Abstract
When a known microimbalance affecting multiple genes is detected in a patient with syndromic intellectual disability, it is usually presumed causative for all observed features. Whole exome sequencing (WES) allows questioning this assumption. In this study of three families with children affected by unexplained syndromic intellectual disability, genome-wide copy number and subsequent analyses revealed a de novo maternal 1.1 Mb microdeletion in the 14q32 imprinted region causing a paternal UPD(14)-like phenotype, and two inherited 22q11.21 microduplications of 2.5 or 2.8 Mb. In patient 1 carrying the 14q32 microdeletion, tall stature and renal malformation were unexplained by paternal UPD(14), and there was no altered DLK1 expression or unexpected methylation status. By WES and filtering with a mining tool, a novel FBN1 missense variant was found in patient 1 and his mother, who both showed clinical features of Marfan syndrome by thorough anthropometric assessment, and a novel EYA1 missense variant as a probable cause of the renal malformation in the patient. In patient 2 with the 22q11.21 microduplication syndrome, skin hypo- and hyperpigmentation and two malignancies were only partially explained. By WES, compound heterozygous BLM stop founder mutations were detected causing Bloom syndrome. In male patient 3 carrying a 22q11.21 microduplication inherited from his unaffected father, WES identified a novel missense variant in the OPHN1 X-linked intellectual disability gene inherited from the unaffected mother as a possible additional cause for developmental delay. Thus, WES seems warranted in patients carrying microdeletions or microduplications, who have unexplained clinical features or microimbalances inherited from an unaffected parent.
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Abdelhak S, Kalatzis V, Heilig R, Compain S, Samson D, Vincent C, Weil D, Cruaud C, Sahly I, Leibovici M, Bitner-Glindzicz M, Francis M, Lacombe D, Vigneron J, Charachon R, Boven K, Bedbeder P, Van Regemorter N, Weissenbach J, Petit C (1997) A human homologue of the Drosophila eyes absent gene underlies branchio-oto-renal (BOR) syndrome and identifies a novel gene family. Nat Genet 15(2):157–164
Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12(11):745–755
Bell DW, Varley JM, Szydlo TE, Kang DH, Wahrer DC, Shannon KE, Lubratovich M, Verselis SJ, Isselbacher KJ, Fraumeni JF, Birch JM, Li FP, Garber JE, Haber DA (1999) Heterozygous germ line hCHK2 mutations in Li-Fraumeni syndrome. Science 286(5449):2528–2531
Bergmann C, Zerres K, Senderek J, Rudnik-Schoneborn S, Eggermann T, Hausler M, Mull M, Ramaekers VT (2003) Oligophrenin 1 (OPHN1) gene mutation causes syndromic X-linked mental retardation with epilepsy, rostral ventricular enlargement and cerebellar hypoplasia. Brain 126:1537–1544
Billuart P, Bienvenu T, Ronce N, des Portes V, Vinet MC, Zemni R, Crollius HR, Carrie A, Fauchereau F, Cherry M, Briault S, Hamel B, Fryns J-P, Beldjord C, Kahn A, Moraine C, Chelly J (1998) Oligophrenin-1 encodes a rhoGAP protein involved in X-linked mental retardation. Nature 392:923–926
Bolar N, Van Laer L, Loeys BL (2012) Marfan syndrome: from gene to therapy. Curr Opin Pediatr 24(4):498–504
Chang VY, Quintero-Rivera F, Baldwin EE, Woo K, Martinez-Agosto JA, Fu C, Gomperts BN (2011) B-acute lymphoblastic leukemia and cystinuria in a patient with duplication 22q11.21 detected by chromosomal microarray analysis. Pediatr Blood Cancer 56(3):470–473
Cybulski C, Górski B, Huzarski T, Masojć B, Mierzejewski M, Debniak T, Teodorczyk U, Byrski T, Gronwald J, Matyjasik J, Zlowocka E, Lenner M, Grabowska E, Nej K, Castaneda J, Medrek K, Szymańska A, Szymańska J, Kurzawski G, Suchy J, Oszurek O, Witek A, Narod SA, Lubiński J (2004) CHEK2 is a multiorgan cancer susceptibility gene. Am J Hum Genet 75(6):1131–1135
de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen C, del Rosario M, Hoischen A, Scheffer H, de Vries BB, Brunner HG, Veltman JA, Vissers LE (2012) Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 367(20):1921–1929
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5):491–498
Desrichard A, Bidet Y, Uhrhammer N, Bignon YJ (2011) CHEK2 contribution to hereditary breast cancer in non-BRCA families. Breast Cancer Res 13(6):R119
Dietz HC, Cutting GR, Pyeritz RE, Maslen CL, Sakai LY, Corson GM, Puffenberger EG, Hamosh A, Nanthakumar EJ, Curristin SM, Stetten G, Meyers DA, Francomano CA (1991) Marfan syndrome caused by a recurrent de novo missense mutation in the fibrillin gene. Nature 352:337–339
El-Maarri O (2004) SIRPH analysis: SNuPE with IP-RP-HPLC for quantitative measurements of DNA methylation at specific CpG sites. Methods Mol Biol 287:195–205
Engels H, Brockschmidt A, Hoischen A, Landwehr C, Bosse K, Walldorf C, Toedt G, Radlwimmer B, Propping P, Lichter P, Weber RG (2007) DNA microarray analysis identifies candidate regions and genes in unexplained mental retardation. Neurology 68(10):743–750
Ensenauer RE, Adeyinka A, Flynn HC, Michels VV, Lindor NM, Dawson DB, Thorland EC, Lorentz CP, Goldstein JL, McDonald MT, Smith WE, Simon-Fayard E, Alexander AA, Kulharya AS, Ketterling RP, Clark RD, Jalal SM (2003) Microduplication 22q11.2, an emerging syndrome: clinical, cytogenetic, and molecular analysis of thirteen patients. Am J Hum Genet 73(5):1027–1040
Faivre L, Masurel-Paulet A, Collod-Béroud G, Callewaert BL, Child AH, Stheneur C, Binquet C, Gautier E, Chevallier B, Huet F, Loeys BL, Arbustini E, Mayer K, Arslan-Kirchner M, Kiotsekoglou A, Comeglio P, Grasso M, Halliday DJ, Béroud C, Bonithon-Kopp C, Claustres M, Robinson PN, Adès L, De Backer J, Coucke P, Francke U, De Paepe A, Boileau C, Jondeau G (2009) Clinical and molecular study of 320 children with Marfan syndrome and related type I fibrillinopathies in a series of 1009 probands with pathogenic FBN1 mutations. Pediatrics 123(1):391–398
Fensterer H, Radlwimmer B, Sträter J, Buchholz M, Aust DE, Julié C, Radvanyi F, Nordlinger B, Belluco C, Van Cutsem E, Köhne CH, Kestler HA, Schwaenen C, Nessling M, Lutz MP, Lichter P, Gress TM, EORTC Gastrointestinal (GI) Group (2007) Matrix-comparative genomic hybridization from multicenter formalin-fixed paraffin-embedded colorectal cancer tissue blocks. BMC Cancer 7:58
Frisancho AR (2008) Anthropometric standards. An interactive nutritional reference of body size and body composition for children and adults. The University of Michigan Press, Ann Arbor
German J (1997) Bloom’s syndrome. XX. The first 100 cancers. Cancer Genet Cytogenet 93(1):100–106
German J, Sanz MM, Ciocci S, Ye TZ, Ellis NA (2007) Syndrome-causing mutations of the BLM gene in persons in the Bloom’s Syndrome Registry. Hum Mutat 28(8):743–753
Girirajan S, Rosenfeld JA, Coe BP, Parikh S, Friedman N, Goldstein A, Filipink RA, McConnell JS, Angle B, Meschino WS, Nezarati MM, Asamoah A, Jackson KE, Gowans GC, Martin JA, Carmany EP, Stockton DW, Schnur RE, Penney LS, Martin DM, Raskin S, Leppig K, Thiese H, Smith R, Aberg E, Niyazov DM, Escobar LF, El-Khechen D, Johnson KD, Lebel RR, Siefkas K, Ball S, Shur N, McGuire M, Brasington CK, Spence JE, Martin LS, Clericuzio C, Ballif BC, Shaffer LG, Eichler EE (2012) Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med 367(14):1321–1331
Hoffmann K, Heller R (2011) Uniparental disomies 7 and 14. Best Pract Res Clin Endocrinol Metab 25(1):77–100
Kagami M, Sekita Y, Nishimura G, Irie M, Kato F, Okada M, Yamamori S, Kishimoto H, Nakayama M, Tanaka Y, Matsuoka K, Takahashi T, Noguchi M, Tanaka Y, Masumoto K, Utsunomiya T, Kouzan H, Komatsu Y, Ohashi H, Kurosawa K, Kosaki K, Ferguson-Smith AC, Ishino F, Ogata T (2008) Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. Nat Genet 40(2):237–242
Kaufman AS, Kaufman N (1983) Kaufman assessment battery for children, manual. American Guidance Service, Circle Pines
Krug P, Morinière V, Marlin S, Koubi V, Gabriel HD, Colin E, Bonneau D, Salomon R, Antignac C, Heidet L (2011) Mutation screening of the EYA1, SIX1, and SIX5 genes in a large cohort of patients harboring branchio-oto-renal syndrome calls into question the pathogenic role of SIX5 mutations. Hum Mutat 32(2):183–190
Le Calvez-Kelm F, Lesueur F, Damiola F, Vallée M, Voegele C, Babikyan D, Durand G, Forey N, McKay-Chopin S, Robinot N, Nguyen-Dumont T, Thomas A, Byrnes GB; Breast Cancer Family Registry, Hopper JL, Southey MC, Andrulis IL, John EM, Tavtigian SV (2011) Rare, evolutionarily unlikely missense substitutions in CHEK2 contribute to breast cancer susceptibility: results from a breast cancer family registry case-control mutation-screening study. Breast Cancer Res 13(1):R6
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25(4):402–408
Loeys BL, Dietz HC, Braverman AC, Callewaert BL, De Backer J, Devereux RB, Hilhorst-Hofstee Y, Jondeau G, Faivre L, Milewicz DM, Pyeritz RE, Sponseller PD, Wordsworth P, De Paepe AM (2010) The revised Ghent nosology for the Marfan syndrome. J Med Genet 47(7):476–485
Lücke T, Franke D, Clewing JM, Boerkoel CF, Ehrich JH, Das AM, Zivicnjak M (2006) Schimke versus non-Schimke chronic kidney disease: an anthropometric approach. Pediatrics 118(2):e400–e407
Mao FJ, Sidorova JM, Lauper JM, Emond MJ, Monnat RJ (2010) The human WRN and BLM RecQ helicases differentially regulate cell proliferation and survival after chemotherapeutic DNA damage. Cancer Res 70(16):6548–6555
Marschalek R (2011) Mechanisms of leukemogenesis by MLL fusion proteins. Br J Haematol 152(2):141–154
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26(16):2069–2070
Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J (2009) Targeted capture and massively parallel sequencing of twelve human exomes. Nature 461(7261):272–276
Pacek M, Tutter AV, Kubota Y, Takisawa H, Walter JC (2006) Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication. Mol Cell 21(4):581–587
Philip N, Chabrol B, Lossi A-M, Cardoso C, Guerrini R, Dobyns WB, Raybaud C, Villard L (2003) Mutations in the oligophrenin-1 gene (OPHN1) cause X linked congenital cerebellar hypoplasia. J Med Genet 40:441–446
Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20(2):207–211
Portnoï MF (2009) Microduplication 22q11.2: a new chromosomal syndrome. Eur J Med Genet 52(2–3):88–93
Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, Dufke A, Cremer K, Hempel M, Horn D, Hoyer J, Joset P, Röpke A, Moog U, Riess A, Thiel CT, Tzschach A, Wiesener A, Wohlleber E, Zweier C, Ekici AB, Zink AM, Rump A, Meisinger C, Grallert H, Sticht H, Schenck A, Engels H, Rappold G, Schröck E, Wieacker P, Riess O, Meitinger T, Reis A, Strom TM (2012) Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380(9854):1674–1682
Robinson PN, Booms P, Katzke S, Ladewig M, Neumann L, Palz M, Pregla R, Tiecke F, Rosenberg T (2002) Mutations of FBN1 and genotype-phenotype correlations in Marfan syndrome and related fibrillinopathies. Hum Mutat 20(3):153–161
Roeb W, Higgins J, King MC (2012) Response to DNA damage of CHEK2 missense mutations in familial breast cancer. Hum Mol Genet 21(12):2738–2744
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Döhner H, Cremer T, Lichter P (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20(4):399–407
Vissers LE, de Vries BB, Veltman JA (2010a) Genomic microarrays in mental retardation: from copy number variation to gene, from research to diagnosis. J Med Genet 47(5):289–297
Vissers LE, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, van Lier B, Arts P, Wieskamp N, del Rosario M, van Bon BW, Hoischen A, de Vries BB, Brunner HG, Veltman JA (2010b) A de novo paradigm for mental retardation. Nat Genet 42(12):1109–1112
Weise A, Mrasek K, Klein E, Mulatinho M, Llerena JC Jr, Hardekopf D, Pekova S, Bhatt S, Kosyakova N, Liehr T (2012) Microdeletion and microduplication syndromes. J Histochem Cytochem 60(5):346–358
Zielinski B, Gratias S, Toedt G, Mendrzyk F, Stange DE, Radlwimmer B, Lohmann DR, Lichter P (2005) Detection of chromosomal imbalances in retinoblastoma by matrix-based comparative genomic hybridization. Genes Chromosomes Cancer 43(3):294–301
Zivicnjak M, Narancic NS, Szirovicza L, Franke D, Hrenovic J, Bisof V (2003) Gender-specific growth patterns for stature, sitting height and limbs length in Croatian children and youth (3 to 18 years of age). Coll Antropol 27:321–334
Zivicnjak M, Franke D, Zenker M, Hoyer J, Lücke T, Pape L, Ehrich JH (2009) SMARCAL1 mutations: a cause of prepubertal idiopathic steroid-resistant nephrotic syndrome. Pediatr Res 65(5):564–568
Acknowledgments
We express our gratitude to the children and their families for kindly participating in this study. We thank Gabriele Krüger and Monika Mix, Rostock, Germany, for excellent patient care; Bernhard Radlwimmer, Heidelberg, Germany, for providing large insert clone arrays; Saskia Biskup, CeGaT GmbH, Tübingen, Germany, and Daniel Swan, OGT, Begbroke, UK, for providing technical details of WES; Christian Kubisch, Ulm, Manfred Stuhrmann-Spangenberg and Mine Arslan-Kirchner, Hannover, Germany, for helpful scientific discussions. Support for this study was obtained from the Else Kröner-Fresenius-Stiftung (2010_A97). The funding organization had no role in the design or conduct of this research. The contents of this publication reflect only the authors’ views and not the views of the funding organization.
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C. F. Classen and V. Riehmer contributed equally as first authors. D. Haffner and R. G. Weber contributed equally as senior authors.
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Classen, C.F., Riehmer, V., Landwehr, C. et al. Dissecting the genotype in syndromic intellectual disability using whole exome sequencing in addition to genome-wide copy number analysis. Hum Genet 132, 825–841 (2013). https://doi.org/10.1007/s00439-013-1296-1
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DOI: https://doi.org/10.1007/s00439-013-1296-1