Incorporating genetic analyses into birth defects cluster investigations: Strategies for identifying candidate genes

Birth Defects Research Part A - Clinical and Molecular Teratology

Volumn 76, Issue 11, 2006, Pages 798-810

  Green, Ridgely Fisk ^a   Moore, Cynthia ^a  

^a NATIONAL CENTER ON BIRTH DEFECTS AND DEVELOPMENTAL DISABILITIES   (United States)

Author keywords

Birth defects; Cluster investigations; Gastroschisis; Genes; Public health

Indexed keywords

BIRTH DEFECT; DATA BASE; ENVIRONMENTAL FACTOR; FEASIBILITY STUDY; GASTROSCHISIS; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC LINKAGE; GENETIC SELECTION; GENOTYPE ENVIRONMENT INTERACTION; HEREDITY; HUMAN; INTERNET; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; REVIEW; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM;

ABNORMALITIES; ANIMALS; CLUSTER ANALYSIS; DISEASE MODELS, ANIMAL; GASTROSCHISIS; GENETIC DISEASES, INBORN; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INTERNET; POPULATION SURVEILLANCE; PUBLIC HEALTH; RISK FACTORS;

ANIMALIA;

EID: 33751246790     PISSN: 15420752     EISSN: 15420760     Source Type: Journal    
DOI: 10.1002/bdra.20280     Document Type: Review

References (96)

1. Alfarano C, Andrade CE, Anthony K, et al. 2005. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 33:D418-D424.
2. Bao L, Cui Y. 2005. Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics 21:2185-2190.
3. Botto LD, Yang Q. 2000. 5,10-Methylenetetrahydrofolate reductase gene variants and congenital anomalies: a HuGE review. Am J Epidemiol 151:862-877.
4. Cappon GD, Cook JC, Hurtt ME. 2003. Relationship between cyclooxygenase 1 and 2 selective inhibitors and fetal development when administered to rats and rabbits during the sensitive periods for heart development and midline closure. Birth Defects Res B Dev Reprod Toxicol 68:47-56.
5. Cardon LR, Abecasis GR. 2003. Using haplotype blocks to map human complex trait loci. Trends Genet 19:135-140.
6. Cartegni L, Wang J, Zhu Z, et al. 2003. ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res 31:3568-3571.
7. Casillas S, Barbadilla A. 2004. PDA: a pipeline to explore and estimate polymorphism in large DNA databases. Nucleic Acids Res 32:W166-W169.
8. Chang H, Fujita T. 2001. PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Biochem Biophys Res Commun 287:288-291.
9. Chekmenev DS, Haid C, Kel AE. 2005. P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res 33:W432-W437.
10. Chen QK, Hertz GZ, Stormo GD. 1995. MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput Appl Biosci 11:563-566.
11. Clark AG. 2004. The role of haplotypes in candidate gene studies. Genet Epidemiol 27:321-333.
12. Colpaert C, Bogers J, Hertveldt K, et al. 2000. Limb-body wall complex: 4 new cases illustrating the importance of examining placenta and umbilical cord. Pathol Res Pract 196:783-790.
13. Conde L, Vaquerizas JM, Ferrer-Costa C, et al. 2005. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res 33:W501-W505.
14. Craven CM, Carey JC, Ward K. 1997. Umbilical cord agenesis in limb body wall defect. Am J Med Genet 71:97-105.
15. Dahlquist KD, Salomonis N, Vranizan K, et al. 2002. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31:19-20.
16. Dantzer J, Moad C, Heiland R, Mooney S. 2005. MutDB services: interactive structural analysis of mutation data. Nucleic Acids Res 33:W311-W314.
17. Das UG, Cronk CE, Martier SS, et al. 2004. Alcohol dehydrogenase 2*3 affects alterations in offspring facial morphology associated with maternal ethanol intake in pregnancy. Alcohol Clin Exp Res 28:1598-1606.
18. Davey Smith G, Ebrahim S. 2003. 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease? Int J Epidemiol 32:1-22.
19. Dennis G Jr, Sherman BT, Hosack DA, et al. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4:P3.
20. Fairbrother WG, Holste D, Burge CB, Sharp PA. 2004. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2:E268.
21. Fox JA, Butland SL, McMillan S, et al. 2005. The Bioinformatics Links Directory: a compilation of molecular biology web servers. Nucleic Acids Res 33:W3-W24.
22. Freudenberg J, Propping P. 2002. A similarity-based method for genomewide prediction of disease-relevant human genes. Bioinformatics 18:S110-S115.
23. Gasteiger E, Gattiker A, Hoogland C, et al. 2003. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784-3788.
24. GeneTests. Medical Genetics Information Resource (online database). University of Washington, Seattle. 1993-2006. Updated weekly. Available at: http://www.genetests.org. Accessed: 13 January 2006.
25. Goujard J. 1999. Clusters of birth defects: emergency and management. A review of some publications. Eur J Epidemiol 15:853-862.
26. Grabe N. 2002. AliBaba2: context specific identification of transcription factor binding sites. In Silico Biol 2:S1-S15.
27. Grossman I, Avidan N, Singer C, et al. 2004. Genomic profiling of interpopulation diversity guides prioritization of candidate-genes for autoimmunity. Genes Immun 5:493-504.
28. Hristovski D, Peterlin B, Mitchell JA, Humphrey SM. 2005. Using literature-based discovery to identify disease candidate genes. Int J Med Inform 74:289-298.
29. Hu Y, Hines LM, Weng H, et al. 2003. Analysis of genomic and proteomic data using advanced literature mining. J Proteome Res 2:405-412.
30. Huang H, Barker WC, Chen Y, Wu CH. 2003. iProClass: an integrated database of protein family, function and structure information. Nucleic Acids Res 31:390-392.
31. Hubbard T, Andrews D, Caccamo M, et al. 2005. Ensembl 2005. Nucleic Acids Res 33:D447-D453.
32. Hubner CA, Stein V, Hermans-Borgmeyer I, et al. 2001. Disruption of KCC2 reveals an essential role of K-Cl cotransport already in early synaptic inhibition. Neuron 30:515-524.
33. International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431:931-945.
34. Ith B, Wei J, Yet SF, et al. 2005. Aortic carboxypeptidase-like protein is expressed in collagen-rich tissues during mouse embryonic development. Gene Expr Patterns 5:533-537.
35. Jenssen TK, Laegreid A, Komorowski J, Hovig E. 2001. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28:21-28.
36. Kanehisa M, Goto S, Hattori M, et al. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354-D357.
37. Kasprzyk A, Keefe D, Smedley D, et al. 2004. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 14:160-169.
38. Kel AE, Kondrakhin YV, Kolpakov Ph A, et al. 1995. Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences. Proc Int Conf Intell Syst Mol Biol 3:197-205.
39. Kel AE, Gossling E, Reuter I, et al. 2003. MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31:3576-3579.
40. Khatri P, Bhavsar P, Bawa G, Draghici S. 2004. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res 32:W449-W456.
41. Komuro H, Mori M, Hayashi Y, et al. 2001. Mutational analysis of the BMP-1 gene in patients with gastroschisis. J Pediatr Surg 36:885-587.
42. Kruglyak L, Nickerson DA. 2001. Variation is the spice of life. Nat Genet 27:234-236.
43. Layne MD, Yet SF, Maemura K, et al. 2001. Impaired abdominal wall development and deficient wound healing in mice lacking aortic carboxypeptidase-like protein. Mol Cell Biol 21:5256-5261.
44. Lee C, Atanelov L, Modrek B, Xing Y. 2003. ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res 31:101-105.
45. Loeken MR. 2006. Advances in understanding the molecular causes of diabetes-induced birth defects. J Soc Gynecol Investig 13:2-10.
46. Maier H, Dohr S, Grote K, et al. 2005. LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts. Nucleic Acids Res 33:W779-W782.
47. Marinescu VD, Kohane IS, Riva A. 2005a. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res 33:D91-D97.
48. Marinescu VD, Kohane IS, Riva A. 2005b. MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics 6:79.
49. Masseroli M, Galati O, Pinciroli F. 2005. GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res 33:W717-W723.
50. Masys DR, Welsh JB, Lynn Fink J, et al. 2001. Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics 17:319-326.
51. McCarver DG, Thomasson HR, Martier SS, et al. 1997. Alcohol dehydrogenase-2*3 allele protects against alcohol-related birth defects among African Americans. J Pharmacol Exp Ther 283:1095-1101.
52. Morrison JJ, Klein N, Chitty LS, et al. 1998. Intra-amniotic inflammation in human gastroschisis: possible aetiology of postnatal bowel dysfunction. Br J Obstet Gynaecol 105:1200-1204.
53. Mulder NJ, Apweiler R, Attwood TK, et al. 2005. InterPro, progress and status in 2005. Nucleic Acids Res 33:D201-D205.
54. Ng PC, Henikoff S. 2003. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812-3814.
55. Nikitin A, Egorov S, Daraselia N, Mazo I. 2003. Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 19:2155-2157.
56. OMIM. 2000. Online Mendelian Inheritance in Man. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD). Available at: http://www.ncbi. nlm.nih.gov/omim. Accessed: 13 January 2006.
57. Overbeek R, Fonstein M, D'Souza M, et al. 1999. Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1:93-108.
58. Pagani F, Stuani C, Tzetis M, et al. 2003. New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12. Hum Mol Genet 12:1111-1120.
59. Pagani F, Baralle FE. 2004. Genomic variants in exons and introns: identifying the splicing spoilers. Nat Rev Genet 5:389-396.
60. Pellegrini M, Marcotte EM, Thompson MJ, et al. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 96:4285-4288.
61. Peltonen L, McKusick VA. 2001. Genomics and medicine. Dissecting human disease in the postgenomic era. Science 291:1224-1229.
62. Peng Y, Yang PH, Ng SS, et al. 2004. A critical role of Pax6 in alcohol-induced fetal microcephaly. Neurobiol Dis 16:370-376.
63. Peng Y, Kwok KH, Yang PH, et al. 2005. Ascorbic acid inhibits ROS production, NF-kappa B activation and prevents ethanol-induced growth retardation and microencephaly. Neuropharmacology 48: 426-434.
64. Perez-Iratxeta C, Bork P, Andrade MA. 2002. Association of genes to genetically inherited diseases using data mining. Nat Genet 31:316-319.
65. Prestridge DS. 1996. SIGNAL SCAN 4.0: additional databases and sequence formats. Comput Appl Biosci 12:157-160.
66. Qu S, Niswender KD, Ji Q, et al. 1997. Polydactyly and ectopic ZPA formation in Alx-4 mutant mice. Development 124:3999-4008.
67. Quandt K, Frech K, Karas H, et al. 1995. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 23:4878-4884.
68. Ramensky V, Bork P, Sunyaev S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30:3894-3900.
69. Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. 1997. GeneCards: encyclopedia for genes, proteins and diseases. Weizmann Institute of Science, Bioinformatics Unit and Genome Center (Rehovot, Israel). Available at: http://bioinformatics.weizmann.ac.il/cards. Accessed: 13 January 2006.
70. Reumers J, Schymkowitz J, Ferkinghoff-Borg J, et al. 2005. SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res 33:D527-D532.
71. Risch NJ. 2000. Searching for genetic determinants in the new millennium. Nature 405:847-856.
72. Riva A, Kohane IS. 2004. A SNP-centric database for the investigation of the human genome. BMC Bioinformatics 5:33.
73. Sandelin A, Wasserman WW, Lenhard B. 2004. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 32:W249-W252.
74. Scholl TO, Johnson WG. 2000. Folic acid: influence on the outcome of pregnancy. Am J Clin Nutr 71:1295S-1303S.
75. Schug J, Overton GC. 1997. Modeling transcription factor binding sites with Gibbs sampling and minimum description length encoding. Proc Int Conf Intell Syst Mol Biol 5:268-271.
76. Stenson PD, Ball EV, Mort M, et al. 2003. Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21:577-581.
77. Stitziel NO, Binkowski TA, Tseng YY, et al. 2004. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res 32:D520-D522.
78. Sunyaev S, Lathe W 3rd, Bork P. 2001a. Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms. Curr Opin Struct Biol 11:125-130.
79. Sunyaev S, Ramensky V, Koch I, et al. 2001b. Prediction of deleterious human alleles. Hum Mol Genet 10:591-597.
80. Suzuki N, Labosky PA, Furuta Y, et al. 1996. Failure of ventral body wall closure in mouse embryos lacking a procollagen C-proteinase encoded by Bmp1, a mammalian gene related to Drosophila tolloid. Development 122:3587-3595.
81. Syvanen AC. 2005. Toward genome-wide SNP genotyping. Nat Genet 37(Suppl):S5-S10.
82. Tabor HK, Risch NJ, Myers RM. 2002. Opinion: candidate-gene approaches for studying complex genetic traits: practical considerations. Nat Rev Genet 3:391-397.
83. Tanabe L, Scherf U, Smith LH, et al. 1999. MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques 27:1210-1214,1216-1217.
84. Tchernitchko D, Goossens M, Wajcman H. 2004. In silico prediction of the deleterious effect of a mutation: proceed with caution in clinical genetics. Clin Chem 50:1974-1978.
85. Teraoka SN, Telatar M, Becker-Catania S, et al. 1999. Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences. Am J Hum Genet 64:1617-1631.
86. Tiffin N, Kelso JF, Powell AR, et al. 2005. Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res 33:1544-1552.
87. Torfs CP, Lam PK, Schaffer DM, Brand RJ. 1998. Association between mothers' nutrient intake and their offspring's risk of gastroschisis. Teratology 58:241-250.
88. Turner FS, Clutterbuck DR, Semple CA. 2003. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol 4:R75.
89. van Driel MA, Cuelenaere K, Kemmeren PP, et al. 2005. GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. Nucleic Acids Res 33:W758-W761.
90. Viljoen DL, Carr LG, Foroud TM, et al. 2001. Alcohol dehydrogenase-2*2 allele is associated with decreased prevalence of fetal alcohol syndrome in the mixed-ancestry population of the Western Cape Province, South Africa. Alcohol Clin Exp Res 25:1719-1722.
91. Wang X, Kim J, McWilliams R, Cutting GR. 2005. Increased prevalence of chronic rhinosinusitis in carriers of a cystic fibrosis mutation. Arch Otolaryngol Head Neck Surg 131:237-240.
92. Williams LJ, Honein MA, Rasmussen SA. 2002. Methods for a public health response to birth defects clusters. Teratology 66:S50-S58.
93. Zaykin DV, Zhivotovsky LA. 2005. Ranks of genuine associations in whole-genome scans. Genetics 171:813-823.
94. Zeeberg BR, Feng W, Wang G, et al. 2003. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4:R28.
95. Zhang K, Qin Z, Chen T, et al. 2005. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 21:131-134.
96. Zucchero TM, Cooper ME, Maher BS, et al. 2004. Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate. N Engl J Med 351:769-780.