BACKGROUND: We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. METHODS: Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis. RESULTS: High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches). CONCLUSIONS: These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.

Clinical and Molecular Genetics Unit Institute of Child Health London UK

Department of Biological Sciences University of Delaware Newark DE USA

Department of Molecular and Human Genetics Baylor College of Medicine One Baylor Plaza Room 604B Houston TX USA

Department of Pediatrics Baylor College of Medicine Houston TX USA

DNA Laboratory Department of Pediatric Neurology 2nd Faculty of Medicine Charles University Prague and University Hospital Motol 150 06 Prague Czech Republic

Graduate Program in Diagnostic Genetics School of Health Professions The University of Texas MD Anderson Cancer Center Houston TX USA

Human Genome Sequencing Center Baylor College of Medicine Houston TX USA

Jefferson Medical College Thomas Jefferson University Philadelphia PA USA

Nemours Biomedical Research Nemours Alfred 1 DuPont Hospital for Children 1600 Rockland Road RC1 Wilmington DE USA

Present address Department of Genetics and Genome Sciences University of Connecticut Health Center and the Jackson Laboratory for Genomic Medicine Farmington CT USA

Present address Diagnostic Genomics PathWest Laboratory Medicine Perth WA Australia

Present address Graduate School of Biomedical Sciences The University of Texas MD Anderson Cancer Center UTHealth Houston TX USA

School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Shatin NT Hong Kong SAR

School of Biomedical Sciences University of Western Australia Perth WA Australia

Texas Children's Hospital Houston TX USA

Zobrazit více v PubMed

Lupski JR. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 1998;14:417–422. doi: 10.1016/S0168-9525(98)01555-8. PubMed DOI

Stankiewicz P, Lupski JR. Genome architecture, rearrangements and genomic disorders. Trends Genet. 2002;18:74–82. doi: 10.1016/S0168-9525(02)02592-1. PubMed DOI

Carvalho CM, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet. 2016;17:224–238. doi: 10.1038/nrg.2015.25. PubMed DOI PMC

Ellis D, Malcolm S. Proteolipid protein gene dosage effect in Pelizaeus-Merzbacher disease. Nat Genet. 1994;6:333–334. doi: 10.1038/ng0494-333. PubMed DOI

Inoue Ken. PLP1-related inherited dysmyelinating disorders: Pelizaeus-Merzbacher disease and spastic paraplegia type 2. Neurogenetics. 2004;6(1):1–16. doi: 10.1007/s10048-004-0207-y. PubMed DOI

Cremers FP, Pfeiffer RA, van de Pol TJ, Hofker MH, Kruse TA, Wieringa B, Ropers HH. An interstitial duplication of the X chromosome in a male allows physical fine mapping of probes from the Xq13-q22 region. Hum Genet. 1987;77:23–27. doi: 10.1007/BF00284707. PubMed DOI

Raskind WH, Williams CA, Hudson LD, Bird TD. Complete deletion of the proteolipid protein gene (PLP) in a family with X-linked Pelizaeus-Merzbacher disease. Am J Hum Genet. 1991;49:1355–60. PubMed PMC

Wang PJ, Hwu WL, Lee WT, Wang TR, Shen YZ. Duplication of proteolipid protein gene: a possible major cause of Pelizaeus-Merzbacher disease. Pediatr Neurol. 1997;17:125–128. doi: 10.1016/S0887-8994(97)00088-X. PubMed DOI

Lee JA, Lupski JR. Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron. 2006;52:103–121. doi: 10.1016/j.neuron.2006.09.027. PubMed DOI

Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009;10:451–481. doi: 10.1146/annurev.genom.9.081307.164217. PubMed DOI PMC

Hobson GM, Garbern JY. Pelizaeus-Merzbacher disease, Pelizaeus-Merzbacher-like disease 1, and related hypomyelinating disorders. Semin Neurol. 2012;32:62–67. doi: 10.1055/s-0032-1306388. PubMed DOI

Sistermans EA, de Coo RF, De Wijs IJ, Van Oost BA. Duplication of the proteolipid protein gene is the major cause of Pelizaeus-Merzbacher disease. Neurology. 1998;50:1749–1754. doi: 10.1212/WNL.50.6.1749. PubMed DOI

Garbern J, Cambi F, Shy M, Kamholz J. The molecular pathogenesis of Pelizaeus-Merzbacher disease. Arch Neurol. 1999;56:1210–1214. doi: 10.1001/archneur.56.10.1210. PubMed DOI

Woodward KJ, Cundall M, Sperle K, Sistermans EA, Ross M, Howell G, Gribble SM, Burford DC, Carter NP, Hobson DL, et al. Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination. Am J Hum Genet. 2005;77:966–987. doi: 10.1086/498048. PubMed DOI PMC

Lee Jennifer A., Inoue Ken, Cheung Sau W., Shaw Chad A., Stankiewicz Pawel, Lupski James R. Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease. Human Molecular Genetics. 2006;15(14):2250–2265. doi: 10.1093/hmg/ddl150. PubMed DOI

Zhang F, Seeman P, Liu P, Weterman MA, Gonzaga-Jauregui C, Towne CF, Batish SD, De Vriendt E, De Jonghe P, Rautenstrauss B, et al. 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. doi: 10.1016/j.ajhg.2010.05.001. PubMed DOI PMC

Lupski JR. Structural variation mutagenesis of the human genome: impact on disease and evolution. Environ Mol Mutagen. 2015;56:419–436. doi: 10.1002/em.21943. PubMed DOI PMC

Lupski JR. 2018 Victor A. McKusick Leadership Award: molecular mechanisms for genomic and chromosomal rearrangements. Am J Hum Genet. 2019;104:391–406. PubMed PMC

Zhang F, Carvalho CM, Lupski JR. Complex human chromosomal and genomic rearrangements. Trends Genet. 2009;25:298–307. doi: 10.1016/j.tig.2009.05.005. PubMed DOI PMC

Zhang L, Wang J, Zhang C, Li D, Carvalho CMB, Ji H, Xiao J, Wu Y, Zhou W, Wang H, et al. Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders. Hum Mol Genet. 2017;26:1927–1941. doi: 10.1093/hmg/ddx102. PubMed DOI PMC

Liu P, Carvalho CM, Hastings PJ, Lupski JR. Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev. 2012;22:211–220. doi: 10.1016/j.gde.2012.02.012. PubMed DOI PMC

Hastings PJ, Ira G, Lupski JR. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 2009;5:e1000327. doi: 10.1371/journal.pgen.1000327. PubMed DOI PMC

Lee JA, Carvalho CM, Lupski JR. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell. 2007;131:1235–1247. doi: 10.1016/j.cell.2007.11.037. PubMed DOI

Shimojima Keiko, Mano Toshiyuki, Kashiwagi Mitsuru, Tanabe Takuya, Sugawara Midori, Okamoto Nobuhiko, Arai Hiroshi, Yamamoto Toshiyuki. Pelizaeus-Merzbacher disease caused by a duplication-inverted triplication-duplication in chromosomal segments including the PLP1 region. European Journal of Medical Genetics. 2012;55(6-7):400–403. doi: 10.1016/j.ejmg.2012.02.013. PubMed DOI

Wolf N. I. Three or more copies of the proteolipid protein gene PLP1 cause severe Pelizaeus-Merzbacher disease. Brain. 2005;128(4):743–751. doi: 10.1093/brain/awh409. PubMed DOI

Carvalho CM, Ramocki MB, Pehlivan D, Franco LM, Gonzaga-Jauregui C, Fang P, McCall A, Pivnick EK, Hines-Dowell S, Seaver LH, et al. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nat Genet. 2011;43:1074–1081. doi: 10.1038/ng.944. PubMed DOI PMC

Waldman AS, Liskay RM. Dependence of intrachromosomal recombination in mammalian cells on uninterrupted homology. Mol Cell Biol. 1988;8:5350–5357. doi: 10.1128/MCB.8.12.5350. PubMed DOI PMC

Reiter LT, Hastings PJ, Nelis E, De Jonghe P, Van Broeckhoven C, Lupski JR. Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients. Am J Hum Genet. 1998;62:1023–1033. doi: 10.1086/301827. PubMed DOI PMC

Liu P, Yuan B, Carvalho CMB, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, et al. An organismal CNV mutator phenotype restricted to early human development. Cell. 2017;168:830–842. doi: 10.1016/j.cell.2017.01.037. PubMed DOI PMC

Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, et al. Megabase length hypermutation accompanies human structural variation at 17p11.2. Cell. 2019;176:1310–1324. doi: 10.1016/j.cell.2019.01.045. PubMed DOI PMC

Beck Christine R., Carvalho Claudia M. B., Banser Linda, Gambin Tomasz, Stubbolo Danielle, Yuan Bo, Sperle Karen, McCahan Suzanne M., Henneke Marco, Seeman Pavel, Garbern James Y., Hobson Grace M., Lupski James R. Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication. PLOS Genetics. 2015;11(3):e1005050. doi: 10.1371/journal.pgen.1005050. PubMed DOI PMC

Dittwald P, Gambin T, Gonzaga-Jauregui C, Carvalho CM, Lupski JR, Stankiewicz P, Gambin A. Inverted low-copy repeats and genome instability--a genome-wide analysis. Hum Mutat. 2013;34:210–220. doi: 10.1002/humu.22217. PubMed DOI PMC

Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. Nucleic Acids Res. 2015;43:2188–2198. doi: 10.1093/nar/gku1394. PubMed DOI PMC

Bilir B, Yapici Z, Yalcinkaya C, Baris I, Carvalho CMB, Bartnik M, Ozes B, Eraksoy M, Lupski JR, Battaloglu E. High frequency ofGJA12/GJC2mutations in Turkish patients with Pelizaeus-Merzbacher disease. Clinical Genetics. 2013;83(1):66–72. doi: 10.1111/j.1399-0004.2012.01846.x. PubMed DOI PMC

Carvalho CM, Bartnik M, Pehlivan D, Fang P, Shen J, Lupski JR. Evidence for disease penetrance relating to CNV size: Pelizaeus-Merzbacher disease and manifesting carriers with a familial 11 Mb duplication at Xq22. Clin Genet. 2012;81:532–541. doi: 10.1111/j.1399-0004.2011.01716.x. PubMed DOI PMC

Ou Z, Kang SH, Shaw CA, Carmack CE, White LD, Patel A, Beaudet AL, Cheung SW, Chinault AC. Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses. Genet Med. 2008;10:278–289. doi: 10.1097/GIM.0b013e31816b4420. PubMed DOI PMC

Gu Shen, Yuan Bo, Campbell Ian M., Beck Christine R., Carvalho Claudia M.B., Nagamani Sandesh C.S., Erez Ayelet, Patel Ankita, Bacino Carlos A., Shaw Chad A., Stankiewicz Paweł, Cheung Sau Wai, Bi Weimin, Lupski James R. Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3. Human Molecular Genetics. 2015;24(14):4061–4077. doi: 10.1093/hmg/ddv146. PubMed DOI PMC

Woodward K, Kendall E, Vetrie D, Malcolm S. Pelizaeus-Merzbacher disease: identification of Xq22 proteolipid-protein duplications and characterization of breakpoints by interphase FISH. Am J Hum Genet. 1998;63:207–217. doi: 10.1086/301933. PubMed DOI PMC

Team RC . R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2013.

Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magrina MA, Bacino CA, Lalani SR, Breman AM, Smith JL, et al. Mechanisms for complex chromosomal insertions. PLoS Genet. 2016;12:e1006446. doi: 10.1371/journal.pgen.1006446. PubMed DOI PMC

Yatsenko SA, Hixson P, Roney EK, Scott DA, Schaaf CP, Ng YT, Palmer R, Fisher RB, Patel A, Cheung SW, Lupski JR. Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage-fusion-bridge for telomere stabilization. Hum Genet. 2012;131:1895–1910. doi: 10.1007/s00439-012-1216-9. PubMed DOI PMC

Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, et al. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell. 2011;146:889–903. doi: 10.1016/j.cell.2011.07.042. PubMed DOI PMC

Boone Philip M, Liu Pengfei, Zhang Feng, Carvalho Claudia M B, Towne Charles F, Batish Sat Dev, Lupski James R. Alu-specific microhomology-mediated deletion of the final exon of SPAST in three unrelated subjects with hereditary spastic paraplegia. Genetics in Medicine. 2011;13(6):582–592. doi: 10.1097/GIM.0b013e3182106775. PubMed DOI PMC

Boone Philip M., Yuan Bo, Campbell Ian M., Scull Jennifer C., Withers Marjorie A., Baggett Brett C., Beck Christine R., Shaw Christine J., Stankiewicz Pawel, Moretti Paolo, Goodwin Wendy E., Hein Nichole, Fink John K., Seong Moon-Woo, Seo Soo Hyun, Park Sung Sup, Karbassi Izabela D., Batish Sat Dev, Ordóñez-Ugalde Andrés, Quintáns Beatriz, Sobrido María-Jesús, Stemmler Susanne, Lupski James R. The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles. The American Journal of Human Genetics. 2014;95(2):143–161. doi: 10.1016/j.ajhg.2014.06.014. PubMed DOI PMC

Song Xiaofei, Beck Christine R., Du Renqian, Campbell Ian M., Coban-Akdemir Zeynep, Gu Shen, Breman Amy M., Stankiewicz Pawel, Ira Grzegorz, Shaw Chad A., Lupski James R. Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements. Genome Research. 2018;28(8):1228–1242. doi: 10.1101/gr.229401.117. PubMed DOI PMC

Genomes Project C. Abecasis GR, Auton A, Brooks LD, MA DP, Durbin RM, Handsaker RE, Kang HM, Marth GT, GA MV. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56–65. doi: 10.1038/nature11632. PubMed DOI PMC

Bonkowsky JL, Nelson C, Kingston JL, Filloux FM, Mundorff MB, Srivastava R. The burden of inherited leukodystrophies in children. Neurology. 2010;75:718–725. doi: 10.1212/WNL.0b013e3181eee46b. PubMed DOI PMC

Stankiewicz P, Lupski JR. Molecular-evolutionary mechanisms for genomic disorders. Curr Opin Genet Dev. 2002;12:312–319. doi: 10.1016/S0959-437X(02)00304-0. PubMed DOI

Stankiewicz P, Shaw CJ, Dapper JD, Wakui K, Shaffer LG, Withers M, Elizondo L, Park SS, Lupski JR. Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am J Hum Genet. 2003;72:1101–1116. doi: 10.1086/374385. PubMed DOI PMC

Carvalho Claudia M.B., Zhang Feng, Liu Pengfei, Patel Ankita, Sahoo Trilochan, Bacino Carlos A., Shaw Chad, Peacock Sandra, Pursley Amber, Tavyev Y. Jane, Ramocki Melissa B., Nawara Magdalena, Obersztyn Ewa, Vianna-Morgante Angela M., Stankiewicz Pawel, Zoghbi Huda Y., Cheung Sau Wai, Lupski James R. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Human Molecular Genetics. 2009;18(12):2188–2203. doi: 10.1093/hmg/ddp151. PubMed DOI PMC

Yuan Bo, Harel Tamar, Gu Shen, Liu Pengfei, Burglen Lydie, Chantot-Bastaraud Sandra, Gelowani Violet, Beck Christine R., Carvalho Claudia M.B., Cheung Sau Wai, Coe Andrew, Malan Valérie, Munnich Arnold, Magoulas Pilar L., Potocki Lorraine, Lupski James R. Nonrecurrent 17p11.2p12 Rearrangement Events that Result in Two Concomitant Genomic Disorders: The PMP22-RAI1 Contiguous Gene Duplication Syndrome. The American Journal of Human Genetics. 2015;97(5):691–707. doi: 10.1016/j.ajhg.2015.10.003. PubMed DOI PMC

Sakofsky CJ, Ayyar S, Deem AK, Chung WH, Ira G, Malkova A. Translesion polymerases drive microhomology-mediated break-induced replication leading to complex chromosomal rearrangements. Mol Cell. 2015;60:860–872. doi: 10.1016/j.molcel.2015.10.041. PubMed DOI PMC

Carvalho CM, Pfundt R, King DA, Lindsay SJ, Zuccherato LW, Macville MV, Liu P, Johnson D, Stankiewicz P, Brown CW, et al. Absence of heterozygosity due to template switching during replicative rearrangements. Am J Hum Genet. 2015;96:555–564. doi: 10.1016/j.ajhg.2015.01.021. PubMed DOI PMC

del Gaudio Daniela, Fang Ping, Scaglia Fernando, Ward Patricia A, Craigen William J, Glaze Daniel G, Neul Jeffrey L, Patel Ankita, Lee Jennifer A, Irons Mira, Berry Susan A, Pursley Amber A, Grebe Theresa A, Freedenberg Debra, Martin Rick A, Hsich Gary E, Khera Jena R, Friedman Neil R, Zoghbi Huda Y, Eng Christine M, Lupski James R, Beaudet Arthur L, Cheung Sau Wai, Roa Benjamin B. Increased MECP2 gene copy number as the result of genomic duplication in neurodevelopmentally delayed males. Genetics in Medicine. 2006;8(12):784–792. doi: 10.1097/01.gim.0000250502.28516.3c. PubMed DOI

Edgar R. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Research. 2002;30(1):207–210. doi: 10.1093/nar/30.1.207. PubMed DOI PMC