the opposite phenomenon-duplication of tens or hundreds of kilobases at the breakpoint junction, so that the same sequence is present on both products of a translocation. When the products of the translocation are mapped on the genome, they overlap. We report several of these "overlapping-breakpoint" duplications in breast cancer cell lines HCC1187, HCC1806, and DU4475. These lines also had deletions and essentially balanced translocations. In HCC1187 and HCC1806, we identified five cases of duplication ranging between 46 kb and 200 kb, with the partner chromosome showing deletions between 29 bp and 31 Mb. DU4475 had a duplication of at least 200 kb. Breakpoints were mapped using array painting, i.e., hybridization of chromosomes isolated by flow cytometry to custom oligonucleotide microarrays. Duplications were verified by fluorescent in situ hybridization (FISH), PCR on isolated chromosomes, and cloning of breakpoints. We propose that these duplications are the counterpart of deletions and that they are produced at a replication bubble, comprising two replication forks with the duplicated sequence in between. Both copies of the duplicated sequence would go to one daughter cell, on different products of the translocation, while the other daughter cell would show deletion. These duplications may have been overlooked because they may be missed by FISH and array-CGH and may be interpreted as insertions by paired-end sequencing. Such duplications may therefore be quite frequent.
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Affiliation(s)
- Karen D Howarth
- Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Cambridge, UK.
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19
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Zhang F, Seeman P, Liu P, Weterman MA, Gonzaga-Jauregui C, Towne CF, Batish SD, De Vriendt E, De Jonghe P, Rautenstrauss B, Krause KH, Khajavi M, Posadka J, Vandenberghe A, Palau F, Van Maldergem L, Baas F, Timmerman V, Lupski JR. Mechanisms for nonrecurrent genomic rearrangements associated with CMT1A or HNPP: rare CNVs as a cause for missing heritability. Am J Hum Genet 2010; 86:892-903. [PMID: 20493460 DOI: 10.1016/j.ajhg.2010.05.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Revised: 04/28/2010] [Accepted: 05/03/2010] [Indexed: 12/20/2022] Open
Abstract
Genomic rearrangements involving the peripheral myelin protein gene (PMP22) in human chromosome 17p12 are associated with neuropathy: duplications cause Charcot-Marie-Tooth disease type 1A (CMT1A), whereas deletions lead to hereditary neuropathy with liability to pressure palsies (HNPP). Our previous studies showed that >99% of these rearrangements are recurrent and mediated by nonallelic homologous recombination (NAHR). Rare copy number variations (CNVs) generated by nonrecurrent rearrangements also exist in 17p12, but their underlying mechanisms are not well understood. We investigated 21 subjects with rare CNVs associated with CMT1A or HNPP by oligonucleotide-based comparative genomic hybridization microarrays and breakpoint sequence analyses, and we identified 17 unique CNVs, including two genomic deletions, ten genomic duplications, two complex rearrangements, and three small exonic deletions. Each of these CNVs includes either the entire PMP22 gene, or exon(s) only, or ultraconserved potential regulatory sequences upstream of PMP22, further supporting the contention that PMP22 is the critical gene mediating the neuropathy phenotypes associated with 17p12 rearrangements. Breakpoint sequence analysis reveals that, different from the predominant NAHR mechanism in recurrent rearrangement, various molecular mechanisms, including nonhomologous end joining, Alu-Alu-mediated recombination, and replication-based mechanisms (e.g., FoSTeS and/or MMBIR), can generate nonrecurrent 17p12 rearrangements associated with neuropathy. We document a multitude of ways in which gene function can be altered by CNVs. Given the characteristics, including small size, structural complexity, and location outside of coding regions, of selected rare CNVs, their identification remains a challenge for genome analysis. Rare CNVs may potentially represent an important portion of "missing heritability" for human diseases.
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20
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Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res 2010; 20:623-35. [PMID: 20308636 DOI: 10.1101/gr.102970.109] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that approximately 16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.
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Affiliation(s)
- Aaron R Quinlan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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21
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Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009. [PMID: 19597530 DOI: 10.1038/nrg2593.mechanisms] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer. CNVs form at a faster rate than other types of mutation, and seem to do so by similar mechanisms in bacteria, yeast and humans. Here we review current models of the mechanisms that cause copy number variation. Non-homologous end-joining mechanisms are well known, but recent models focus on perturbation of DNA replication and replication of non-contiguous DNA segments. For example, cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
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Affiliation(s)
- P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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22
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Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009; 10:551-64. [PMID: 19597530 DOI: 10.1038/nrg2593] [Citation(s) in RCA: 846] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer. CNVs form at a faster rate than other types of mutation, and seem to do so by similar mechanisms in bacteria, yeast and humans. Here we review current models of the mechanisms that cause copy number variation. Non-homologous end-joining mechanisms are well known, but recent models focus on perturbation of DNA replication and replication of non-contiguous DNA segments. For example, cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
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Affiliation(s)
- P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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23
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Vissers LE, Bhatt SS, Janssen IM, Xia Z, Lalani SR, Pfundt R, Derwinska K, de Vries BB, Gilissen C, Hoischen A, Nesteruk M, Wisniowiecka-Kowalnik B, Smyk M, Brunner HG, Cheung SW, van Kessel AG, Veltman JA, Stankiewicz P. Rare pathogenic microdeletions and tandem duplications are microhomology-mediated and stimulated by local genomic architecture. Hum Mol Genet 2009; 18:3579-93. [DOI: 10.1093/hmg/ddp306] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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24
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Zhang F, Carvalho CMB, Lupski JR. Complex human chromosomal and genomic rearrangements. Trends Genet 2009; 25:298-307. [PMID: 19560228 DOI: 10.1016/j.tig.2009.05.005] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 05/14/2009] [Accepted: 05/19/2009] [Indexed: 01/08/2023]
Abstract
Copy number variation (CNV) is a major source of genetic variation among humans. In addition to existing as benign polymorphisms, CNVs can also convey clinical phenotypes, including genomic disorders, sporadic diseases and complex human traits. CNV results from genomic rearrangements that can represent simple deletion or duplication of a genomic segment, or be more complex. Complex chromosomal rearrangements (CCRs) have been known for some time but their mechanisms have remained elusive. Recent technology advances and high-resolution human genome analyses have revealed that complex genomic rearrangements can account for a large fraction of non-recurrent rearrangements at a given locus. Various mechanisms, most of which are DNA-replication-based, for example fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR), have been proposed for generating such complex genomic rearrangements and are probably responsible for CCR.
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Affiliation(s)
- Feng Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA
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25
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D'Angelo CS, Gajecka M, Kim CA, Gentles AJ, Glotzbach CD, Shaffer LG, Koiffmann CP. Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements. Hum Genet 2009; 125:551-63. [PMID: 19271239 DOI: 10.1007/s00439-009-0650-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 02/25/2009] [Indexed: 12/23/2022]
Abstract
The mechanisms involved in the formation of subtelomeric rearrangements are now beginning to be elucidated. Breakpoint sequencing analysis of 1p36 rearrangements has made important contributions to this line of inquiry. Despite the unique architecture of segmental duplications inherent to human subtelomeres, no common mechanism has been identified thus far and different nonexclusive recombination-repair mechanisms seem to predominate. In order to gain further insights into the mechanisms of chromosome breakage, repair, and stabilization mediating subtelomeric rearrangements in humans, we investigated the constitutional rearrangements of 1p36. Cloning of the breakpoint junctions in a complex rearrangement and three non-reciprocal translocations revealed similarities at the junctions, such as microhomology of up to three nucleotides, along with no significant sequence identity in close proximity to the breakpoint regions. All the breakpoints appeared to be unique and their occurrence was limited to non-repetitive, unique DNA sequences. Several recombination- or cleavage-associated motifs that may promote non-homologous recombination were observed in close proximity to the junctions. We conclude that NHEJ is likely the mechanism of DNA repair that generates these rearrangements. Additionally, two apparently pure terminal deletions were also investigated, and the refinement of the breakpoint regions identified two distinct genomic intervals ~25-kb apart, each containing a series of 1p36 specific segmental duplications with 90-98% identity. Segmental duplications can serve as substrates for ectopic homologous recombination or stimulate genomic rearrangements.
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Affiliation(s)
- Carla S D'Angelo
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano, Instituto de Biociências, Universidade de São Paulo, SP CEP, Brazil.
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26
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Gajecka M, Saadeh R, Mackay KL, Glotzbach CD, Spodar K, Chitayat D, Shaffer LG. Clinical and molecular cytogenetic characterization of four patients with unbalanced translocation der(1)t(1;22)(p36;q13). Am J Med Genet A 2008; 146A:2777-84. [DOI: 10.1002/ajmg.a.32427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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