Medical sequencing of candidate genes for nonsyndromic cleft lip and palate

PLoS Genetics

Volumn 1, Issue 6, 2005, Pages 0651-0659

  Vieira, Alexandre R ^a   Avila, Joseph R ^a   Daack Hirsch, Sandra ^a   Dragan, Ecaterina ^a   Félix, Têmis M ^a   Rahimov, Fedik ^b   Harrington, Jill ^a   Schultz, Rebecca R ^a   Watanabe, Yoriko ^a   Johnson, Maria ^a   Fang, Jennifer ^a   O'Brien, Sarah E ^a   Orioli, Iêda M ^c   Castilla, Eduardo E ^d,e   FitzPatrick, David R ^f   Jiang, Rulang ^g   Marazita, Mary L ^h,i   Murray, Jeffrey C ^a  

^a UNIVERSITY OF IOWA   (United States)

^b UNIVERSITY OF IOWA   (United States)

^c FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^d INSTITUTO OSWALDO CRUZ   (Brazil)

^e Department of Gynecology and Obstetrics   (Argentina)

^f UNIVERSITY OF EDINBURGH   (United Kingdom)

^g UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^h UNIVERSITY OF PITTSBURGH   (United States)

ⁱ UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MSX1 PROTEIN, HUMAN; TRANSCRIPTION FACTOR MSX1;

ARTICLE; CLEFT LIP; CLEFT PALATE; DNA SEQUENCE; FAMILY HEALTH; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETIC DATABASE; GENETIC LINKAGE; GENETIC POLYMORPHISM; GENETIC PREDISPOSITION; GENETICS; HUMAN; MALE; PEDIGREE; POINT MUTATION;

CLEFT LIP; CLEFT PALATE; DATABASES, GENETIC; FAMILY HEALTH; FEMALE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; MALE; MSX1 TRANSCRIPTION FACTOR; PEDIGREE; POINT MUTATION; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 34547516140     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0010064     Document Type: Article

References (60)

1. Mossey PA, Little J (2002) Epidemiology of oral clefts: An international perspective. In: Wyszynski DF, editor. Cleft lip and palate. From origin to treatment. New York: Oxford Press, pp. 127-158.
2. Schliekelman P, Slatkin M (2002) Multiplex relative risk and estimation of the number of loci underlying an inherited disease. Am J Hum Genet 71: 1369-1385.
3. Murray JC, Schutte BC (2004) Cleft palate: Players, pathways, and pursuits. J Clin Invest 113: 1676-1678.
4. Jezewski PA, Vieira AR, Nishimura C, Ludwig B, Johnson M, et al. (2003) Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate. J Med Genet 40: 399-407.
5. Suzuki Y, Jezewski PA, Machida J, Watanabe Y, Shi M, et al. (2004) In a Vietnamese population, MSX1 variants contribute to cleft lip and palate. Genet Med 6: 117-125.
6. Kariyazono H, Ohno T, Ihara K, Igarashi H, Joh-o K, et al. (2001) Rapid detection of the 22q11-2 deletion with quantitative real-time PCR. Mol Cellular Probes 15: 71-73.
7. Marazita ML, Murray JC, Lidral AC, Arcos-Burgos M, Cooper ME, et al. (2004) Meta-analysis of 13 genome scans reveals multiple cleft lip/palate genes with novel loci on 9q21 and 2p32-35. Am J Hum Genet 75: 161-173.
8. Collins JS, Schwartz CE (2002) Detecting polymorphisms and mutations in candidate genes. Am J Hum Genet 71: 1251-1252.
9. van den Boogard MJH, Dorland M, Beemer FA, van Amstel HKP (2000) MSX1 mutation is associated with orofacial clefting and tooth agenesis in humans. Nat Genet 24: 342-343.
10. Dodé C, Levilliers J, Dupont JM, De Paepe A, Le Dû N, et al. (2003) Loss-of-function mutations in FGFR1 cause autosomal dominant Kallmann syndrome. Nat Genet 33: 463-465.
11. Hong K, Brugada J, Oliva A, Berruezo-Sanchez A, Potenza D, et al. (2004) Value of electrocardiographic parameters and ajmaline test in the diagnosis of Brugada syndrome caused by SCN5A mutations. Circulation 110: 3023-3027.
12. Kondo S, Schutte BC, Richardson RJ, Bjork BC, Knight AS, et al. (2002) Mutations in interferon regulatory factor 6 cause Van der Woude and popliteal pterygium syndromes. Nat Genet 32: 285-289.
13. Watanabe Y, Benson DW, Yano S, Akagi T, Yoshino M, et al. (2002) Two novel frameshift mutations in NKX2.5 result in novel features including visceral inversus and sinus venosus type ASD. J Med Genet 39: 807-811.
14. Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR (2003) ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acid Res 31: 3568-3571.
15. Zucchero T, Cooper ME, Maher BS, Daack-Hirsch S, Nepomuceno B, et al. (2004) Interferon regulatory factor (IRF6) is a modifier for isolated cleft lip and palate. New Engl J Med 351: 769-780.
16. Scapoli L, Palmieri A, Martinelli M, Pezetti F, Carinci P, et al. (2005) Strong evidence of linkage disequilibrium between polymorphisms at the IRF6 locus and nonsyndromic cleft lip with or without cleft palate, in an Italian population. Am J Hum Genet 76: 180-183.
17. Machida J, Yoshiura K, Funkhauser CD, Natsume N, Kawai T, et al. (1999) Transforming growth factor-α (TGFA): Genomic structure, boundary sequences, and mutation analysis in nonsyndromic cleft lip/palate and cleft palate only. Genomics 61: 237-242.
18. Mitchell LE (1997) Transforming growth factor α locus and nonsyndromic cleft lip with or without cleft palate: A reappraisal. Genet Epidemiol 14: 231-240.
19. Lidral AC, Romitti PA, Basart AM, Doetschman T, Leysens NJ, et al. (1998) Association of MSX1 and TGFB3 with nonsyndromic clefting in humans. Am J Hum Genet 63: 557-568.
20. Roessler E, Du YZ, Mullor JL, Casas E, Allen WP, et al. (2003) Loss-of-function mutations in the human GLI2 gene are associated with pituitary anomalies and holoprosencephaly-like features. Proc Natl Acad Sci U S A 100: 13424-13429.
21. Prescott NJ, Lees MM, Winter RM, Malcolm S (2000) Identification of susceptibility loci for nonsyndromic cleft lip with or without cleft palate in a two stage genome scan of affected sib-pairs. Hum Genet 106: 345-350.
22. -/- mice. Nat Genet 30: 106-109.
23. FitzPatrick DR, Carr IM, McLaren L, Leek JP, Wightman P, et al. (2003) Identification of SATB2 as the cleft palate gene on 2q32-q33. Hum Mol Genet 12: 2491-2501.
24. Murray JC, Daack-Hirsch S, Buetow KH, Munger R, Espina L, et al. (1997) Clinical and epidemiologic studies of cleft lip and palate in the Philippines. Cleft Palate Craniofac J 34: 7-10.
25. Romitti PA, Munger RG, Murray JC, Daack-Hirsch S, Hanson JW, et al. (1998) The effect of follow-up on limiting participation bias in genetic epidemiologic investigations. Eur J Epidemiol 14: 129-138.
26. Wilkie AOM, Tang Z, Elanko N, Walsh S, Twigg SRF, et al. (2000) Functional haploinsufflciency of the human homeobox gene MSX2 causes defects in skull ossification. Nat Genet 24: 387-390.
27. Castanet M, Park SM, Smith A, Bost M, Léger J, et al. (2002) A novel loss-of-function mutation in TTF-2 is associated with congenital hypothyroidsm, thyroid agenesis and cleft palate. Hum Mol Genet 11: 2051-2059.
28. Debeer P, de Ravel TJL, Devriendt K, Fryns JP, Huysmans C, et al. (2002) Human homologues of Osr1 and Osr2 are not involved in a syndrome with distal limb deficiencies, oral abnormalities, and renal defects. Am J Hum Genet 111: 455-456.
29. Zhang HT, Fei QY, Chen F, Qi QY, Zou W, et al. (2003) Mutational analysis of the transforming growth factor β receptor type I gene in primary non-small cell lung cancer. Lung Cancer 40: 281-287.
30. Nickerson DA, Tobe VO, Taylor SL (1997) PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res 25: 2745-2751.
31. Cann HM, Toma C, Cazes L, Legrand MF, Morel V, et al. (2002) A human diversity cell line panel. Science 296: 261-262.
32. Blencowe BJ (2000) Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases. Trends Biochem Sci 25: 106-110.
33. Graveley BR (2000) Sorting out the complexity of SR protein functions. RNA 6: 1197-1211.
34. Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, et al. (2004) Systematic identification and analysis of exonic splicing silencers. Cell 119: 831-845.
35. Sunyaev S, Ramensky V, Bork P (2000) Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet 16: 198-200.
36. Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, et al. (2001) Prediction of deleterious human alleles. Hum Mol Genet 10: 591-597.
37. Ramesnky V, Bork P, Sunyaev S (2002) Human non-synonymous SNPs: Server and survey. Nucleic Acids Res 30: 3894-3900.
38. Ranade K, Chang MS, Ting CT, Pei D, Hsiao CF, et al. (2001) High-throughput genotyping with single nucleotide polymorphisms. Genome Res 11: 1262-1268.
39. Shi M, Caprau D, Dagle J, Christiansen L, Christensen K, et al. (2004) Application of kinetic polymarase chain reaction and molecular beacon assays to pooled analyses and high-throughput genotyping for candidate genes. Birth Defects Res A Clin Mol Teratol 70: 65-74.
40. Laird NM, Horvath S, Xu X (2000) Implementing a unified approach to family-based tests of association. Genet Epidemiol 19 Suppl 1: S36-42.
41. Rabinowitz D, Laird N (2000) A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum Hered 50: 211-223.
42. Horvath S, Xu X, Laird NM (2001) The family based association test method: strategies for studying general genotype-phenotype associations. Eur J Hum Genet 9: 301-306.
43. Bonferroni CE (1936) Teoria statistica delle classi e calcolo delle probabilità. Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8: 3-62.
44. Vieira AR, Karras JC, Orioli IM, Castilla EE, Murray JC (2002) Genetic origins in a South American clefting population. Clin Genet 62: 458-463.
45. Vieira AR, Orioli IM, Castilla EE, Cooper ME, Marazita ML, et al. (2003) MSX1 and TGFB3 contribute to clefting in South America. J Dent Res 82: 289-292.
46. Weinberg CR (1999) Allowing for missing parents in genetic studies of case-parent triads. Am J Hum Genet 64: 1186-1193.
47. De Felice M, Ovitt C, Biffali E, Rodriguez-Mallon A, Arra C, et al. (1998) A mouse model for hereditary thyroid dysgenesis and cleft palate. Nat Genet 19: 395-398.
48. Jiang R, Lan Y, Chapman HD, Shawber C, Norton CR, et al. (1998) Defects in limb, craniofacial, and thymic development in Jagged2 mutant mice. Genes Dev 12: 1046-1057.
49. Zhao Y, Guo YJ, Tomac AC, Taylor NR, Grinberg A, et al. (1999) Isolated cleft palate in mice with a targeted mutation of the LIM homeobox gene Lhx8. Proc Natl Acad Sci U S A 96: 15002-15006.
50. Karolyi J, Erickson RP, Liu S, Killewald L (1990) Major effect on teratogen-induced facial clefting in mice determined by a single genetic region. Genetics 126: 201-205.
51. Lammer EJ, Shaw GM, Iovannisci DM, van Waes J, Finnell RH (2004) Maternal smoking and the risk of orofacial clefts: Susceptibility with NAT1 and NAT2 polymorphisms. Epidemiology 15: 150-156.
52. Lan Y, Ovitt CE, Cho ES, Maltby KM, Wang Q et al. (2004) Odd-skipped related 2 (Osr2) encodes a key intrinsic regulator of secondary palate growth and morphogenesis. Development 131: 3207-3216.
53. Celli J, Duijf P, Hamel BCJ, Bamshad M, Kramer B, et al. (1999) Heterozygous germline mutations in the p53 homolog p63 are the cause of EEC syndrome. Cell 99: 143-153.
54. Peters H, Neubuser A, Kratochwil K, Balling R (1998) Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities. Genes Dev 12: 2735-2747.
55. Reich A, Sapir A, Shilo B (1999) Sprouty is a general inhibitor of receptor tyrosine kinase signaling. Development 126: 4139-4147.
56. Jerome LA, Papaioannou VE (2001) DiGeorge syndrome phenotype in mice mutant for the T-box gene, Tbx1. Nat Genet 27: 286-291.
57. Yagi H, Furutani Y, Hamada H, Sasaki T, Asakawa S, et al. (2003) Role of TBX1 in human del22q11-2 syndrome. Lancet 362: 1366-1373.
58. Bush JO, Lan Y, Jiang R (2004) The cleft lip and palate defects in Dancer mutant mice result from gain of function of the Tbx10 gene. Proc Natl Acad Sci U S A 101: 7022-7027.
59. Kaartinen V, Voncken JW, Shuler C, Warburton D, Bu D, et al. (1995) Abnormal lung development and cleft palate in mice lacking TGF-beta-3 indicates defects of epithelial-mesenchymal interaction. Nat Genet 11: 415-421.
60. Proetzel G, Pawlowski SA, Wiles MV, Yin M, Boivin GP, et al. (1995) Transforming growth factor-B3 is required for secondary palate fusion. Nat Genet 11: 409-414.