Sequencing of a Patient with Balanced Chromosome Abnormalities and Neurodevelopmental Disease Identifies Disruption of Multiple High Risk Loci by Structural Variation
Balanced chromosome abnormalities (BCAs) occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD) and complex de novo BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (LINC00299, NUP205, PSMD14) that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor ZNF804A as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of ZNF804A in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception.
References
[1]
Currall BB, Chiang C, Talkowski ME, Morton CC (2013) Mechanisms for Structural Variation in the Human Genome. Curr Genet Med Rep 1: 81–90. doi: 10.1007/s40142-013-0012-8
[2]
Ravel C, Berthaut I, Bresson JL, Siffroi JP (2006) Genetics Commission of the French Federation of CECOS (2006) Prevalence of chromosomal abnormalities in phenotypically normal and fertile adult males: large-scale survey of over 10,000 sperm donor karyotypes. Hum Reprod 21: 1484–1489. doi: 10.1093/humrep/del024
[3]
Gardner RJM, Sutherland GR, Shaffer LG (2012) Chromosome abnormalities and genetic counseling. 4th ed. (New York: Oxford University Press).
[4]
Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, et al. (2008) Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82: 477–488. doi: 10.1016/j.ajhg.2007.12.009
[5]
Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, et al. (2012) Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell 149: 525–537. doi: 10.1016/j.cell.2012.03.028
[6]
Talkowski ME, Ordulu Z, Pillalamarri V, Benson CB, Blumenthal I, et al. (2012) Clinical diagnosis by whole-genome sequencing of a prenatal sample. N Engl J Med 367: 2226–2232. doi: 10.1056/nejmoa1208594
[7]
Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420–426. doi: 10.1126/science.1149504
[8]
Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, et al. (2008) Mapping translocation breakpoints by next-generation sequencing. Genome Res 18: 1143–1149. doi: 10.1101/gr.076166.108
[9]
Talkowski ME, Ernst C, Heilbut A, Chiang C, Hanscom C, et al. (2011) Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research. Am J Hum Genet 88: 469–481. doi: 10.1016/j.ajhg.2011.03.013
[10]
Kloosterman WP, Guryev V, van Roosmalen M, Duran KJ, de Bruijn E, et al. (2011) Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet 20: 1916–1924. doi: 10.1093/hmg/ddr073
[11]
Talkowski ME, Maussion G, Crapper L, Rosenfeld JA, Blumenthal I, et al. (2012) Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities. Am J Hum Genet 91: 1128–1134. doi: 10.1016/j.ajhg.2012.10.016
[12]
Burrage LC, Eble TN, Hixson PM, Roney EK, Cheung SW, et al. (2013) A mosaic 2q24.2 deletion narrows the critical region to a 0.4 Mb interval that includes TBR1, TANK, and PSMD14. Am J Med Genet A 161: 841–844. doi: 10.1002/ajmg.a.35751
[13]
Byrne A, McLaren RP, Mason P, Chai L, Dufault MR, et al. (2010) Knockdown of human deubiquitinase PSMD14 induces cell cycle arrest and senescence. Exp Cell Res 316: 258–271. doi: 10.1016/j.yexcr.2009.08.018
[14]
Tsai NP, Wilkerson JR, Guo W, Maksimova MA, DeMartino GN, et al. (2012) Multiple autism-linked genes mediate synapse elimination via proteasomal degradation of a synaptic scaffold PSD-95. Cell 151: 1581–1594. doi: 10.1016/j.cell.2012.11.040
[15]
Galy V, Mattaj IW, Askjaer P (2003) Caenorhabditis elegans nucleoporins Nup93 and Nup205 determine the limit of nuclear pore complex size exclusion in vivo. Mol Biol Cell 14: 5104–5115. doi: 10.1091/mbc.e03-04-0237
[16]
Hachet V, Busso C, Toya M, Sugimoto A, Askjaer P, et al. (2012) The nucleoporin Nup205/NPP-3 is lost near centrosomes at mitotic onset and can modulate the timing of this process in Caenorhabditis elegans embryos. Mol Biol Cell 23: 3111–3121. doi: 10.1091/mbc.e12-03-0204
[17]
Stevenson J, Richman N (1976) The prevalence of language delay in a population of three-year-old children and its association with general retardation. Dev Med Child Neurol 18: 431–441. doi: 10.1111/j.1469-8749.1976.tb03682.x
[18]
Al-Holou WN, Yew AY, Boomsaad ZE, Garton HJ, Muraszko KM, et al. (2010) Prevalence and natural history of arachnoid cysts in children. J Neurosurg Pediatr 5: 578–585. doi: 10.3171/2010.2.peds09464
[19]
Cocchella A, Malacarne M, Forzano F, Marciano C, Pierluigi M, et al. (2010) The refinement of the critical region for the 2q31.2q32.3 deletion syndrome indicates candidate genes for mental retardation and speech impairment. Am J Med Genet B Neuropsychiatr Genet 153B: 1342–1346. doi: 10.1002/ajmg.b.31107
[20]
Lim J, Hao T, Shaw C, Patel AJ, Szabó G, et al. (2006) A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125: 801–814. doi: 10.1016/j.cell.2006.03.032
[21]
Girgenti MJ, LoTurco JJ, Maher BJ (2012) ZNF804a regulates expression of the schizophrenia-associated genes PRSS16, COMT, PDE4B, and DRD2. PLoS One 7: e32404. doi: 10.1371/journal.pone.0032404
[22]
Hill MJ, Jeffries AR, Dobson RJ, Price J, Bray NJ (2012) Knockdown of the psychosis susceptibility gene ZNF804A alters expression of genes involved in cell adhesion. Hum Mol Genet 21: 1018–1024. doi: 10.1093/hmg/ddr532
[23]
O’Donovan MC, Craddock N, Norton N, Williams H, Peirce T, et al. (2008) Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nat Genet 40: 1053–1055. doi: 10.1038/ng.201
[24]
Steinberg S, Mors O, B？rglum AD, Gustafsson O, Werge T, et al. (2011) Expanding the range of ZNF804A variants conferring risk of psychosis. Mol Psychiatry 16: 59–66. doi: 10.1038/mp.2009.149
[25]
Williams HJ, Norton N, Dwyer S, Moskvina V, Nikolov I, et al. (2011) Fine mapping of ZNF804A and genome-wide significant evidence for its involvement in schizophrenia and bipolar disorder. Mol Psychiatry 16: 429–441. doi: 10.1038/mp.2010.36
[26]
Riley B, Thiselton D, Maher BS, Bigdeli T, Wormley B (2010) Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample. Mol Psychiatry 15: 29–37. doi: 10.1038/mp.2009.109
[27]
Walter H, Schnell K, Erk S, Arnold C, Kirsch P, et al. (2011) Effects of a genome-wide supported psychosis risk variant on neural activation during a theory-of-mind task. Mol Psychiatry 16: 462–470. doi: 10.1038/mp.2010.18
[28]
Huang N, Lee I, Marcotte EM, Hurles ME (2010) Characterising and predicting haploinsufficiency in the human genome. PLoS Genet 6: e1001154. doi: 10.1371/journal.pgen.1001154
[29]
Esslinger C, Walter H, Kirsch P, Erk S, Schnell K, et al. (2009) Neural mechanisms of a genome-wide supported psychosis variant. Science 324: 605. doi: 10.1126/science.1167768
[30]
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, et al. (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335: 823–828. doi: 10.1126/science.1215040
[31]
Edmondson AC, Braund PS, Stylianou IM, Khera AV, Nelson CP, et al. (2011) Dense genotyping of candidate gene loci identifies variants associated with high-density lipoprotein cholesterol. Circ Cardiovasc Genet 4: 145–155. doi: 10.1161/circgenetics.110.957563
[32]
Ng BL, Carter NP (2006) Factors Affecting Flow Karyotype Resolution. Cytometry Part A 69: 1028–1036. doi: 10.1002/cyto.a.20330
[33]
Gribble SM, Ng BL, Prigmore E, Fitzgerald T, Carter NP (2009) Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays. Nat Protocols 4: 1722–1736. doi: 10.1038/nprot.2009.183
