[en] BACKGROUND: Array-CGH is considered as the first-tier investigation used to identify copy number variations. Right now, there is no available data about the genetic etiology of patients with development delay/intellectual disability and congenital malformation in East Africa. METHODS: Array comparative genomic hybridization was performed in 50 Rwandan patients with development delay/intellectual disability and multiple congenital abnormalities, using the Agilent's 180 K microarray platform. RESULTS: Fourteen patients (28%) had a global development delay whereas 36 (72%) patients presented intellectual disability. All patients presented multiple congenital abnormalities. Clinically significant copy number variations were found in 13 patients (26%). Size of CNVs ranged from 0,9 Mb to 34 Mb. Six patients had CNVs associated with known syndromes, whereas 7 patients presented rare genomic imbalances. CONCLUSION: This study showed that CNVs are present in African population and show the importance to implement genetic testing in East-African countries.
Disciplines :
Genetics & genetic processes
Author, co-author :
Uwineza, Annette; Centre Hospitalier Universitaire de Liège - CHU > Génétique
CABERG, Jean-Hubert ; Centre Hospitalier Universitaire de Liège - CHU > Génétique
Hitayezu, Janvier
JAMAR, Mauricette ; Centre Hospitalier Universitaire de Liège - CHU > Génétique
DIDEBERG, Vinciane ; Centre Hospitalier Universitaire de Liège - CHU > Génétique
Rusingiza, Emmanuel K.
Bours, Vincent ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > GIGA-R : Génétique humaine
Mefford HC, Batshaw ML, Hoffman EP: Genomics, intellectual disability, and autism. N Engl J Med 2012,366(8):733-743.
de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen Cdel Rosario M, Hoischen A, Scheffer H, de Vries BB, Brunner HG, Veltman JA, Vissers LE: Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 2012,367(20):1921-1929.
Shevell M, Ashwal S, Donley D, Flint J, Gingold M, Hirtz D, Majnemer A, Noetzel M, Sheth RD: Practice parameter: evaluation of the child with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society. Neurology 2003,60(3):367-380.
Topper S, Ober C, Das S: Exome sequencing and the genetics of intellectual disability. Clin Genet 2011,80(2):117-126.
Menten B, Maas N, Thienpont B, Buysse K, Vandesompele J, Melotte C, de Ravel T, Van Vooren S, Balikova I, Backx L, Janssens S, De Paepe A, De Moor B, Moreau Y, Marynen P, Fryns JP, Mortier G, Devriendt K, Speleman F, Vermeesch JR: Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports. J Med Genet 2006,43(8):625-633.
Rauch A, Hoyer J, Guth S, Zweier C, Kraus C, Becker C, Zenker M, Huffmeier U, Thiel C, Ruschendorf F, Nürnberg P, Reis A, Trautmann U: Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation. Am J Med Genet A 2006,140(19):2063-2074.
Ropers HH: Genetics of early onset cognitive impairment. Annu Rev Genomics Hum Genet 2010, 11:161-187.
Durkin M: The epidemiology of developmental disabilities in low-income countries. Ment Retard Dev Disabil Res Rev 2002,8(3):206-211.
Jauhari P, Boggula R, Bhave A, Bhargava R, Singh C, Kohli N, Yadav R, Kumar R: Aetiology of intellectual disability in paediatric outpatients in Northern India. Dev Med Child Neurol 2011,53(2):167-172.
Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, et al.: Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010,86(5):749-764.
Delahaye A, Bitoun P, Drunat S, Gerard-Blanluet M, Chassaing N, Toutain A, Verloes A, Gatelais F, Legendre M, Faivre L, Passemard S, Aboura A, Kaltenbach S, Quentin S, Dupont C, Tabet AC, Amselem S, Elion J, Gressens P, Pipiras E, Benzacken B: Genomic imbalances detected by array-CGH in patients with syndromal ocular developmental anomalies. Eur J Hum Genet 2012,20(5):527-533.
Siggberg L, Ala-Mello S, Jaakkola E, Kuusinen E, Schuit R, Kohlhase J, Bohm D, Ignatius J, Knuutila S: Array CGH in molecular diagnosis of mental retardation - A study of 150 Finnish patients. Am J Med Genet A 2010,152a(6):1398-1410.
Stankiewicz P, Beaudet AL: Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr Opin Genet Dev 2007,17(3):182-192.
Koolen DA, Pfundt R, de Leeuw N, Hehir-Kwa JY, Nillesen WM, Neefs I, Scheltinga I, Sistermans E, Smeets D, Brunner HG, van Kessel AG, Veltman JA, de Vries BB: Genomic microarrays in mental retardation: a practical workflow for diagnostic applications. Hum Mutat 2009,30(3):283-292.
Iourov IY, Vorsanova SG, Kurinnaia OS, Zelenova MA, Silvanovich AP, Yurov YB: Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies. Mol Cytogenet 2012,5(1):46.
Eussen BH, Bartalini G, Bakker L, Balestri P, Di Lucca C, Van Hemel JO, Dauwerse H, van Den Ouweland AM, Ris-Stalpers C, Verhoef S, Halley DJ, Fois A: An unbalanced submicroscopic translocation t(8;16)(q24.3;p13.3)pat associated with tuberous sclerosis complex, adult polycystic kidney disease, and hypomelanosis of Ito. J Med Genet 2000,37(4):287-291.
Ewart AK, Morris CA, Atkinson D, Jin W, Sternes K, Spallone P, Stock AD, Leppert M, Keating MT: Hemizygosity at the elastin locus in a developmental disorder, Williams syndrome. Nat Genet 1993,5(1):11-16.
Frangiskakis JM, Ewart AK, Morris CA, Mervis CB, Bertrand J, Robinson BF, Klein BP, Ensing GJ, Everett LA, Green ED, Proschel C, Gutowski NJ, Noble M, Atkinson DL, Odelberg SJ, Keating MT: LIM-kinase1 hemizygosity implicated in impaired visuospatial constructive cognition. Cell 1996,86(1):59-69.
Tassabehji M, Hammond P, Karmiloff-Smith A, Thompson P, Thorgeirsson SS, Durkin ME, Popescu NC, Hutton T, Metcalfe K, Rucka A, Stewart H, Read AP, Maconochie M, Donnai D: GTF2IRD1 in craniofacial development of humans and mice. Science 2005,310(5751):1184-1187.
Somerville MJ, Mervis CB, Young EJ, Seo EJ, del Campo M, Bamforth S, Peregrine E, Loo W, Lilley M, Perez-Jurado LA, Morris CA, Scherer SW, Osborne LR: Severe expressive-language delay related to duplication of the Williams-Beuren locus. N Engl J Med 2005,353(16):1694-1701.
Chieffo C, Garvey N, Gong W, Roe B, Zhang G, Silver L, Emanuel BS, Budarf ML: Isolation and characterization of a gene from the DiGeorge chromosomal region homologous to the mouse Tbx1 gene. Genomics 1997,43(3):267-277.
Veerapandiyan A, Abdul-Rahman OA, Adam MP, Lyons MJ, Manning M, Coleman K, Kobrynski L, Taneja D, Schoch K, Zimmerman HH, Shashi V: Chromosome 22q11.2 deletion syndrome in African-American patients: a diagnostic challenge. Am J Med Genet A 2011,155a(9):2186-2195.
Pehlivan T, Pober BR, Brueckner M, Garrett S, Slaugh R, Van Rheeden R, Wilson DB, Watson MS, Hing AV: GATA4 haploinsufficiency in patients with interstitial deletion of chromosome region 8p23.1 and congenital heart disease. Am J Med Genet 1999,83(3):201-206.
Huang WY, Cukerman E, Liew CC: Identification of a GATA motif in the cardiac alpha-myosin heavy-chain-encoding gene and isolation of a human GATA-4 cDNA. Gene 1995,155(2):219-223.
Koolen DA, Kramer JM, Neveling K, Nillesen WM, Moore-Barton HL, Elmslie FV, Toutain A, Amiel J, Malan V, Tsai AC, Cheung SW, Gilissen C, Verwiel ET, Martens S, Feuth T, Bongers EM, de Vries P, Scheffer H, Vissers LE, de Brouwer AP, Brunner HG, Veltman JA, Schenck A, Yntema HG, de Vries BB: Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome. Nat Genet 2012,44(6):639-641.
Koolen DA, Sharp AJ, Hurst JA, Firth HV, Knight SJ, Goldenberg A, Saugier-Veber P, Pfundt R, Vissers LE, Destree A, Grisart B, Rooms L, Van der Aa N, Field M, Hackett A, Bell K, Nowaczyk MJ, Mancini GM, Poddighe PJ, Schwartz CE, Rossi E, De Gregori M, Antonacci-Fulton LL, McLellan MD 2nd, Garrett JM, Wiechert MA, Miner TL, Crosby S, Ciccone R, Willatt L, Rauch A, et al.: Clinical and molecular delineation of the 17q21.31 microdeletion syndrome. J Med Genet 2008,45(11):710-720.
Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE: Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat Genet 2012,44(8):872-880.
Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V, Abdel-Hamid H, Bader P, McCracken E, Niyazov D, Leppig K, Thiese H, Hummel M, Alexander N, Gorski J, Kussmann J, Shashi V, Johnson K, Rehder C, Ballif BC, Shaffer LG, Eichler EE: A copy number variation morbidity map of developmental delay. Nat Genet 2011,43(9):838-846.
Plaja A, Lloveras E, Martinez-Bouzas C, Barrena B, Del Campo M, Fernandez A, Herrero M, Barranco L, Palau N, Lopez-Ariztegui MA, Catala V, Tejada MI: Trisomy 18p caused by a supernumerary marker with a chromosome 13/21 centromere: a possible recurrent chromosome aberration. Am J Med Genet A 2013,161(9):2363-2368.
Rodriguez L, Liehr T, Mrasek K, Mansilla E, Martinez-Fernandez ML, Garcia A, Martinez-Frias ML: Small supernumerary chromosome marker generating complete and pure trisomy 18p, characterized by molecular cytogenetic techniques and review. Am J Med Genet A 2007,143a(22):2727-2732.
Palmer A, Klein R: Multiple roles of ephrins in morphogenesis, neuronal networking, and brain function. Genes & development 2003,17(12):1429-1450.
Motazacker MM, Rost BR, Hucho T, Garshasbi M, Kahrizi K, Ullmann R, Abedini SS, Nieh SE, Amini SH, Goswami C, Tzschach A, Jensen LR, Schmitz D, Ropers HH, Najmabadi H, Kuss AW: A defect in the ionotropic glutamate receptor 6 gene (GRIK2) is associated with autosomal recessive mental retardation. Am J Hum Genet 2007,81(4):792-798.
Bonaglia MC, Ciccone R, Gimelli G, Gimelli S, Marelli S, Verheij J, Giorda R, Grasso R, Borgatti R, Pagone F, Rodriguez L, Martinez-Frias ML, van Ravenswaaij C, Zuffardi O: Detailed phenotype-genotype study in five patients with chromosome 6q16 deletion: narrowing the critical region for Prader-Willi-like phenotype. Eur J Hum Genet 2008,16(12):1443-1449.
Klein OD, Cotter PD, Moore MW, Zanko A, Gilats M, Epstein CJ, Conte F, Rauen KA: Interstitial deletions of chromosome 6q: genotype-phenotype correlation utilizing array CGH. Clin Genet 2007,71(3):260-266.
Rosenfeld JA, Amrom D, Andermann E, Andermann F, Veilleux M, Curry C, Fisher J, Deputy S, Aylsworth AS, Powell CM, Manickam K, Heese B, Maisenbacher M, Stevens C, Ellison JW, Upton S, Moeschler J, Torres-Martinez W, Stevens A, Marion R, Pereira EM, Babcock M, Morrow B, Sahoo T, Lamb AN, Ballif BC, Paciorkowski AR, Shaffer LG: Genotype-phenotype correlation in interstitial 6q deletions: a report of 12 new cases. Neurogenetics 2012,13(1):31-47.
Piccione M, Antona V, Antona R, Gambino G, Pierluigi M, Malacarne M, Cavani S, Corsello G: Array-CGH defined chromosome 1p duplication in a patient with autism spectrum disorder, mild mental deficiency, and minor dysmorphic features. Am J Med Genet A 2010,152a(2):486-489.
Puffenberger EG, Jinks RN, Sougnez C, Cibulskis K, Willert RA, Achilly NP, Cassidy RP, Fiorentini CJ, Heiken KF, Lawrence JJ, Mahoney MH, Miller CJ, Nair DT, Politi KA, Worcester KN, Setton RA, Dipiazza R, Sherman EA, Eastman JT, Francklyn C, Robey-Bond S, Rider NL, Gabriel S, Morton DH, Strauss KA: Genetic mapping and exome sequencing identify variants associated with five novel diseases. PloS one 2012,7(1):e28936.
Baker S, Booth C, Fillman C, Shapiro M, Blair MP, Hyland JC, Ala-Kokko L: A loss of function mutation in the COL9A2 gene causes autosomal recessive Stickler syndrome. Am J Med Genet A 2011,155a(7):1668-1672.
Watabe T, Matsunaga T, Namba K, Mutai H, Inoue Y, Ogawa K: Moderate hearing loss associated with a novel KCNQ4 non-truncating mutation located near the N-terminus of the pore helix. Biochem Biophys Res Comm 2013,432(3):475-479.
Xia JH, Liu CY, Tang BS, Pan Q, Huang L, Dai HP, Zhang BR, Xie W, Hu DX, Zheng D, Shi XL, Wang DA, Xia K, Yu KP, Liao XD, Feng Y, Yang YF, Xiao JY, Xie DH, Huang JZ: Mutations in the gene encoding gap junction protein beta-3 associated with autosomal dominant hearing impairment. Nat genet 1998,20(4):370-373.
Mullen SA, Suls A, De Jonghe P, Berkovic SF, Scheffer IE: Absence epilepsies with widely variable onset are a key feature of familial GLUT1 deficiency. Neurology 2010,75(5):432-440.
Hu H, Eggers K, Chen W, Garshasbi M, Motazacker MM, Wrogemann K, Kahrizi K, Tzschach A, Hosseini M, Bahman I, Hucho T, Muhlenhoff M, Gerardy-Schahn R, Najmabadi H, Ropers HH, Kuss AW: ST3GAL3 mutations impair the development of higher cognitive functions. Am J Hum Genet 2011,89(3):407-414.
Crane J, Fagerness J, Osiecki L, Gunnell B, Stewart SE, Pauls DL, Scharf JM: Family-based genetic association study of DLGAP3 in Tourette Syndrome. Am J Med Genet B Neuropsychiatr Genet 2011,156b(1):108-114.
Bisgaard AM, Rackauskaite G, Thelle T, Kirchhoff M, Bryndorf T: Twins with mental retardation and an interstitial deletion 7q34q36.2 leading to the diagnosis of long QT syndrome. Am J Med Genet A 2006,140(6):644-648.
Caselli R, Mencarelli MA, Papa FT, Ariani F, Longo I, Meloni I, Vonella G, Acampa M, Auteri A, Vicari S, Orsi A, Hayek G, Renieri A, Mari F: Delineation of the phenotype associated with 7q36.1q36.2 deletion: long QT syndrome, renal hypoplasia and mental retardation. Am J Med Genet A 2008,146a(9):1195-1199.
Rush ET, Stevens JM, Sanger WG, Olney AH: Report of a patient with developmental delay, hearing loss, growth retardation, and cleft lip and palate and a deletion of 7q34-36.1: review of distal 7q deletions. Am J Med Genet A 2013,161a(7):1726-1732.
Mefford HC, Muhle H, Ostertag P, von Spiczak S, Buysse K, Baker C, Franke A, Malafosse A, Genton P, Thomas P, Grunett CA, Schreiber S, Bassuk AG, Guipponi M, Stephani U, Helbig I, Eichler EE: Genome-wide copy number variation in epilepsy: novel susceptibility loci in idiopathic generalized and focal epilepsies. PLoS genetics 2010,6(5):e1000962.
Curran ME, Splawski I, Timothy KW, Vincent GM, Green ED, Keating MT: A molecular basis for cardiac arrhythmia: HERG mutations cause long QT syndrome. Cell 1995,80(5):795-803.
Sehested LT, Moller RS, Bache I, Andersen NB, Ullmann R, Tommerup N, Tumer Z: Deletion of 7q34-q36.2 in two siblings with mental retardation, language delay, primary amenorrhea, and dysmorphic features. Am J Med Genet A 2010,152a(12):3115-3119.
Dobreva G, Dambacher J, Grosschedl R: SUMO modification of a novel MAR-binding protein, SATB2, modulates immunoglobulin mu gene expression. Gene Dev 2003,17(24):3048-3061.
Leoyklang P, Suphapeetiporn K, Siriwan P, Desudchit T, Chaowanapanja P, Gahl WA, Shotelersuk V: Heterozygous nonsense mutation SATB2 associated with cleft palate, osteoporosis, and cognitive defects. Hum Mutat 2007,28(7):732-738.
Rosenfeld JA, Ballif BC, Lucas A, Spence EJ, Powell C, Aylsworth AS, Torchia BA, Shaffer LG: Small deletions of SATB2 cause some of the clinical features of the 2q33.1 microdeletion syndrome. PloS one 2009,4(8):e6568.
DeScipio C, Conlin L, Rosenfeld J, Tepperberg J, Pasion R, Patel A, McDonald MT, Aradhya S, Ho D, Goldstein J, McGuire M, Mulchandani S, Medne L, Rupps R, Serrano AH, Thorland EC, Tsai AC, Hilhorst-Hofstee Y, Ruivenkamp CA, Van Esch H, Addor MC, Martinet D, Mason TB, Clark D, Spinner NB, Krantz ID: Subtelomeric deletion of chromosome 10p15.3: clinical findings and molecular cytogenetic characterization. Am J Med Genet A 2012,158a(9):2152-2161.
Chen CX, Cho DS, Wang Q, Lai F, Carter KC, Nishikura K: A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains. RNA (New York, NY) 2000,6(5):755-767.
Van Esch H, Groenen P, Nesbit MA, Schuffenhauer S, Lichtner P, Vanderlinden G, Harding B, Beetz R, Bilous RW, Holdaway I, Shaw NJ, Fryns JP, Van de Ven W, Thakker RV, Devriendt K: GATA3 haplo-insufficiency causes human HDR syndrome. Nature 2000,406(6794):419-422.
Papanikolaou K, Paliokosta E, Gyftodimou J, Kolaitis G, Vgenopoulou S, Sarri C, Tsiantis J: A case of partial trisomy of chromosome 8p associated with autism. J Autism Dev Disord 2006,36(5):705-709.
Weatherall DJ, Higgs DR, Bunch C, Old JM, Hunt DM, Pressley L, Clegg JB, Bethlenfalvay NC, Sjolin S, Koler RD, Magenis E, Francis JL, Bebbington D: Hemoglobin H disease and mental retardation: a new syndrome or a remarkable coincidence? New Engl J Med 1981,305(11):607-612.
Pfeifer D, Poulat F, Holinski-Feder E, Kooy F, Scherer G: The SOX8 gene is located within 700 kb of the tip of chromosome 16p and is deleted in a patient with ATR-16 syndrome. Genomics 2000,63(1):108-116.
Gibson WT, Harvard C, Qiao Y, Somerville MJ, Lewis ME, Rajcan-Separovic E: Phenotype-genotype characterization of alpha-thalassemia mental retardation syndrome due to isolated monosomy of 16p13.3. Am J Med Genet A 2008,146a(2):225-232.