Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes
- Zhishuo Ou1,9,
- Paweł Stankiewicz1,9,
- Zhilian Xia1,
- Amy M. Breman1,
- Brian Dawson1,
- Joanna Wiszniewska1,
- Przemyslaw Szafranski1,
- M. Lance Cooper1,
- Mitchell Rao1,
- Lina Shao1,
- Sarah T. South2,
- Karlene Coleman3,
- Paul M. Fernhoff3,
- Marcel J. Deray4,
- Sally Rosengren5,
- Elizabeth R. Roeder6,
- Victoria B. Enciso6,
- A. Craig Chinault1,
- Ankita Patel1,
- Sung-Hae L. Kang1,
- Chad A. Shaw1,
- James R. Lupski1,7,8 and
- Sau W. Cheung1,10
- 1 Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA;
- 2 Departments of Pediatrics and Pathology, University of Utah, Salt Lake City, Utah 84112, USA;
- 3 Children's Healthcare of Atlanta, Atlanta, Georgia 30033, USA;
- 4 Department of Neurology, Miami Children's Hospital, Miami, Florida 33155, USA;
- 5 Hartford Hospital, Hartford, Connecticut 06102, USA;
- 6 Department of Pediatrics, UTHSCSA, San Antonio, Texas 78229, USA;
- 7 Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA;
- 8 Texas Children's Hospital, Houston, Texas 77030, USA
Abstract
Four unrelated families with the same unbalanced translocation der(4)t(4;11)(p16.2;p15.4) were analyzed. Both of the breakpoint regions in 4p16.2 and 11p15.4 were narrowed to large ∼359-kb and ∼215-kb low-copy repeat (LCR) clusters, respectively, by aCGH and SNP array analyses. DNA sequencing enabled mapping the breakpoints of one translocation to 24 bp within interchromosomal paralogous LCRs of ∼130 kb in length and 94.7% DNA sequence identity located in olfactory receptor gene clusters, indicating nonallelic homologous recombination (NAHR) as the mechanism for translocation formation. To investigate the potential involvement of interchromosomal LCRs in recurrent chromosomal translocation formation, we performed computational genome-wide analyses and identified 1143 interchromosomal LCR substrate pairs, >5 kb in size and sharing >94% sequence identity that can potentially mediate chromosomal translocations. Additional evidence for interchromosomal NAHR mediated translocation formation was provided by sequencing the breakpoints of another recurrent translocation, der(8)t(8;12)(p23.1;p13.31). The NAHR sites were mapped within 55 bp in ∼7.8-kb paralogous subunits of 95.3% sequence identity located in the ∼579-kb (chr 8) and ∼287-kb (chr 12) LCR clusters. We demonstrate that NAHR mediates recurrent constitutional translocations t(4;11) and t(8;12) and potentially many other interchromosomal translocations throughout the human genome. Furthermore, we provide a computationally determined genome-wide “recurrent translocation map.”
Footnotes
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↵9 These authors contributed equally to this work.
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↵10 Corresponding author.
E-mail scheung{at}bcm.edu; fax (713) 798-8937.
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[Supplemental material is available online at http://www.genome.org. The sequence data from this study have been submitted to GenBank (http://www.ncbi.nlm.nih.gov/genbank/) under accession nos. HM989976 and HM989977 and to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession nos. GSM578535–GSM578540, GSM578936–GSM578940, GSM578965, and GSM579028.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.111609.110.
- Received June 14, 2010.
- Accepted October 6, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
Freely available online through the Genome Research Open Access option.