Mapping the deletion endpoints in individuals with 22q11.2 Deletion Syndrome by droplet digital PCR

BMC Medical Genetics

Volumn 15, Issue 1, 2014, Pages

  Hwang, Vicki J ^a   Maar, Dianna ^b   Regan, John ^b   Angkustsiri, Kathleen ^d   Simon, Tony J ^c,d   Tassone, Flora ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BIO RAD LABORATORIES   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

22q11DS; Copy number; Droplet digital PCR; LCR; QPCR

Indexed keywords

ADOLESCENT; ARTICLE; ATTENTION DEFICIT DISORDER; CHILD; CHROMOSOMAL MAPPING; CHROMOSOME 22Q; CHROMOSOME BREAKAGE; CHROMOSOME DELETION 22Q11; CONTROLLED STUDY; DROPLET DIGITAL POLYMERASE CHAIN REACTION; FEMALE; GENE DOSAGE; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HYPOCALCEMIA; INTERMETHOD COMPARISON; ISCHEMIC HEART DISEASE; MAJOR CLINICAL STUDY; MALE; MEASUREMENT PRECISION; POLYMERASE CHAIN REACTION; QUANTITATIVE POLYMERASE CHAIN REACTION; RELIABILITY; SEIZURE; THYROID DISEASE; CHROMOSOME 22; COPY NUMBER VARIATION; DIGEORGE SYNDROME; ECONOMICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DELETION; GENETIC ASSOCIATION STUDY; GENETICS; PROCEDURES;

ADOLESCENT; CHILD; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 22; DIGEORGE SYNDROME; DNA COPY NUMBER VARIATIONS; FEMALE; GENE DELETION; GENETIC ASSOCIATION STUDIES; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; POLYMERASE CHAIN REACTION;

EID: 84989288335     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/s12881-014-0106-5     Document Type: Article

References (62)

1. Botto LD, May K, Fernhoff PM, Correa A, Coleman K, Rasmussen SA, Merritt RK, O'Leary LA, Wong LY, Elixson EM, Mahle WT, Campbell RM: A population-based study of the 22q11.2 deletion: phenotype, incidence, and contribution to major birth defects in the population. Pediatrics 2003, 112(1 Pt 1):101-107.
2. Goodship J, Cross I, LiLing J, Wren C: A population study of chromosome 22q11 deletions in infancy. Arch Dis Child 1998, 79(4):348-351.
3. Tezenas Du Montcel S, Mendizabai H, Ayme S, Levy A, Philip N: Prevalence of 22q11 microdeletion. J Med Genet 1996, 33(8):719.
4. Wilson DI, Burn J, Scambler P, Goodship J: DiGeorge syndrome: part of CATCH 22. J Med Genet 1993, 30(10):852-856.
5. McDonald-McGinn DM, Sullivan KE: Chromosome 22q11.2 deletion syndrome (DiGeorge syndrome/velocardiofacial syndrome). Medicine 2011, 90(1):1-18.
6. Edelmann L, Pandita RK, Spiteri E, Funke B, Goldberg R, Palanisamy N, Chaganti RS, Magenis E, Shprintzen RJ, Morrow BE: A common molecular basis for rearrangement disorders on chromosome 22q11. Hum Mol Genet 1999, 8(7):1157-1167.
7. Shaikh TH, Kurahashi H, Emanuel BS: Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: an update and literature review. Genet Med: Off J Am College Med Genet 2001, 3(1):6-13.
8. Oskarsdottir S: Incidence and prevalence of the 22q11 deletion syndrome: a population-based study in Western Sweden. Arch Dis Child 2004, 89(2):148-151.
9. Kobrynski LJ, Sullivan KE: Velocardiofacial syndrome, DiGeorge syndrome: the chromosome 22q11.2 deletion syndromes. Lancet 2007, 370 (9596):1443-1452.
10. Carlson C, Sirotkin H, Pandita R, Goldberg R, McKie J, Wadey R, Patanjali SR, Weissman SM, Anyane-Yeboa K, Warburton D, Scambler P, Shprintzen R, Kucherlapati R, Morrow BE: Molecular definition of 22q11 deletions in 151 velo-cardio-facial syndrome patients. Am J Hum Genet 1997, 61(3):620-629.
11. Garcia-Minaur S, Fantes J, Murray RS, Porteous ME, Strain L, Burns JE, Stephen J, Warner JP: A novel atypical 22q11.2 distal deletion in father and son. J Med Genet 2002, 39(10):E62.
12. Rauch A, Zink S, Zweier C, Thiel CT, Koch A, Rauch R, Lascorz J, Huffmeier U, Weyand M, Singer H, Hofbeck M: Systematic assessment of atypical deletions reveals genotype-phenotype correlation in 22q11.2. J Med Genet 2005, 42(11):871-876.
13. Rauch A, Pfeiffer RA, Leipold G, Singer H, Tigges M, Hofbeck M: A novel 22q11.2 microdeletion in DiGeorge syndrome. Am J Hum Genet 1999, 64(2):659-666.
14. Amati F, Conti E, Novelli A, Bengala M, Diglio MC, Marino B, Giannotti A, Gabrielli O, Novelli G, Dallapiccola B: Atypical deletions suggest five 22q11.2 critical regions related to the DiGeorge/velo-cardio-facial syndrome. Eur J Hum Genet 1999, 7(8):903-909.
15. Kurahashi H, Tsuda E, Kohama R, Nakayama T, Masuno M, Imaizumi K, Kamiya T, Sano T, Okada S, Nishisho I: Another critical region for deletion of 22q11: a study of 100 patients. Am J Med Genet 1997, 72(2):180-185.
16. Wieser R, Fritz B, Ullmann R, Muller I, Galhuber M, Storlazzi CT, Ramaswamy A, Christiansen H, Shimizu N, Rehder H: Novel rearrangement of chromosome band 22q11.2 causing 22q11 microdeletion syndrome-like phenotype and rhabdoid tumor of the kidney. Hum Mutat 2005, 26(2):78-83.
17. O'Donnell H, McKeown C, Gould C, Morrow B, Scambler P: Detection of an atypical 22q11 deletion that has no overlap with the DiGeorge syndrome critical region. Am J Hum Genet 1997, 60(6):1544-1548.
18. Saitta SC, McGrath JM, Mensch H, Shaikh TH, Zackai EH, Emanuel BS: A 22q11.2 deletion that excludes UFD1L and CDC45L in a patient with conotruncal and craniofacial defects. Am J Hum Genet 1999, 65(2):562-566.
19. Lu JH, Chung MY, Betau H, Chien HP, Lu JK: Molecular characterization of tetralogy of fallot within Digeorge critical region of the chromosome 22. Pediatr Cardiol 2001, 22(4):279-284.
20. Yamagishi H, Garg V, Matsuoka R, Thomas T, Srivastava D: A molecular pathway revealing a genetic basis for human cardiac and craniofacial defects. Science 1999, 283(5405):1158-1161.
21. Kurahashi H, Nakayama T, Osugi Y, Tsuda E, Masuno M, Imaizumi K, Kamiya T, Sano T, Okada S, Nishisho I: Deletion mapping of 22q11 in CATCH22 syndrome: identification of a second critical region. Am J Hum Genet 1996, 58(6):1377-1381.
22. Verhoeven W, Egger J, Brunner H, de Leeuw N: A patient with a de novo distal 22q11.2 microdeletion and anxiety disorder. Am J Med Genet 2011, 155A(2):392-397.
23. Ben-Shachar S, Ou Z, Shaw CA, Belmont JW, Patel MS, Hummel M, Amato S, Tartaglia N, Berg J, Sutton VR, Lalani SR, Chinault AC, Cheung SW, Lupski JR, Patel A: 22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome. Am J Hum Genet 2008, 82(1):214-221.
24. McQuade L, Christodoulou J, Budarf M, Sachdev R, Wilson M, Emanuel B, Colley A: Patient with a 22q11.2 deletion with no overlap of the minimal DiGeorge syndrome critical region (MDGCR). Am J Med Genet 1999, 86(1):27-33.
25. Rodningen OK, Prescott T, Eriksson AS, Rosby O: 1.4Mb recurrent 22q11.2 distal deletion syndrome, two new cases expand the phenotype. Eur J Med Genet 2008, 51(6):646-650.
26. Newbern J, Zhong J, Wickramasinghe RS, Li X, Wu Y, Samuels I, Cherosky N, Karlo JC, O'Loughlin B, Wikenheiser J, Gargesha M, Doughman YQ, Charron J, Ginty DD, Watanabe M, Saitta SC, Snider WD, Landreth GE: Mouse and human phenotypes indicate a critical conserved role for ERK2 signaling in neural crest development. Proc Natl Acad Sci USA 2008, 105(44):17115-17120.
27. Verhagen JM, Diderich KE, Oudesluijs G, Mancini GM, Eggink AJ, Verkleij-Hagoort AC, Groenenberg IA, Willems PJ, du Plessis FA, de Man SA, Srebniak MI, van Opstal D, Hulsman LO, van Zutven LJ, Wessels MW: Phenotypic variability of atypical 22q11.2 deletions not including TBX1. Am J Med Genet 2012, 158A(10):2412-2420.
28. Breckpot J, Thienpont B, Bauters M, Tranchevent LC, Gewillig M, Allegaert K, Vermeesch JR, Moreau Y, Devriendt K: Congenital heart defects in a novel recurrent 22q11.2 deletion harboring the genes CRKL and MAPK1. Am J Med Genet 2012, 158A(3):574-580.
29. Ogilvie CM, Ahn JW, Mann K, Roberts RG, Flinter F: A novel deletion in proximal 22q associated with cardiac septal defects and microcephaly: a case report. Mol Cytogenet 2009, 2:9.
30. D'Angelo CS, Jehee FS, Koiffmann CP: An inherited atypical 1 Mb 22q11.2 deletion within the DGS/VCFS 3 Mb region in a child with obesity and aggressive behavior. Am J Med Genet 2007, 143A(16):1928-1932.
31. Mikhail FM, Descartes M, Piotrowski A, Andersson R, de Diaz Stahl T, Komorowski J, Bruder CE, Dumanski JP, Carroll AJ: A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene. Am J Med Genet 2007, 143A(18):2178-2184.
32. Fernandez L, Nevado J, Santos F, Heine-Suner D, Martinez-Glez V, Garcia-Minaur S, Palomo R, Delicado A, Pajares IL, Palomares M, Garcia-Guereta L, Valverde E, Hawkins F, Lapunzina P: A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review. BMC Med Genet 2009, 10:48.
33. Garavelli L, Rosato S, Wischmeijer A, Gelmini C, Esposito A, Mazzanti L, Franchi F, De Crescenzo A, Palumbo O, Carella M, Riccio A: 22q11.2 Distal Deletion Syndrome: Description of a New Case with Truncus Arteriosus Type 2 and Review. Mol Syndromol 2011, 2(1):35-44.
34. Vorstman JA, Jalali GR, Rappaport EF, Hacker AM, Scott C, Emanuel BS: MLPA: a rapid, reliable, and sensitive method for detection and analysis of abnormalities of 22q. Human Mutat 2006, 27(8):814-821.
35. Weksberg R, Hughes S, Moldovan L, Bassett AS, Chow EW, Squire JA: A method for accurate detection of genomic microdeletions using real-time quantitative PCR. BMC Genomics 2005, 6:180.
36. Mantripragada KK, Tapia-Paez I, Blennow E, Nilsson P, Wedell A, Dumanski JP: DNA copy-number analysis of the 22q11 deletion-syndrome region using array-CGH with genomic and PCR-based targets. Int J Mol Med 2004, 13(2):273-279.
37. Miller KA: FISH Diagnosis of 22q11.2 Deletion Syndrome. Newborn Infant Nurs Rev 2008, 8(1):e11-e19.
38. Jalali GR, Vorstman JA, Errami A, Vijzelaar R, Biegel J, Shaikh T, Emanuel BS: Detailed analysis of 22q11.2 with a high density MLPA probe set. Hum Mutat 2008, 29(3):433-440.
39. Bittel DC, Yu S, Newkirk H, Kibiryeva N, Holt A 3rd, Butler MG, Cooley LD: Refining the 22q11.2 deletion breakpoints in DiGeorge syndrome by aCGH. Cytogen Genome Res 2009, 124(2):113-120.
40. Coffa J, van de Wiel MA, Diosdado B, Carvalho B, Schouten J, Meijer GA: MLPAnalyzer: data analysis tool for reliable automated normalization of MLPA fragment data. Cell Oncol 2008, 30(4):323-335.
41. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G: Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002, 30(12):e57.
42. Frigerio M, Passeri E, de Filippis T, Rusconi D, Valaperta R, Carminati M, Donnangelo A, Costa E, Persani L, Finelli P, Corbetta S: SNPs and real-time quantitative PCR method for constitutional allelic copy number determination, the VPREB1 marker case. BMC Med Genet 2011, 12:61.
43. Schwab CJ, Jones LR, Morrison H, Ryan SL, Yigittop H, Schouten JP, Harrison CJ: Evaluation of multiplex ligation-dependent probe amplification as a method for the detection of copy number abnormalities in B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2010, 49(12):1104-1113.
44. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang S, Stumbo DP, Hodges SP, et al.: High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 2011, 83(22):8604-8610.
45. Pinheiro LB, Coleman VA, Hindson CM, Herrmann J, Hindson BJ, Bhat S, Emslie KR: Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal Chem 2012, 84(2):1003-1011.
46. Wechsler D: Wechsler intelligence scale for children-Fourth Edition (WISC-IV). San Antonio, TX: The Psychological Corporation; 2003.
47. Swanson J: SNAP-IV Scale. Irvine, Calif: University of California Child Development Center; 1994.
48. Wechsler D: Wechsler abbreviated scale of intelligence. San Antonio, TX: Psychological Corporation; 1999.
49. Lindsay EA, Botta A, Jurecic V, Carattini-Rivera S, Cheah YC, Rosenblatt HM, Bradley A, Baldini A: Congenital heart disease in mice deficient for the DiGeorge syndrome region. Nature 1999, 401(6751):379-383.
50. Gong W, Gottlieb S, Collins J, Blescia A, Dietz H, Goldmuntz E, McDonald-McGinn DM, Zackai EH, Emanuel BS, Driscoll DA, Budarf ML: Mutation analysis of TBX1 in non-deleted patients with features of DGS/VCFS or isolated cardiovascular defects. J Med Genet 2001, 38(12):E45.
51. Conti E, Grifone N, Sarkozy A, Tandoi C, Marino B, Digilio MC, Mingarelli R, Pizzuti A, Dallapiccola B: DiGeorge subtypes of nonsyndromic conotruncal defects: evidence against a major role of TBX1 gene. Eur J Hum Genet 2003, 11(4):349-351.
52. Ambros V: microRNAs: tiny regulators with great potential. Cell 2001, 107(7):823-826.
53. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ: Processing of primary microRNAs by the Microprocessor complex. Nature 2004, 432(7014):231-235.
54. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R: The Microprocessor complex mediates the genesis of microRNAs. Nature 2004, 432(7014):235-240.
55. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN: Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006, 125(5):887-901.
56. Lai EC: microRNAs: runts of the genome assert themselves. Current Biol 2003, 13(23):R925-R936.
57. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN: The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425(6956):415-419.
58. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN: The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 2004, 18(24):3016-3027.
59. Wang Y, Medvid R, Melton C, Jaenisch R, Blelloch R: DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat Genet 2007, 39(3):380-385.
60. Rao PK, Toyama Y, Chiang HR, Gupta S, Bauer M, Medvid R, Reinhardt F, Liao R, Krieger M, Jaenisch R, Lodish HF, Blelloch R: Loss of cardiac microRNA-mediated regulation leads to dilated cardiomyopathy and heart failure. Circ Res 2009, 105(6):585-594.
61. Huang ZP, Chen JF, Regan JN, Maguire CT, Tang RH, Dong XR, Majesky MW, Wang DZ: Loss of microRNAs in neural crest leads to cardiovascular syndromes resembling human congenital heart defects. Arterioscler Thromb Vasc Biol 2010, 30(12):2575-2586.
62. de la Morena MT, Eitson JL, Dozmorov IM, Belkaya S, Hoover AR, Anguiano E, Pascual MV, van Oers NS: Signature MicroRNA expression patterns identified in humans with 22q11.2 deletion/DiGeorge syndrome. Clin Immunol 2013, 147(1):11-22.