Rapid identification of kidney cyst mutations by whole exome sequencing in zebrafish

Development (Cambridge)

Volumn 140, Issue 21, 2013, Pages 4445-4451

  Ryan, Sean ^a   Willer, Jason ^a   Marjoram, Lindsay ^a   Bagwell, Jennifer ^a   Mankiewicz, Jamie ^a   Leshchiner, Ignaty ^b   Goessling, Wolfram ^b,c   Bagnat, Michel ^a   Katsanis, Nicholas ^a  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c HARVARD STEM CELL INSTITUTE   (United States)

Author keywords

Cilia; Exome sequencing; Kidney cyst

Indexed keywords

ANIMAL TISSUE; ARTICLE; CHROMOSOME 15; CHROMOSOME 19; CONTROLLED STUDY; DNA EXTRACTION; DONOR SITE; EXOME; FEMALE; FISH STOCK; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENETIC IDENTIFICATION; GENETIC SCREENING; HISTOLOGY; HOMOZYGOSITY; HUMAN; KIDNEY CYST; LINKAGE ANALYSIS; MUTAGENESIS; NONHUMAN; NONSENSE MUTATION; OPEN READING FRAME; PHENOTYPE; POINT MUTATION; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; ZEBRA FISH;

CILIA; EXOME SEQUENCING; KIDNEY CYST;

ANIMALS; CYSTS; DNA MUTATIONAL ANALYSIS; EXOME; GENETIC LINKAGE; KIDNEY; MICROSCOPY, CONFOCAL; MUTAGENESIS; OLIGONUCLEOTIDES; ZEBRAFISH;

EID: 84885620415     PISSN: 09501991     EISSN: 14779129     Source Type: Journal    
DOI: 10.1242/dev.101170     Document Type: Article

References (32)

1. Badano, J. L., Mitsuma, N., Beales, P. L. and Katsanis, N. (2006). The ciliopathies: an emerging class of human genetic disorders. Annu. Rev. Genomics Hum. Genet. 7, 125-148.
2. Bagnat, M., Navis, A., Herbstreith, S., Brand-Arzamendi, K., Curado, S., Gabriel, S., Mostov, K., Huisken, J. and Stainier, D. Y. (2010). Cse1l is a negative regulator of CFTR-dependent fluid secretion. Curr. Biol. 20, 1840-1845.
3. Bakkers, J. (2011). Zebrafish as a model to study cardiac development and human cardiac disease. Cardiovasc. Res. 91, 279-288.
4. Bamshad, M. J., Ng, S. B., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A. and Shendure, J. (2011). Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745-755.
5. Bowen, M. E., Henke, K., Siegfried, K. R., Warman, M. L. and Harris, M. P. (2012). Efficient mapping and cloning of mutations in zebrafish by lowcoverage whole-genome sequencing. Genetics 190, 1017-1024.
6. Dagoneau, N., Goulet, M., Geneviève, D., Sznajer, Y., Martinovic, J., Smithson, S., Huber, C., Baujat, G., Flori, E., Tecco, L. et al. (2009). DYNC2H1 mutations cause asphyxiating thoracic dystrophy and short rib-polydactyly syndrome, type III. Am. J. Hum. Genet. 84, 706-711.
7. Davis, E. E. and Katsanis, N. (2012). The ciliopathies: a transitional model into systems biology of human genetic disease. Curr. Opin. Genet. Dev. 22, 290-303.
8. El Hokayem, J., Huber, C., Couvé, A., Aziza, J., Baujat, G., Bouvier, R., Cavalcanti, D. P., Collins, F. A., Cordier, M. P., Delezoide, A. L. et al. (2012). NEK1 and DYNC2H1 are both involved in short rib polydactyly Majewski type but not in Beemer Langer cases. J. Med. Genet. 49, 227-233.
9. Ellis, K., Bagwell, J. and Bagnat, M. (2013). Notochord vacuoles are lysosomerelated organelles that function in axis and spine morphogenesis. J. Cell Biol. 200, 667-679.
10. Fairfield, H., Gilbert, G. J., Barter, M., Corrigan, R. R., Curtain, M., Ding, Y., D'Ascenzo, M., Gerhardt, D. J., He, C., Huang, W. et al. (2011). Mutation discovery in mice by whole exome sequencing. Genome Biol. 12, R86.
11. Gherman, A., Davis, E. E. and Katsanis, N. (2006). The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia. Nat. Genet. 38, 961-962.
12. Hildebrandt, F., Benzing, T. and Katsanis, N. (2011). Ciliopathies. N. Engl. J. Med. 364, 1533-1543.
13. Hill, J. T., Demarest, B. L., Bisgrove, B. W., Gorsi, B., Su, Y. C. and Yost, H. J. (2013). MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Genome Res. 23, 687-697.
14. Horani, A., Ferkol, T. W., Shoseyov, D., Wasserman, M. G., Oren, Y. S., Kerem, B., Amirav, I., Cohen-Cymberknoh, M., Dutcher, S. K., Brody, S. L. et al. (2013). LRRC6 mutation causes primary ciliary dyskinesia with dynein arm defects. PLoS ONE 8, e59436.
15. Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L. et al. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498-503.
16. Kettleborough, R. N., Busch-Nentwich, E. M., Harvey, S. A., Dooley, C. M., de Bruijn, E., van Eeden, F., Sealy, I., White, R. J., Herd, C., Nijman, I. J. et al. (2013). A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature 496, 494-497.
17. Kodani, A., Salomé Sirerol-Piquer, M., Seol, A., Garcia-Verdugo, J. M. and Reiter, J. F. (2013). Kif3a interacts with Dynactin subunit p150 Glued to organize centriole subdistal appendages. EMBO J. 32, 597-607.
18. Krock, B. L., Mills-Henry, I. and Perkins, B. D. (2009). Retrograde intraflagellar transport by cytoplasmic dynein-2 is required for outer segment extension in vertebrate photoreceptors but not arrestin translocation. Invest. Ophthalmol. Vis. Sci. 50, 5463-5471.
19. Lawson, N. D. and Wolfe, S. A. (2011). Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish. Dev. Cell 21, 48-64.
20. Leshchiner, I., Alexa, K., Kelsey, P., Adzhubei, I., Austin-Tse, C. A., Cooney, J. D., Anderson, H., King, M. J., Stottmann, R. W., Garnaas, M. K. et al. (2012). Mutation mapping and identification by whole-genome sequencing. Genome Res. 22, 1541-1548.
21. Merrill, A. E., Merriman, B., Farrington-Rock, C., Camacho, N., Sebald, E. T., Funari, V. A., Schibler, M. J., Firestein, M. H., Cohn, Z. A., Priore, M. A. et al. (2009). Ciliary abnormalities due to defects in the retrograde transport protein DYNC2H1 in short-rib polydactyly syndrome. Am. J. Hum. Genet. 84, 542-549.
22. Miller, A. C., Obholzer, N. D., Shah, A. N., Megason, S. G. and Moens, C. B. (2013). RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res. 23, 679-686.
23. Navis, A., Marjoram, L. and Bagnat, M. (2013). Cftr controls lumen expansion and function of Kupffer's vesicle in zebrafish. Development 140, 1703-1712.
24. Noël, E. S., Casal-Sueiro, A., Busch-Nentwich, E., Verkade, H., Dong, P. D., Stemple, D. L. and Ober, E. A. (2008). Organ-specific requirements for Hdac1 in liver and pancreas formation. Dev. Biol. 322, 237-250.
25. Obholzer, N., Swinburne, I. A., Schwab, E., Nechiporuk, A. V., Nicolson, T. and Megason, S. G. (2012). Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing. Development 139, 4280-4290.
26. Ocbina, P. J., Eggenschwiler, J. T., Moskowitz, I. and Anderson, K. V. (2011). Complex interactions between genes controlling trafficking in primary cilia. Nat. Genet. 43, 547-553.
27. Patton, E. E. and Zon, L. I. (2001). The art and design of genetic screens: zebrafish. Nat. Rev. Genet. 2, 956-966.
28. Schmidts, M., Arts, H. H., Bongers, E. M., Yap, Z., Oud, M. M., Antony, D., Duijkers, L., Emes, R. D., Stalker, J., Yntema, J. B. et al.; UK10K (2013). Exome sequencing identifies DYNC2H1 mutations as a common cause of asphyxiating thoracic dystrophy (Jeune syndrome) without major polydactyly, renal or retinal involvement. J. Med. Genet. 50, 309-323.
29. Sun, Z., Amsterdam, A., Pazour, G. J., Cole, D. G., Miller, M. S. and Hopkins, N. (2004). A genetic screen in zebrafish identifies cilia genes as a principal cause of cystic kidney. Development 131, 4085-4093.
30. Voz, M. L., Coppieters, W., Manfroid, I., Baudhuin, A., Von Berg, V., Charlier, C., Meyer, D., Driever, W., Martial, J. A. and Peers, B. (2012). Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing. PLoS ONE 7, e34671.
31. Westerfield, M. (2000) The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio). Eugene, OR: University of Oregon Press.
32. Zhou, Y. and Zon, L. I. (2011). The Zon laboratory guide to positional cloning in zebrafish. Methods Cell Biol. 104, 287-309.