Mechanisms for Nonrecurrent Genomic Rearrangements Associated with CMT1A or HNPP: Rare CNVs as a Cause for Missing Heritability

The American Journal of Human Genetics - Tập 86 Số 6 - Trang 892-903 - 2010
Feng Zhang1,2, Pavel Seeman3, Pengfei Liu1, Marian A. J. Weterman4, Claudia Gonzaga‐Jauregui1, Charles F. Towne5, Sat Dev Batish5, Els De Vriendt6, Peter De Jonghe6, Bernd Rautenstrauß7,8, Klaus-Henning Krause7, Mehrdad Khajavi1, Jan Posadka3, Antoon Vandenberghe9, Francesc Palau10, Lionel Van Maldergem11, Frank Baas4, Vincent Timmerman6, James R. Lupski1,12,13
1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
2State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
3Department of Child Neurology, DNA Laboratory, 2nd School of Medicine, Charles University Prague and University Hospital Motol, V Úvalu 84, 15006 Praha 5, Czech Republic
4Neurogenetics Lab, Academic Medical Center Amsterdam, 1105 AZ Amsterdam, The Netherlands
5Athena Diagnositics, Inc., Worcester, MA 01605, USA
6Department of Molecular Genetics, VIB and University of Antwerp, B-2610 Antwerpen, Belgium
7Friedrich-Baur-Institute of the Ludwig-Maximilians-University, Ziemssenstrasse 1, 80336 Munich, Germany
8Medical Genetics Center, Bayerstrasse 3-5, 80335 Munich, Germany
9Biomnis Inc., F-69357 Lyon, France
10Institut de Biomedicina, Consejo Superior de Investigaciones Cientificas, and CIBER de Enfermedades Raras (CIBERER), Valencia 46010, Spain
11Centre de Génétique Humaine, Université de Liège, B-4000 Liège, Belgium
12Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
13Texas Children's Hospital, Houston, TX, 77030, USA

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Lupski, 1998, Genomic disorders: Structural features of the genome can lead to DNA rearrangements and human disease traits, Trends Genet., 14, 417, 10.1016/S0168-9525(98)01555-8

Stankiewicz, 2002, Genome architecture, rearrangements and genomic disorders, Trends Genet., 18, 74, 10.1016/S0168-9525(02)02592-1

Lupski, 2009, Genomic disorders ten years on, Genome Med., 1, 42, 10.1186/gm42

Lupski, 1991, DNA duplication associated with Charcot-Marie-Tooth disease type 1A, Cell, 66, 219, 10.1016/0092-8674(91)90613-4

Chance, 1993, DNA deletion associated with hereditary neuropathy with liability to pressure palsies, Cell, 72, 143, 10.1016/0092-8674(93)90058-X

Raeymaekers, 1991, Duplication in chromosome 17p11.2 in Charcot-Marie-Tooth neuropathy type 1a (CMT 1a), Neuromuscul. Disord., 1, 93, 10.1016/0960-8966(91)90055-W

Lupski, 2005, Hereditary motor and sensory neuropathies involving altered dosage or mutation of PMP22: The CMT1A duplication and HNPP deletion, 1659

Lupski, 1992, Gene dosage is a mechanism for Charcot-Marie-Tooth disease type 1A, Nat. Genet., 1, 29, 10.1038/ng0492-29

Gu, 2008, Mechanisms for human genomic rearrangements, PathoGenetics, 1, 4, 10.1186/1755-8417-1-4

Turner, 2008, Germline rates of de novo meiotic deletions and duplications causing several genomic disorders, Nat. Genet., 40, 90, 10.1038/ng.2007.40

Bailey, 2002, Recent segmental duplications in the human genome, Science, 297, 1003, 10.1126/science.1072047

Pentao, 1992, Charcot-Marie-Tooth type 1A duplication appears to arise from recombination at repeat sequences flanking the 1.5 Mb monomer unit, Nat. Genet., 2, 292, 10.1038/ng1292-292

Reiter, 1997, The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs, Hum. Mol. Genet., 6, 1595, 10.1093/hmg/6.9.1595

Reiter, 1998, Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients, Am. J. Hum. Genet., 62, 1023, 10.1086/301827

Valentijn, 1992, Identical point mutations of PMP-22 in Trembler-J mouse and Charcot-Marie-Tooth disease type 1A, Nat. Genet., 2, 288, 10.1038/ng1292-288

Patel, 1992, The gene for the peripheral myelin protein PMP-22 is a candidate for Charcot-Marie-Tooth disease type 1A, Nat. Genet., 1, 159, 10.1038/ng0692-159

Timmerman, 1992, The peripheral myelin protein gene PMP-22 is contained within the Charcot-Marie-Tooth disease type 1A duplication, Nat. Genet., 1, 171, 10.1038/ng0692-171

Valentijn, 1992, The peripheral myelin gene PMP-22/GAS-3 is duplicated in Charcot-Marie-Tooth disease type 1A, Nat. Genet., 1, 166, 10.1038/ng0692-166

Roa, 1993, Charcot-Marie-Tooth disease type 1A. Association with a spontaneous point mutation in the PMP22 gene, N. Engl. J. Med., 329, 96, 10.1056/NEJM199307083290205

Zhang, 2009, The DNA replication FoSTeS/MMBIR mechanism can generate human genomic, genic, and exonic complex rearrangements, Nat. Genet., 41, 849, 10.1038/ng.399

Palau, 1993, Origin of the de novo duplication in Charcot-Marie-Tooth disease type 1A: Unequal nonsister chromatid exchange during spermatogenesis, Hum. Mol. Genet., 2, 2031, 10.1093/hmg/2.12.2031

Timmerman, 1997, Detection of the CMT1A/HNPP recombination hotspot in unrelated patients of European descent, J. Med. Genet., 34, 43, 10.1136/jmg.34.1.43

Seeman, 2000, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP): reliable detection of the CMT1A duplication and HNPP deletion using 8 microsatellite markers in 2 multiplex PCRs, Int. J. Mol. Med., 6, 421

Weterman, 2010, Copy number variation upstream of PMP22 in Charcot-Marie-Tooth disease, Eur. J. Hum. Genet., 18, 421, 10.1038/ejhg.2009.186

Lee, 2007, A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders, Cell, 131, 1235, 10.1016/j.cell.2007.11.037

Bi, 2009, Increased LIS1 expression affects human and mouse brain development, Nat. Genet., 41, 168, 10.1038/ng.302

Stankiewicz, 2003, Genome architecture catalyzes nonrecurrent chromosomal rearrangements, Am. J. Hum. Genet., 72, 1101, 10.1086/374385

Chen, 2005, Meta-analysis of gross insertions causing human genetic disease: Novel mutational mechanisms and the role of replication slippage, Hum. Mutat., 25, 207, 10.1002/humu.20133

Chen, 2005, Complex gene rearrangements caused by serial replication slippage, Hum. Mutat., 26, 125, 10.1002/humu.20202

Lieber, 2010, The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway, Annu. Rev. Biochem., 10.1146/annurev.biochem.052308.093131

Kidd, 2008, Mapping and sequencing of structural variation from eight human genomes, Nature, 453, 56, 10.1038/nature06862

Kang, 2010, Insertional translocation detected using FISH confirmation of array-comparative genomic hybridization (aCGH) results, Am. J. Med. Genet. A., 152A, 1111, 10.1002/ajmg.a.33278

Stankiewicz, 2010, Challenges in clinical interpretation of microduplications detected by array CGH analysis, Am. J. Med. Genet. A., 152A, 1089, 10.1002/ajmg.a.33216

Roy, 2004, Tektin3 encodes an evolutionarily conserved putative testicular microtubules-related protein expressed preferentially in male germ cells, Mol. Reprod. Dev., 67, 295, 10.1002/mrd.20025

Lee, 2006, Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect, Ann. Neurol., 59, 398, 10.1002/ana.20732

Kleinjan, 2005, Long-range control of gene expression: emerging mechanisms and disruption in disease, Am. J. Hum. Genet., 76, 8, 10.1086/426833

Carvalho, 2009, Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching, Hum. Mol. Genet., 18, 2188, 10.1093/hmg/ddp151

Lieber, 2008, The mechanism of human nonhomologous DNA end joining, J. Biol. Chem., 283, 1, 10.1074/jbc.R700039200

Hastings, 2009, A microhomology-mediated break-induced replication model for the origin of human copy number variation, PLoS Genet., 5, e1000327, 10.1371/journal.pgen.1000327

Payen, 2008, Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms, PLoS Genet., 4, e1000175, 10.1371/journal.pgen.1000175

Zhang, 2009, Complex human chromosomal and genomic rearrangements, Trends Genet., 25, 298, 10.1016/j.tig.2009.05.005

Hastings, 2009, Mechanisms of change in gene copy number, Nat. Rev. Genet., 10, 551, 10.1038/nrg2593

Bailey, 2003, An Alu transposition model for the origin and expansion of human segmental duplications, Am. J. Hum. Genet., 73, 823, 10.1086/378594

Sen, 2006, Human genomic deletions mediated by recombination between Alu elements, Am. J. Hum. Genet., 79, 41, 10.1086/504600

Gajecka, 2008, Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13), Genome Res., 18, 1733, 10.1101/gr.077453.108

Elliott, 2005, Chromosomal translocation mechanisms at intronic alu elements in mammalian cells, Mol. Cell, 17, 885, 10.1016/j.molcel.2005.02.028

Vissers, 2009, Rare pathogenic microdeletions and tandem duplications are microhomology-mediated and stimulated by local genomic architecture, Hum. Mol. Genet., 18, 3579, 10.1093/hmg/ddp306

Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062

Inoue, 2001, The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes, Genome Res., 11, 1018, 10.1101/gr.180401

Stankiewicz, 2004, Serial segmental duplications during primate evolution result in complex human genome architecture, Genome Res., 14, 2209, 10.1101/gr.2746604

Wells, 2007, Non-B DNA conformations, mutagenesis and disease, Trends Biochem. Sci., 32, 271, 10.1016/j.tibs.2007.04.003

Argueso, 2008, Double-strand breaks associated with repetitive DNA can reshape the genome, Proc. Natl. Acad. Sci. USA, 105, 11845, 10.1073/pnas.0804529105

Voineagu, 2008, Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins, Proc. Natl. Acad. Sci. USA, 105, 9936, 10.1073/pnas.0804510105

Manolio, 2009, Finding the missing heritability of complex diseases, Nature, 461, 747, 10.1038/nature08494