Amiel J, Sproat-Emison E, Garcia-Barcelo M, Lantieri F, Burzynski G, Borrego S, Pelet A, Arnold S, Miao X, Griseri P, et al. Hirschsprung disease, associated syndromes and genetics: a review. J Med Genet. 2008;45:1–14.
Article
CAS
PubMed
Google Scholar
Garcia-Barcelo MM, Tang CS, Ngan ES, Lui VC, Chen Y, So MT, Leon TY, Miao XP, Shum CK, Liu FQ, et al. Genome-wide association study identifies NRG1 as a susceptibility locus for Hirschsprung's disease. Proc Natl Acad Sci U S A. 2009;106:2694–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang Q, Arnold S, Heanue T, Kilambi KP, Doan B, Kapoor A, Ling AY, Sosa MX, Guy M, Jiang Q, et al. Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability. Am J Hum Genet. 2015;96:581–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Emison ES, Garcia-Barcelo M, Grice EA, Lantieri F, Amiel J, Burzynski G, Fernandez RM, Hao L, Kashuk C, West K, et al. Differential contributions of rare and common, coding and noncoding Ret mutations to multifactorial Hirschsprung disease liability. Am J Hum Genet. 2010;87:60–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature. 2012;488:471–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature. 2012;485:237–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee YH, Narzisi G, Leotta A, et al. De novo gene disruptions in children on the autistic spectrum. Neuron. 2012;74:285–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu B, Roos JL, Dexheimer P, Boone B, Plummer B, Levy S, Gogos JA, Karayiorgou M. Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet. 2011;43:864–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 2014;515:216–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 2012;485:246–50.
Article
PubMed
PubMed Central
Google Scholar
Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet. 2012;380:1674–82.
Article
CAS
PubMed
Google Scholar
Heanue TA, Pachnis V. Enteric nervous system development and Hirschsprung's disease: advances in genetic and stem cell studies. Nat Rev Neurosci. 2007;8:466–79.
Article
CAS
PubMed
Google Scholar
Samocha KE, Robinson EB, Sanders SJ, Stevens C, Sabo A, McGrath LM, Kosmicki JA, Rehnstrom K, Mallick S, Kirby A, et al. A framework for the interpretation of de novo mutation in human disease. Nat Genet. 2014;46:944–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Acuna-Hidalgo R, Bo T, Kwint MP, van de Vorst M, Pinelli M, Veltman JA, Hoischen A, Vissers LE, Gilissen C. Post-zygotic point mutations are an underrecognized source of de novo genomic variation. Am J Hum Genet. 2015;97:67–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nat Rev Genet. 2012;13:565–75.
Article
CAS
PubMed
Google Scholar
MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, et al. Guidelines for investigating causality of sequence variants in human disease. Nature. 2014;508:469–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shepherd I, Eisen J. Development of the zebrafish enteric nervous system. Methods Cell Biol. 2011;101:143–60.
Article
PubMed
PubMed Central
Google Scholar
Harrison C, Wabbersen T, Shepherd IT. In vivo visualization of the development of the enteric nervous system using a Tg(-8.3bphox2b:Kaede) transgenic zebrafish. Genesis. 2014;52:985–90.
Article
CAS
PubMed
Google Scholar
Robu ME, Larson JD, Nasevicius A, Beiraghi S, Brenner C, Farber SA, Ekker SC. p53 activation by knockdown technologies. PLoS Genet. 2007;3:e78.
Article
PubMed
PubMed Central
Google Scholar
Jao LE, Wente SR, Chen W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci U S A. 2013;110:13904–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Emison ES, McCallion AS, Kashuk CS, Bush RT, Grice E, Lin S, Portnoy ME, Cutler DJ, Green ED, Chakravarti A. A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk. Nature. 2005;434:857–63.
Article
CAS
PubMed
Google Scholar
Bedell VM, Westcot SE, Ekker SC. Lessons from morpholino-based screening in zebrafish. Brief Funct Genomics. 2011;10:181–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li MX, Kwan JS, Bao SY, Yang W, Ho SL, Song YQ, Sham PC. Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS Genet. 2013;9:e1003143.
Article
CAS
PubMed
PubMed Central
Google Scholar
Matsui T, Noguchi K, Fukuda M. Dennd3 functions as a guanine nucleotide exchange factor for small GTPase Rab12 in mouse embryonic fibroblasts. J Biol Chem. 2014;289:13986–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Piloto S, Schilling TF. Ovo1 links Wnt signaling with N-cadherin localization during neural crest migration. Development. 2010;137:1981–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Srinivasan S, Anitha M, Mwangi S, Heuckeroth RO. Enteric neuroblasts require the phosphatidylinositol 3-kinase/Akt/Forkhead pathway for GDNF-stimulated survival. Mol Cell Neurosci. 2005;29:107–19.
Article
CAS
PubMed
Google Scholar
Haffner C, Frauli M, Topp S, Irmler M, Hofmann K, Regula JT, Bally-Cuif L, Haass C. Nicalin and its binding partner Nomo are novel Nodal signaling antagonists. EMBO J. 2004;23:3041–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schier AF. Nodal signaling in vertebrate development. Annu Rev Cell Dev Biol. 2003;19:589–621.
Article
CAS
PubMed
Google Scholar
Smith JR, Vallier L, Lupo G, Alexander M, Harris WA, Pedersen RA. Inhibition of Activin/Nodal signaling promotes specification of human embryonic stem cells into neuroectoderm. Dev Biol. 2008;313:107–17.
Article
CAS
PubMed
Google Scholar
Chambers SM, Fasano CA, Papapetrou EP, Tomishima M, Sadelain M, Studer L. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat Biotechnol. 2009;27:275–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fontoura BM, Blobel G, Matunis MJ. A conserved biogenesis pathway for nucleoporins: proteolytic processing of a 186-kilodalton precursor generates Nup98 and the novel nucleoporin, Nup96. J Cell Biol. 1999;144:1097–112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tran EJ, Wente SR. Dynamic nuclear pore complexes: life on the edge. Cell. 2006;125:1041–53.
Article
CAS
PubMed
Google Scholar
Chakraborty P, Wang Y, Wei JH, van Deursen J, Yu H, Malureanu L, Dasso M, Forbes DJ, Levy DE, Seemann J, Fontoura BM. Nucleoporin levels regulate cell cycle progression and phase-specific gene expression. Dev Cell. 2008;15:657–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lupu F, Alves A, Anderson K, Doye V, Lacy E. Nuclear pore composition regulates neural stem/progenitor cell differentiation in the mouse embryo. Dev Cell. 2008;14:831–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
D'Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer MW. A change in nuclear pore complex composition regulates cell differentiation. Dev Cell. 2012;22:446–58.
Article
PubMed
PubMed Central
Google Scholar
Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer MW. Dynamic association of NUP98 with the human genome. PLoS Genet. 2013;9:e1003308.
Article
CAS
PubMed
PubMed Central
Google Scholar
Irla M, Puthier D, Granjeaud S, Saade M, Victorero G, Mattei MG, Nguyen C. Genomic organization and the tissue distribution of alternatively spliced isoforms of the mouse Spatial gene. BMC Genomics. 2004;5:41.
Article
PubMed
PubMed Central
Google Scholar
Irla M, Saade M, Fernandez C, Chasson L, Victorero G, Dahmane N, Chazal G, Nguyen C. Neuronal distribution of spatial in the developing cerebellum and hippocampus and its somatodendritic association with the kinesin motor KIF17. Exp Cell Res. 2007;313:4107–19.
Article
CAS
PubMed
Google Scholar
Yammine M, Saade M, Chauvet S, Nguyen C. Spatial gene's (Tbata) implication in neurite outgrowth and dendrite patterning in hippocampal neurons. Mol Cell Neurosci. 2014;59:1–9.
Article
CAS
PubMed
Google Scholar
Tang CS, Sribudiani Y, Miao XP, de Vries AR, Burzynski G, So MT, Leon YY, Yip BH, Osinga J, Hui KJ, et al. Fine mapping of the 9q31 Hirschsprung's disease locus. Hum Genet. 2010;127:675–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pingault V, Guiochon-Mantel A, Bondurand N, Faure C, Lacroix C, Lyonnet S, Goossens M, Landrieu P. Peripheral neuropathy with hypomyelination, chronic intestinal pseudo-obstruction and deafness: a developmental "neural crest syndrome" related to a SOX10 mutation. Ann Neurol. 2000;48:671–6.
Article
CAS
PubMed
Google Scholar
Harrison PJ, Law AJ. Neuregulin 1 and schizophrenia: genetics, gene expression, and neurobiology. Biol Psychiatry. 2006;60:132–40.
Article
CAS
PubMed
Google Scholar
Winge K, Rasmussen D, Werdelin LM. Constipation in neurological diseases. J Neurol Neurosurg Psychiatry. 2003;74:13–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bernier R, Golzio C, Xiong B, Stessman HA, Coe BP, Penn O, Witherspoon K, Gerdts J, Baker C, Vulto-van Silfhout AT, et al. Disruptive CHD8 mutations define a subtype of autism early in development. Cell. 2014;158:263–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van Ginneken C, Schafer KH, Van Dam D, Huygelen V, De Deyn PP. Morphological changes in the enteric nervous system of aging and APP23 transgenic mice. Brain Res. 2011;1378:43–53.
Article
PubMed
Google Scholar
Wahba G, Schock SC, Claridge E, Bettolli M, Grynspan D, Humphreys P, Staines WA. MeCP2 in the enteric nervous system. Neurogastroenterol Motil. 2015;27:1156–61.
Article
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome Project Data Processing S. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
Google Scholar
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li MX, Gui HS, Kwan JS, Bao SY, Sham PC. A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. Nucleic Acids Res. 2012;40:e53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
Article
PubMed
PubMed Central
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gulsuner S, Walsh T, Watts AC, Lee MK, Thornton AM, Casadei S, Rippey C, Shahin H. Consortium on the Genetics of S, Group PS, et al. Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell. 2013;154:518–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li B, Leal SM. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008;83:311–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Desmet FO, Hamroun D, Lalande M, Collod-Beroud G, Claustres M, Beroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37:e67.
Article
PubMed
PubMed Central
Google Scholar
Churkin A, Barash D. RNAmute: RNA secondary structure mutation analysis tool. BMC Bioinforma. 2006;7:221.
Article
Google Scholar
Jiang Q, Ho YY, Hao L, Berrios CN, Chakravarti A. Copy number variants in candidate genes are genetic modifiers of Hirschsprung disease. Plos One. 2011;6(6):e21219.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gui HS, Bao JY, Tang CSM, So MT, Ngo DN, Tran AQ, Bui DH, Pham DH, Nguyen TL, Tong A, et al. Targeted next-generation sequencing on Hirschsprung disease: a pilot study exploits DNA pooling. Ann Hum Genet. 2014;78:381–7.
Article
CAS
PubMed
Google Scholar
Alves MM, Sribudiani Y, Brouwer RW, Amiel J, Antinolo G, Borrego S, Ceccherini I, Chakravarti A, Fernandez RM, Garcia-Barcelo MM, et al. Contribution of rare and common variants determine complex diseases-Hirschsprung disease as a model. Dev Biol. 2013;382:320–9.
Article
CAS
PubMed
Google Scholar
Westerfield M. The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio), 4th Edition. University of Oregon Press, Eugene; 2000.
Google Scholar
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015;12:982–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods. 2001;25:402–8.
Article
CAS
PubMed
Google Scholar
Thisse C, Thisse B, Schilling TF, Postlethwait JH. Structure of the zebrafish Snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos. Development. 1993;119:1203–15.
CAS
PubMed
Google Scholar