A method for accurate detection of genomic microdeletions using real-time quantitative PCR

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Weksberg, Rosanna ^a,b   Hughes, Simon ^c   Moldovan, Laura ^a   Bassett, Anne S ^d   Chow, Eva W C ^d   Squire, Jeremy A ^d,e  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^d UNIVERSITY OF TORONTO   (Canada)

^e PRINCESS MARGARET HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PRIMER DNA;

ARTICLE; CHROMOSOME 22Q; CHROMOSOME DELETION; CHROMOSOME DUPLICATION; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DNA DETERMINATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC SCREENING; HUMAN; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; TRISOMY; VALIDATION PROCESS; CHEMISTRY; CHROMOSOME 22; GENE DELETION; GENE DUPLICATION; GENETIC PROCEDURES; GENETICS; GENOMICS; HUMAN GENOME; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

CHROMOSOMES, HUMAN, PAIR 22; DNA; DNA PRIMERS; GENE DELETION; GENE DUPLICATION; GENETIC TECHNIQUES; GENOME, HUMAN; GENOMICS; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE DELETION;

EID: 29244433760     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-180     Document Type: Article

References (48)

1. Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, et al: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004, 36:299-303.
2. Koolen DA, Vissers LE, Nillesen W, Smeets D, van Ravenswaaij CM, Sistermans EA, Veltman JA, de Vries BB: A novel microdeletion, del(2)(q22.3q23.3) in a mentally retarded patient, detected by array-based comparative genomic hybridization. Clin Genet 2004, 65:429-432.
3. Shaw-Smith C, Redon R, Rickman L, Rio M, Willatt L, Fiegler H, Firth H, Sanlaville D, Winter R, Colleaux L, et al: Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 2004, 41:241-248.
4. Babovic-Vuksanovic D, Jenkins SC, Ensenauer R, Newman DC, Jalal SM: Subtelomeric deletion of 18p in an adult with paranoid schizophrenia and mental retardation. Am J Med Genet A 2004, 124:318-322.
5. Mantripragada KK, Buckley PG, de Stahl TD, Dumanski JP: Genomic microarrays in the spotlight. Trends Genet 2004, 20:87-94.
6. 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, 13:273-279.
7. Saitta SC, Harris SE, Gaeth AP, Driscoll DA, McDonald-McGinn DM, Maisenbacher MK, Yersak JM, Chakraborty PK, Hacker AM, Zackai EH, et al: Aberrant interchromosomal exchanges are the predominant cause of the 22q11.2 deletion. Hum Mol Genet 2004, 13:417-428.
8. 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, 72:180-185.
9. 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, 7:903-909.
10. 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, 22:279-284.
11. 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, 64:659-666.
12. 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, 65:562-566.
13. Ensenauer RE, Adeyinka A, Flynn HC, Michels VV, Lindor NM, Dawson DB, Thorland EC, Lorentz CP, Goldstein JL, McDonald MT, et al: Microduplication 22q11.2, an emerging syndrome: clinical, cytogenetic, and molecular analysis of thirteen patients. Am J Hum Genet 2003, 73:1027-1040.
14. Ikeuchi T: Extending the capabilities of human chromosome analysis: from high-resolution banding to chromatin fiber-FISH. Hum Cell 1997, 10:121-134.
15. Sellner LN, Taylor GR: MLPA and MAPH: new techniques for detection of gene deletions. Hum Mutat 2004, 23:413-419.
16. UCSC Genome Bioinformatics [http://genome.ucsc.edu/]
17. NCBI [http://www.ncbi.nlm.nih.gov/]
18. Roe Lab Human Genomic DNA Sequencing Progress [http://www.genome.ou.edu/hum_totals.html]
19. Egenome [http://egenome.chop.edu/]
20. Human BAC Resource [http://www.ncbi.nlm.nih.gov/genome/cyto/hbrc.shtml]
21. Human Organized Whole Genome Database [http://www-alis.tokyo.jst.go.jp/HOWDY/]
22. YACs on Chromosome 22 [http://www.biologia.uniba.it/rmc/2-YAC-BAC/YAC/YAC-22.html]
23. Genatlas [http://www.dsi.univ-paris5.fr/genatlas/]
24. Human Genome Segmental Duplication Database [http://projects.tcag.ca/humandup/]
25. Yobb TM, Somerville MJ, Willatt L, Firth HV, Harrison K, Mackenzie J, Gallo N, Morrow BE, Shaffer LG, Babcock M, et al: Microduplication and triplication of 22q11.2: a highly variable syndrome. Am J Hum Genet 2005, 76:865-876.
26. Carlson C, Sirotkin H, Pandita R, Goldberg R, McKie J, Wadey R, Patanjali SR, Weissman SM, Anyane-Yeboa K, Warburton D, et al: Molecular definition of 22q11 deletions in 151 velo-cardio-facial syndrome patients. Am J Hum Genet 1997, 61:620-629.
27. Demczuk S, Aledo R, Zucman J, Delattre O, Desmaze C, Dauphinot L, Jalbert P, Rouleau GA, Thomas G, Aurias A: Cloning of a balanced translocation breakpoint in the DiGeorge syndrome critical region and isolation of a novel potential adhesion receptor gene in its vicinity. Hum Mol Genet 1995, 4:551-558.
28. Funke B, Edelmann L, McCain N, Pandita RK, Ferreira J, Merscher S, Zohouri M, Cannizzaro L, Shanske A, Morrow BE: Der(22) syndrome and velo-cardiofacial syndrome/DiGeorge syndrome share a 1.5-Mb region of overlap on chromosome 22q11. Am J Hum Genet 1999, 64:747-758.
29. Kurahashi H, Akagi K, Inazawa J, Ohta T, Niikawa N, Kayatani F, Sano T, Okada S, Nishisho I: Isolation and characterization of a novel gene deleted in DiGeorge syndrome. Hum Mol Genet 1995, 4:541-549.
30. Lindsay EA: Chromosomal microdeletions: dissecting del22q11 syndrome. Nat Rev Genet 2001, 2:858-868.
31. Lindsay EA, Vitelli F, Su H, Morishima M, Huynh T, Pramparo T, Jurecic V, Ogunrinu G, Sutherland HF, Scambler PJ, et al: Tbx1 haploinsufficieny in the DiGeorge syndrome region causes aortic arch defects in mice. Nature 2001, 410:97-101.
32. 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, 86:27-33.
33. Perez E, Sullivan KE: Chromosome 22q11.2 deletion syndrome (DiGeorge and velocardiofacial syndromes). Curr Opin Pediatr 2002, 14:678-683.
34. Shaikh TH, Kurahashi H, Saitta SC, O'Hare AM, Hu P, Roe BA, Driscoll DA, McDonald-McGinn DM, Zackai EH, Budarf ML, Emanuel BS: Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis. Hum Mol Genet 2000, 9:489-501.
35. Johnson A, Minoshima S, Asakawa S, Shimizu N, Shizuya H, Roe BA, McDermid HE: A 1.5-Mb contig within the cat eye syndrome critical region at human chromosome 22q11.2. Genomics 1999, 57:306-309.
36. Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
37. Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A: Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 2004, 313:856-862.
38. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
39. Meijerink J, Mandigers C, van de Locht L, Tonnissen E, Goodsaid F, Raemaekers J: A novel method to compensate for different amplification efficiencies between patient DNA samples in quantitative real-time PCR. J Mol Diagn 2001, 3:55-61.
40. Tichopad A, Dilger M, Schwarz G, Pfaffl MW: Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res 2003, 31:e122.
41. Moody A, Sellers S, Bumstead N: Measuring infectious bursal disease virus RNA in blood by multiplex real-time quantitative RT-PCR. J Virol Methods 2000, 85:55-64.
42. Sijben JW, Klasing KC, Schrama JW, Parmentier HK, van der Poel JJ, Savelkoul HF, Kaiser P: Early in vivo cytokine genes expression in chickens after challenge with Salmonella typhimurium lipopolysaccharide and modulation by dietary n - 3 polyunsaturated fatty acids. Dev Comp Immunol 2003, 27:611-619.
43. Parr C, Jiang WG: Quantitative analysis of lymphangiogenic markers in human colorectal cancer. Int J Oncol 2003, 23:533-539.
44. Cairns JP, Chiang PW, Ramamoorthy S, Kurnit DM, Sidransky D: A comparison between microsatellite and quantitative PCR analyses to detect frequent p16 copy number changes in primary bladder tumors. Clin Cancer Res 1998, 4:441-444.
45. Ivanov D, Kirov G, Norton N, Williams HJ, Williams NM, Nikolov I, Tzwetkova R, Stambolova SM, Murphy KC, Toncheva D, et al: Chromosome 22q11 deletions, velo-cardio-facial syndrome and early-onset psychosis. Molecular genetic study. Br J Psychiatry 2003, 183:409-413.
46. Kariyazono H, Ohno T, Ihara K, Igarashi H, Joh-o K, Ishikawa S, Hara T: Rapid detection of the 22q11.2 deletion with quantitative real-time PCR. Mol Cell Probes 2001, 15:71-73.
47. Shi YR, Hsieh KS, Wu JY, Lee CC, Tsai CH, Yu MT, Chang JS, Tsai FJ: Genetic analysis of chromosome 22q11.2 markers in congenital heart disease. J Clin Lab Anal 2003, 17:28-35.
48. Nicholas C. Dracopoli, Jonathan L. Haines, Bruce R. Korf, Cynthia C. Morton, Christine E. Seidman, J.G. Seidman, Smith DR: Short Protocols in Human Genetics. John Wiley & Sons, Inc.; 1994-2004.