A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk (original) (raw)

• Bolk, S. et al. A human model for multigenic inheritance: phenotypic expression in Hirschsprung disease requires both the RET gene and a new 9q31 locus. Proc. Natl Acad. Sci. USA 97, 268–273 (2000)
  Article ADS CAS Google Scholar
• Gabriel, S. B. et al. Segregation at three loci explains familial and population risk in Hirschsprung disease. Nature Genet. 31, 89–93 (2002)
  Article CAS Google Scholar
• Chakravarti, A. & Lyonnet, S. in The Metabolic and Molecular Bases of Inherited Disease 8th edn (eds Scriver, C. R., Beaudet, A. R., Sly, W. & Valle, D.) Ch. 251, 6231–6255 (McGraw-Hill, New York, 2001)
  Google Scholar
• Carrasquillo, M. M. et al. Genome-wide association study and mouse model identify interaction between RET and EDNRB pathways in Hirschsprung disease. Nature Genet. 32, 237–244 (2002)
  Article CAS Google Scholar
• Borrego, S. et al. RET genotypes comprising specific haplotypes of polymorphic variants predispose to isolated Hirschsprung disease. J. Med. Genet. 37, 572–578 (2000)
  Article CAS Google Scholar
• Garcia-Barcelo, M. M. et al. Chinese patients with sporadic Hirschsprung's disease are predominantly represented by a single RET haplotype. J. Med. Genet. 40, e122 (2003)
  Article Google Scholar
• Sancandi, M. et al. Single nucleotide polymorphic alleles in the 5′ region of the RET proto-oncogene define a risk haplotype in Hirschsprung's disease. J. Med. Genet. 40, 714–718 (2003)
  Article CAS Google Scholar
• McCallion, A. S. et al. Genomic variation in multigenic traits: Hirschsprung disease. Cold Spring Harb. Symp. Quant. Biol. 68, 373–381 (2003)
  Article CAS Google Scholar
• Uyama, T. et al. Molecular cloning and expression of a second chondroitin _N_-acetylgalactosaminyltransferase involved in the initiation and elongation of chondroitin/dermatan sulfate. J. Biol. Chem. 278, 3072–3078 (2003)
  Article CAS Google Scholar
• Sato, T. et al. Molecular cloning and characterization of a novel human β1,4-_N_-acetylgalactosaminyltransferase, β4GalNAc-T3, responsible for the synthesis of N,_N_′-diacetyllactosediamine, galNAc β1-4GlcNAc. J. Biol. Chem. 278, 47534–47544 (2003)
  Article CAS Google Scholar
• Spielman, R. S., McGinnis, R. E. & Ewens, W. J. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52, 506–516 (1993)
  CAS PubMed PubMed Central Google Scholar
• Lin, S., Chakravarti, A. & Cutler, D. J. Haplotype and missing data inference in nuclear families. Genome Res. 14, 1624–1632 (2004)
  Article CAS Google Scholar
• Lin, S., Chakravarti, A. & Cutler, D. J. Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies. Nature Genet. 36, 1181–1188 (2004)
  Article CAS Google Scholar
• Loots, G. G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136–140 (2000)
  Article ADS CAS Google Scholar
• Thomas, J. W. et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424, 788–793 (2003)
  Article ADS CAS Google Scholar
• Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003)
  Article ADS CAS Google Scholar
• Nobrega, M. & Pennacchio, L. A. Comparative genomic analysis as a tool for biological discovery. J. Physiol. 554, 31–39 (2003)
  Article Google Scholar
• Bray, N., Dubchak, I. & Pachter, L. AVID: A global alignment program. Genome Res. 13, 97–102 (2003)
  Article CAS Google Scholar
• Margulies, E. H., Blanchette, M., Haussler, D. & Green, E. D. Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507–2518 (2003)
  Article CAS Google Scholar
• Shepherd, I. T., Pietsch, J., Elworthy, S., Kelsh, R. N. & Raible, D. W. Roles for GFRalpha1 receptors in zebrafish enteric nervous system development. Development 131, 241–249 (2004)
  Article CAS Google Scholar
• Shepherd, I. T., Beattie, C. E. & Raible, D. W. Functional analysis of zebrafish GDNF. Dev. Biol. 231, 420–435 (2001)
  Article CAS Google Scholar
• Rivas, E. & Eddy, S. R. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2, 8 (2001)
  Article CAS Google Scholar
• Shoba, T., Dheen, S. T. & Tay, S. S. Retinoic acid influences the expression of the neuronal regulatory genes Mash-1 and c-ret in the developing rat heart. Neurosci. Lett. 318, 129–132 (2002)
  Article CAS Google Scholar
• Batourina, E. et al. Vitamin A controls epithelial/mesenchymal interactions through Ret expression. Nature Genet. 27, 74–78 (2001)
  Article CAS Google Scholar
• Pitera, J. E., Smith, V. V., Woolf, A. S. & Milla, P. J. Embryonic gut anomalies in a mouse model of retinoic Acid-induced caudal regression syndrome: delayed gut looping, rudimentary cecum, and anorectal anomalies. Am. J. Pathol. 159, 2321–2329 (2001)
  Article CAS Google Scholar
• ENCODE Project Consortium . The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636–640 (2004)
  Article ADS Google Scholar
• Haldane, J. B. S. The rate of mutation of human genes. Hereditas 35 (suppl.), 267–273 (1948)
  MathSciNet Google Scholar
• Allison, A. C. G-6-PD deficiency in red blood cells of East Africans. Nature 186, 531–532 (1960)
  Article ADS CAS Google Scholar
• Allison, A. C. & Clyde, D. F. Malaria in African children with deficient erythrocyte glucose-6-phosphate dehydrogenase. Br. Med. J. 5236, 1346–1349 (1961)
  Article Google Scholar
• Motulsky, A. Metabolic polymorphisms and the role of infectious disease in human evolution. Hum. Biol. 32, 28–62 (1960)
  CAS PubMed Google Scholar
• Hill, A. V. et al. Common west African HLA antigens are associated with protection from severe malaria. Nature 352, 595–600 (1991)
  Article ADS CAS Google Scholar
• Miller, L. H., Mason, S. J., Clyde, D. F. & McGinniss, M. H. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype, FyFy. N. Engl. J. Med. 295, 302–304 (1976)
  Article CAS Google Scholar
• Samson, M. et al. Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382, 722–725 (1996)
  Article ADS CAS Google Scholar
• Dean, M. et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273, 1856–1862 (1996)
  Article ADS CAS Google Scholar
• Huang, Y. et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nature Med. 2, 1240–1243 (1996)
  Article CAS Google Scholar
• Collins, F. S. et al. New goals for the U.S. Human Genome Project: 1998–2003. Science 282, 682–689 (1998)
  Article ADS CAS Google Scholar
• Lander, E. S. The new genomics: global views of biology. Science 274, 536–539 (1996)
  Article ADS CAS Google Scholar
• Falconer, D. S. The inheritance of liability to diseases with variable age of onset, with particular reference to diabetes mellitus. Ann. Hum. Genet. 31, 1–20 (1967)
  Article CAS Google Scholar
• Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)
  Article ADS CAS Google Scholar
• Cann, H. M. et al. A human genome diversity cell line panel. Science 296, 261–262 (2002)
  Article CAS Google Scholar
• Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978–989 (2001)
  Article CAS Google Scholar
• Cutler, D. J. et al. High-throughput variation detection and genotyping using microarrays. Genome Res. 11, 1913–1925 (2001)
  Article CAS Google Scholar