Multiplex ligation-dependent probe amplification workflow for the detection of submicroscopic chromosomal abnormalities in patients with developmental delay/intellectual disability
Tóm tắt
Array based comparative genomic hybridization (arrayCGH) has been increasingly used as the method of choice for diagnosis of patients with unexplained developmental delay/intellectual disability (DD/ID) but is not universally available for the high throughput use in routine practice. The next-generation sequencing (NGS) techniques, emerging as a new tool in clinical diagnostics, are at present quite labour-intensive and expensive. Since multiplex ligation-dependent probe amplification (MLPA) is relatively fast, easily interpreted and cost-effective, it is still a method of choice for screening large cohorts of patients with DD/ID. We prospectively studied a cohort of 150 patients with DD/ID with or without dysmorphic features or additional congenital abnormalities. We used two distinct MLPA kits, SALSA P036 and P070, for subtelomere screening and MLPA kit SALSA P245 for the 21 common microdeletion syndromes. Subtelomere analysis was performed by both kits in all patients. All imbalances were verified by follow-up MLPA kits. The MLPA analysis revealed chromosome aberrations in 21 (14%) cases: 11 subtelomeric rearrangements and 10 microdeletions. We have presented the results of the investigation of patients with DD/ID obtained by using a combination of the MLPA sets for subtelomere aberrations and microdeletion syndromes followed by the confirmation of the aberrant results by the region-specific MLPA kits. The use of two subtelomeric kits per patient and investigation of all aberrations by follow-up sets has reduced the rate of false positive and negative results and improved the diagnostic yield. The relatively low cost, simplicity and reliability makes MLPA an effective first-tier cytogenetic diagnostic test for screening large cohorts of DD/ID patients.
Tài liệu tham khảo
Moeschler JB, Shevell M: American academy of pediatrics committee on genetics. Clinical genetic evaluation of the child with mental retardation or developmental delays. Pediatrics 2006, 117: 2304–2316. 10.1542/peds.2006-1006
Knight SJ, Horsley SW, Regan R, Lawrie NM, Maher EJ, Cardy DL, Flint J, Kearney L: Development and clinical application of an innovative fluorescence in situ hybridization technique which detects submicroscopic rearrangements involving telomeres. Eur J Hum Genet 1997, 5(1):1–8.
Carpenter NJ: Molecular cytogenetics. Semin Pediatr Neurol 2001, 8(3):135–146. 10.1053/spen.2001.26447
Shaffer LG, Bejjani BA, Torchia B, Kirkpatrick S, Coppinger J, Ballif BC: The identification of microdeletion syndromes and other chromosome abnormalities: cytogenetic methods of the past, new technologies for the future. Am J Med Genet C Semin Med Genet 2007, 145: 335–345.
Rooms L, Vandeweyer G, Reyniers E, van Mol K, de Canck I, Van der Aa N, Rossau R, Kooy RF: Array-based MLPA to detect recurrent copy number variations in patients with idiopathic mental retardation. Am J Med Genet A 2011, 155A(2):343–348.
Su Z, Ning B, Fang H, Hong H, Perkins R, Tong W, Shi L: Next-generation sequencing and its applications in molecular diagnostics. Expert Rev Mol Diagn 2011, 11(3):333–343.
Desai AN, Jere A: Next-generation sequencing: ready for the clinics? Clin Genet 2012, 81(6):503–510. 10.1111/j.1399-0004.2012.01865.x
Jehee FS, Takamori JT, Medeiros PF, Pordeus AC, Latini FR, Bertola DR, Kim CA, Passos-Bueno MR: Using a combination of MLPA kits to detect chromosomal imbalances in patients with multiple congenital anomalies and mental retardation is a valuable choice for developing countries. Eur J Med Genet 2011, 54(4):425–432. 10.1016/j.ejmg.2011.03.007
Keren B, Le Caignec C: Oligonucleotide microarrays in constitutional genetic diagnosis. Expert Rev Mol Diagn 2011, 11(5):521–532. 10.1586/erm.11.32
Gijsbers AC, Lew JY, Bosch CA, Schuurs-Hoeijmakers JH, van Haeringen A, den Hollander NS, Kant SG, Bijlsma EK, Breuning MH, Bakker E, Ruivenkamp CA: A new diagnostic workflow for patients with mental retardation and/or multiple congenital abnormalities: test arrays first. Eur J Hum Genet 2009, 17(11):1394–1402. 10.1038/ejhg.2009.74
Ahn JW, Mann K, Walsh S, Shehab M, Hoang S, Docherty Z, Mohammed S, Mackie Ogilvie C: Validation and implementation of array comparative genomic hybridisation as a first line test in place of postnatal karyotyping for genome imbalance. Mol Cytogenet 2010, 3: 9. 10.1186/1755-8166-3-9
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, Martin CL, Ledbetter DH: 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. 10.1016/j.ajhg.2010.04.006
Koolen DA, Nillesen WM, Versteeg MH, Merkx GF, Knoers NV, Kets M, Vermeer S, van Ravenswaaij CM, de Kovel CG, Brunner HG, Smeets D, de Vries BB, Sistermans EA: Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA). J Med Genet 2004, 41(12):892–899. 10.1136/jmg.2004.023671
Rooms L, Reyniers E, van Luijk R, Scheers S, Wauters J, Ceulemans B, Van Den Ende J, Van Bever Y, Kooy RF: Subtelomeric deletions detected in patients with idiopathic mental retardation using multiplex ligation-dependent probe amplification (MLPA). Hum Mutat 2004, 23(1):17–21. 10.1002/humu.10300
Mandal K, Mandal K, Boggula VR, Borkar M, Agarwal S, Phadke SR: Use of multiplex ligation-dependent probe amplification (MLPA) in screening of subtelomeric regions in children with idiopathic mental retardation. Indian J Pediatr 2009, 76(10):1027–1031. 10.1007/s12098-009-0218-7
Kirchhoff M, Gerdes T, Brunebjerg S, Bryndorf T: Investigation of patients with mental retardation and dysmorphic features using comparative genomic hybridization and subtelomeric multiplex ligation dependent probe amplification. Am J Med Genet A 2005, 139(3):231–233.
Rooms L, Reyniers E, Wuyts W, Storm K, van Luijk R, Scheers S, Wauters J, van den Ende J, Biervliet M, Eyskens F, van Goethem G, Laridon A, Ceulemans B, Courtens W, Kooy RF: Multiplex ligation- dependent probe amplification to detect subtelomeric rearrangements in routine diagnostics. Clin Genet 2006, 69(1):58–64.
Stegmann AP, Jonker LM, Engelen JJ: Prospective screening of patients with unexplained mental retardation using subtelomeric MLPA strongly increases the detection rate of cryptic unbalanced chromosomal rearrangements. Eur J Med Genet 2008, 51(2):93–105. 10.1016/j.ejmg.2007.10.003
Northrop EL, Ren H, Bruno DL, McGhie JD, Coffa J, Schouten J, Choo KH, Slater HR: Detection of cryptic subtelomeric chromosome abnormalities and identification of anonymous chromatin using a quantitative multiplex ligation-dependent probe amplification (MLPA) assay. Hum Mutat 2005, 26(5):477–486. 10.1002/humu.20243
Kirchhoff M, Bisgaard AM, Bryndorf T, Gerdes T: MLPA analysis for a panel of syndromes with mental retardation reveals imbalances in 5.8% of patients with mental retardation and dysmorphic features, including duplications of the sotos syndrome and williams-beuren syndrome regions. Eur J Med Genet 2007, 50: 33–42. 10.1016/j.ejmg.2006.10.002