A novel, single nucleotide polymorphism-based assay to detect 22q11 deletions

Genetic Testing

Volumn 11, Issue 1, 2007, Pages 91-100

  Funke, Birgit H ^a,b,f   Brown, Alison C ^a,b   Ramoni, Marco F ^a,b,c   Regan, Maura E ^a,b   Baglieri, Chris ^a,b   Finn, Christine T ^a,b   Babcock, Melanie ^d   Shprintzen, Robert J ^e   Morrow, Bernice E ^d   Kucherlapati, Raju ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b Harvard MIT Division of Health Sciences and Technology ^*

^c HARVARD MIT DIVISION OF HEALTH SCIENCES AND TECHNOLOGY   (United States)

^d ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^e State University of New York Upstate Medical University: College of Medicine   (United States)

^f LABORATORY FOR MOLECULAR MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CHROMOSOME 22Q; CHROMOSOME ANALYSIS; CHROMOSOME DELETION; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC VALUE; DIGEORGE SYNDROME; FACE MALFORMATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC ANALYSIS; GENOTYPE; HEMIZYGOSITY; HUMAN; MAJOR CLINICAL STUDY; PREDICTIVE VALIDITY; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY; VELOCARDIOFACIAL SYNDROME;

BASE SEQUENCE; BAYES THEOREM; CHROMOSOME DELETION; CHROMOSOMES, HUMAN, PAIR 22; DNA; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY;

EID: 34147106503     PISSN: 10906576     EISSN: None     Source Type: Journal    
DOI: 10.1089/gte.2006.0507     Document Type: Article

References (45)

1. Bender HU, Almashanu S, Steel G, Hu CA, Lin WW, Willis A, Pulver A, Valle D (2005) Functional consequences of PRODH missense mutations. Am J Hum Genet 76:409-420.
2. Bonnet D, Cormier-Daire V, Kachaner J, Szezepanski I, Souillard P, Sidi D, Munnich A, Lyonnet S (1997) Microsatellite DNA markers detects 95% of chromosome 22q11 deletions. Am J Med Genet 68:182-184.
3. 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 (2003) A population-based study of the 22q11.2 deletion: phenotype, incidence, and contribution to major birth defects in the population. Pediatrics 112:101-107.
4. Bum J, Goodship J (1996) Congenitcal heart disease. In: Rimoin DL, Connor JM, Pyeritz RE (eds) Emery and Rimoin's principles and practice of medical genetics, vol 1. 3rd ed. Churchill Livingston, New York, pp 767-828.
5. Carl son C, Sirotkin H, Pandita R, Goldberg R, McKie J, Wadey R, Patanjali SR, Weissman SM, Anyane-Yeboa K, Warburton D, Scambier P, Shprintzen R, Kucherlapati R, Morrow BE (1997) Molecular definition of 22q11 deletions in 151 velo-cardio-facial syndrome patients. Am J Hum Genet 61:620-629.
6. Chen YF, Kou PL, Tsai SJ, Chen KF, Chan HH, Chen CM, Sun HS (2006) Computational analysis and refinement of sequence structure on chromosome 22q11.2 region: application to the development of quantitative real-time PCR assay for clinical diagnosis. Genomics 87:290-297.
7. Cheung SW, Shaw CA, Yu W, Li J, Ou Z, Patel A, Yatsenko SA, Cooper ML, Furmun P, Stankiewicz P, Lupski JR, Chinault AC, Beaud et al (2005) Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet Med 7:422-432.
8. Cowell RG, Dawid AP, Lauritzen SL, und Spiegelhalter DJ (1999) Probabilistic Networks and Expert Systems. Springer Verlag. New York.
9. De la Vega FM, Luzaruk KD, Rhodes MD, Wenz MH (2005) Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPleX Genotyping System. Mutat Res 573:111-135.
10. Desmaze C, Prieur M, Amblard F, Aikem M, LeDeist F, Demczuk S, Zucman J, Plougastel B, Delattre O, Croquette MF, et al. (1993) Physical mapping by FISH of the DiGeorge critical region (DGCR): involvement of the region in familial eases. Am J Hum Genet 53:1239-1249.
11. Driscoll DA, Emanuel BS, Mitchell LE, Budarf ML (1997) PCR assay for screening patients at risk for 22q11.2 deletion. Genet Test 1:109-113.
12. Edelmann L, Pandita RK, Morrow BE (1999a) Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. Am J Hum Genet 64:1076-1086.
13. Edelmann L, Pandita RK, Spiteri E, Funke B, Goldberg R, Palanisamy N, Chaganii RS, Magenis E, Shprintzen RJ, Morrow BE (1999b) A common molecular basis for rearrangement disorders on chromosome 22q11. Hum Mol Genet 8:1157-1167.
14. Fan JB, Chce MS, Gunderson KL (2006) Highly parallel genomic assays. Nature Rev Genet 7:632-644.
15. Farrall M, Morris AP (2005) Gearing up for genome-wide gene-association studies. Hum Mol Genet 14 Spec No. 2:R157-R162.
16. Friedman N (2004) Inferring cellular networks using probabilistic graphical models. Science 303:799-805.
17. Funke B, Edelmann L, McCain N, Pandita RK, Ferreira J, Merscher S, Zohouri M, Cannizzaro L, Shanske A, Morrow BE (1999) Der(22) syndrome and velo-cardio-facial syndrome/DiGeorge syndrome share a 1.5-Mb region of overlap on chromosome 22q11. Am J Hum Genet 64:747-758.
18. Guris DL, Fantes J, Tara D, Druker BJ, Imamoto A (2001) Mice lacking the homologue of the human 22q11.2 gene CRKL phenocopy neurocristopathies of DiGeorge syndrome. Nature Genet 27:293-298.
19. Jacquet H, Raux G, Thibaut F, Hecketsweiler B, Houy E, Demilly C, Haouzir S, Allio G, Fouldrin G,. Drouin V, Bou J, Petit M, Campion D, Frebourg T (2002) PRODH mutations and hyperprolinemia in a subset of schizophrenic patients. Hum Mol Genet 11:2243-2249.
20. Janscn R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein, M (2003) A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-453.
21. Jerome LA, Papaioannou VE (2001) DiGeorge syndrome phenotype in mice mutant for the T-box gene. Thx1. Nature Genet 27:286-291.
22. Karayiorgou M, Gogos JA (2004) The molecular genetics of the 22q44-associated schizophrenia. Brain Res Mol Brain Res 132:95-104.
23. Kariyazono H, Ohno T, Ihara K, Igarashi H, Joh-o K, Ishikawa S, Hara T (2001) Rapid detection of the 22q11.2 deletion with quantitative real-time PCR. Mol Cell Probes 15:71-73.
24. Kerstjens-Frederikse WS, Kurahashi H, Driscoll DA, Budarf ML, Emanuel BS, Beatty B, Scheidl T, Siegel-Bartelt J, Henderson K, Cytrynbaum C, Nie G, Teshima I (1999) Microdeletion 22q11.2: clinical data and deletion size. J Med Genet 36:721-723.
25. Kotzot D (2001) Complex and segmental uniparental disomy (UPD): review and lessons from rare chromosomal complements. J Med Genet 38:497-507.
26. Lauritzen SL, Sheehan NA (2004) Graphical models for genetic analysis. Statist Sci 18:489-514.
27. Lindblad-Toh K, Tanenhaum DM, Daly MJ, Winchester E, Lui WO, Villapakkam A, Slanton SE, Larsson C, Hudson TJ, Johnson BE, Lander ES, Meyerson M (2000) Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nature Biotechnol 18:1001-1005.
28. Lindsay EA, Greenberg F, Shaffer LG, Shapira SK, Scambler PJ, Baldini A (1995) Submicroscopic deletions at 22q11.2: variability of the clinical picture and delineation of a commonly deleted region. Am J Med Genet 56:191-197.
29. Lindsay EA, Vitelli F, Su H, Morishima M, Huynh T, Pramparo T, Jurecic V, Ogunrinu G, Sutherland HF, Scambler PJ, Bradley A, Baldini A (2001) Tbx1 haploinsuffieieny in the DiGeorge syndrome region causes aortic arch defects in mice. Nature 410:97-101.
30. Liu H, Heath SC, Sohin C, Roos JL, Galke BL, Blundell ML, Lenane M, Robertson B, Wijsman EM, Rapoporl JL, Gogos JA, Karayiorgou M (2002) Genetic variation at the 22q11 PRODH2/DGCR6 locus presents an unusual pattern and increases susceptibility to schizophrenia. Proc Natl Acad Sci USA 99:3717-3722.
31. McDonald-McGinn DM, LaRossa D, Goldmuntz E, Sullivan K, Eicher P, Gerdes M, Moss E, Wang P, Solot C, Schultz P, Lynch D, Bingham P, Keenan G, Weinzimer S, Ming JE, Driscoll D, Clark BJ, 3rd, Markowitz R, Cohen A, Moshang T, Pasquariello P, Randall P, Emanuel BS, Zackai EH (1997) The 22q11.2 deletion: screening, diagnostic workup, and outcome of results: report on 181 patients. Genet Test 1:99-108.
32. McDonald-McGinn DM, Kirschner R, Goldmuntz E, Sullivan K, Eicher P, Gerdes M, Moss E, Solot C, Wang P, Jacobs I, Handler S, Knightly C, Heher K, Wilson M, Ming JE, Grace K, Driscoll D, Pasquariello P, Randall P, Larossa D, Emanuel BS, Zackai EH (1999) The Philadelphia story: the 22q11.2 deletion: report on 250 patients. Genet Counsel 10:11-24.
33. Mei R, Galipeau PC, Prass C, Berno A, Ghandour G, Patil N, Wolff RK, Chee MS, Reid BJ, Lockhart DJ (2000) Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res 10:1126-1137.
34. Merscher S, Funke B, Epstein JA, Heyer J, Puech A, Lu MM, Xavier RJ, Demay MB, Russell RG, Factor S, Tokooya K, Jore BS, Lopez M, Pandita RK, Lia M, Carrion D, Xu H, Schorle H, Kohler JB, Scambler P, Wynshaw-Boris A, Skoultchi AI, Morrow BE, Kucherlapati R (2001) TBX1 is responsible for cardiovascular defects in velo-cardio-facial/DiGeorge syndrome. Cell 104:619-629.
35. Schinzel AA, Basaran S, Bernasconi F, Karaman B, Yuksel-Apak M, Robinson WP (1994) Maternal uniparental disomy 22 has no impact on the phenotype. Am J Hum Genet 54:21-24.
36. Schonten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G (2002) Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30:e57.
37. Sebastiani P, Ramuni MF, Nokin V, Baldwin CT, Steinberg MH (2005) Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia. Nature Genet 37:435-440.
38. Shaikh TH, Kurahashi H, Saitla SC, O'Hare AM, Hu P, Roe BA, Driscoll DA, McDonald-McGinn DM, Zackai EH, Budarf ML, Emanuel BS (2000) Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis. Hum Mol Genet 9:489-501.
39. Sugama S, Namihira T, Matsuoka R, Taira N, Eto Y, Mackawa K (1999) Psychiatric inpatients and chromosome deletions within 22q11.2. J Neurol Neurosurg Psychiatry 67:803-806.
40. Urban AE, Korbel JO, Selzer R, Richmond T, Haeker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M (2006) High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci USA 103:4534-4539.
41. Verzilli CJ, Stallard N, Whittaker JC (2006) Bayesian graphical models for genomewide association studies. Am J Hum Genet 79:100-112.
42. Weksberg R, Hughes S, Moldovan L, Bassett AS, Chow EW, Squire JA (2005) A method for accurate detection of genomic microdeletions using real-time quantitative PCR. BMC Genomics 6:180.
43. Yu W, Ballif BC, Kashork CD, Heilstedt HA, Howard LA, Cai WW, White LD, Liu W, Beaud et al. Bejjani BA, Shaw CA, Shaffer LG (2003) Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 well-characterized lp36 deletions. Hum Mol Genet 12:2145-2152.
44. Zhou X, Li C, Mok SC, Chen Z, Wong DT (2004) Whole genome loss of heterozygosity profiling on oral squamous cell carcinoma by high-density single nucleotide polymorphic allele (SNP) array. Cancer Genet Cytogenet 151:82-84.
45. Zhou X, Rao NP, Cole SW, Mok SC, Chen Z, Wong DT (2005) Progress in concurrent analysis of loss of heterozygosity and comparative genomic hybridization utilizing high density single nucleotide polymorphism arrays. Cancer Genet Cytogenet 159:53-57.