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Volumn 13, Issue 1, 2012, Pages

Exon capture and bulk segregant analysis: Rapid discovery of causative mutations using high-throughput sequencing

Author keywords

Bulk segregant analysis; ccdc40; Cilia; Exon capture sequencing; Forward genetics; Genome assembly; Kidney development; pax8; SNP discovery; Xenopus tropicalis

Indexed keywords

ARTICLE; BULK SEGREGANT ANALYSIS; EMBRYO; EXON CAPTURE SEQUENCING; GENE IDENTIFICATION; GENE MAPPING; GENE MUTATION; GENE OVEREXPRESSION; GENETIC PROCEDURES; GENETIC SCREENING; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; LINKAGE ANALYSIS; MOLECULAR CLONING; MUTATIONAL ANALYSIS; NONHUMAN; SEGREGATION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; XENOPUS TROPICALIS;

EID: 84871218754     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-649     Document Type: Article
Times cited : (17)

References (51)
  • 2
    • 53249091939 scopus 로고    scopus 로고
    • Caenorhabditis elegans mutant allele identification by whole-genome sequencing
    • 10.1038/nmeth.1249, 2574580, 18677319
    • Sarin S, Prabhu S, O'Meara MM, Pe'er I, Hobert O. Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods 2008, 5:865-867. 10.1038/nmeth.1249, 2574580, 18677319.
    • (2008) Nat Methods , vol.5 , pp. 865-867
    • Sarin, S.1    Prabhu, S.2    O'Meara, M.M.3    Pe'er, I.4    Hobert, O.5
  • 3
    • 79953217082 scopus 로고    scopus 로고
    • Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis
    • 10.1534/genetics.110.124586, 3063661, 21196518
    • Arnold CN, Xia Y, Lin P, Ross C, Schwander M, Smart NG, Muller U, Beutler B. Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. Genetics 2011, 187:633-641. 10.1534/genetics.110.124586, 3063661, 21196518.
    • (2011) Genetics , vol.187 , pp. 633-641
    • Arnold, C.N.1    Xia, Y.2    Lin, P.3    Ross, C.4    Schwander, M.5    Smart, N.G.6    Muller, U.7    Beutler, B.8
  • 5
    • 84859354783 scopus 로고    scopus 로고
    • Fast Homozygosity Mapping and Identification of a Zebrafish ENU-Induced Mutation by Whole-Genome Sequencing
    • 10.1371/journal.pone.0034671, 3319596, 22496837
    • Voz ML, Coppieters W, Manfroid I, Baudhuin A, Von Berg V, Charlier C, Meyer D, Driever W, Martial JA, Peers B. Fast Homozygosity Mapping and Identification of a Zebrafish ENU-Induced Mutation by Whole-Genome Sequencing. PLoS One 2012, 7:e34671. 10.1371/journal.pone.0034671, 3319596, 22496837.
    • (2012) PLoS One , vol.7
    • Voz, M.L.1    Coppieters, W.2    Manfroid, I.3    Baudhuin, A.4    Von Berg, V.5    Charlier, C.6    Meyer, D.7    Driever, W.8    Martial, J.A.9    Peers, B.10
  • 8
    • 35748959649 scopus 로고    scopus 로고
    • Microarray-based genomic selection for high-throughput resequencing
    • 10.1038/nmeth1109, 17934469
    • Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray-based genomic selection for high-throughput resequencing. Nat Methods 2007, 4:907-909. 10.1038/nmeth1109, 17934469.
    • (2007) Nat Methods , vol.4 , pp. 907-909
    • Okou, D.T.1    Steinberg, K.M.2    Middle, C.3    Cutler, D.J.4    Albert, T.J.5    Zwick, M.E.6
  • 13
    • 80052835338 scopus 로고    scopus 로고
    • Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice
    • 10.1186/gb-2011-12-9-r90, 3308053, 21936904
    • Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ, Steel KP. Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice. Genome Biol 2011, 12:R90. 10.1186/gb-2011-12-9-r90, 3308053, 21936904.
    • (2011) Genome Biol , vol.12
    • Hilton, J.M.1    Lewis, M.A.2    Grati, M.3    Ingham, N.4    Pearson, S.5    Laskowski, R.A.6    Adams, D.J.7    Steel, K.P.8
  • 14
    • 79953742752 scopus 로고    scopus 로고
    • Grainyhead-like 2 regulates neural tube closure and adhesion molecule expression during neural fold fusion
    • 10.1016/j.ydbio.2011.02.027, 3114429, 21377456
    • Pyrgaki C, Liu A, Niswander L. Grainyhead-like 2 regulates neural tube closure and adhesion molecule expression during neural fold fusion. Dev Biol 2011, 353:38-49. 10.1016/j.ydbio.2011.02.027, 3114429, 21377456.
    • (2011) Dev Biol , vol.353 , pp. 38-49
    • Pyrgaki, C.1    Liu, A.2    Niswander, L.3
  • 16
    • 79960041626 scopus 로고    scopus 로고
    • Lampe1: an ENU-germline mutation causing spontaneous hepatosteatosis identified through targeted exon-enrichment and next-generation sequencing
    • 10.1371/journal.pone.0021979, 3131302, 21760938
    • Sheridan R, Lampe K, Shanmukhappa SK, Putnam P, Keddache M, Divanovic S, Bezerra J, Hoebe K. Lampe1: an ENU-germline mutation causing spontaneous hepatosteatosis identified through targeted exon-enrichment and next-generation sequencing. PLoS One 2011, 6:e21979. 10.1371/journal.pone.0021979, 3131302, 21760938.
    • (2011) PLoS One , vol.6
    • Sheridan, R.1    Lampe, K.2    Shanmukhappa, S.K.3    Putnam, P.4    Keddache, M.5    Divanovic, S.6    Bezerra, J.7    Hoebe, K.8
  • 18
    • 84857996686 scopus 로고    scopus 로고
    • From expression cloning to gene modeling: the development of Xenopus gene sequence resources
    • 10.1002/dvg.22008, 3488295, 22344767
    • Gilchrist MJ. From expression cloning to gene modeling: the development of Xenopus gene sequence resources. Genesis 2012, 50:143-154. 10.1002/dvg.22008, 3488295, 22344767.
    • (2012) Genesis , vol.50 , pp. 143-154
    • Gilchrist, M.J.1
  • 19
    • 84858000598 scopus 로고    scopus 로고
    • The hitchhiker's guide to Xenopus genetics
    • 10.1002/dvg.22007, 22344745
    • Abu-Daya A, Khokha MK, Zimmerman LB. The hitchhiker's guide to Xenopus genetics. Genesis 2012, 50:164-175. 10.1002/dvg.22007, 22344745.
    • (2012) Genesis , vol.50 , pp. 164-175
    • Abu-Daya, A.1    Khokha, M.K.2    Zimmerman, L.B.3
  • 20
    • 33644748173 scopus 로고    scopus 로고
    • Genetic and genomic prospects for Xenopus tropicalis research
    • 10.1016/j.semcdb.2005.11.009, 16427790
    • Carruthers S, Stemple DL. Genetic and genomic prospects for Xenopus tropicalis research. Semin Cell Dev Biol 2006, 17:146-153. 10.1016/j.semcdb.2005.11.009, 16427790.
    • (2006) Semin Cell Dev Biol , vol.17 , pp. 146-153
    • Carruthers, S.1    Stemple, D.L.2
  • 21
    • 81055157765 scopus 로고    scopus 로고
    • Xenopus research: metamorphosed by genetics and genomics
    • 10.1016/j.tig.2011.08.003, 21963197
    • Harland RM, Grainger RM. Xenopus research: metamorphosed by genetics and genomics. Trends Genet 2011, 27:507-515. 10.1016/j.tig.2011.08.003, 21963197.
    • (2011) Trends Genet , vol.27 , pp. 507-515
    • Harland, R.M.1    Grainger, R.M.2
  • 22
    • 84858000785 scopus 로고    scopus 로고
    • Xenopus white papers and resources: folding functional genomics and genetics into the frog
    • 10.1002/dvg.22015, 22287484
    • Khokha MK. Xenopus white papers and resources: folding functional genomics and genetics into the frog. Genesis 2012, 50:133-142. 10.1002/dvg.22015, 22287484.
    • (2012) Genesis , vol.50 , pp. 133-142
    • Khokha, M.K.1
  • 23
    • 33745698558 scopus 로고    scopus 로고
    • Genetic screens for mutations affecting development of Xenopus tropicalis
    • 10.1371/journal.pgen.0020091, 1475704, 16789825
    • Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL, Zimmerman LB. Genetic screens for mutations affecting development of Xenopus tropicalis. PLoS Genet 2006, 2:e91. 10.1371/journal.pgen.0020091, 1475704, 16789825.
    • (2006) PLoS Genet , vol.2
    • Goda, T.1    Abu-Daya, A.2    Carruthers, S.3    Clark, M.D.4    Stemple, D.L.5    Zimmerman, L.B.6
  • 24
    • 14844320115 scopus 로고    scopus 로고
    • Identification of mutants in inbred Xenopus tropicalis
    • 10.1016/j.mod.2004.11.003, 15763207
    • Grammer TC, Khokha MK, Lane MA, Lam K, Harland RM. Identification of mutants in inbred Xenopus tropicalis. Mech Dev 2005, 122:263-272. 10.1016/j.mod.2004.11.003, 15763207.
    • (2005) Mech Dev , vol.122 , pp. 263-272
    • Grammer, T.C.1    Khokha, M.K.2    Lane, M.A.3    Lam, K.4    Harland, R.M.5
  • 25
    • 14844302829 scopus 로고    scopus 로고
    • A gynogenetic screen to isolate naturally occurring recessive mutations in Xenopus tropicalis
    • 10.1016/j.mod.2004.11.001, 15763208
    • Noramly S, Zimmerman L, Cox A, Aloise R, Fisher M, Grainger RM. A gynogenetic screen to isolate naturally occurring recessive mutations in Xenopus tropicalis. Mech Dev 2005, 122:273-287. 10.1016/j.mod.2004.11.001, 15763208.
    • (2005) Mech Dev , vol.122 , pp. 273-287
    • Noramly, S.1    Zimmerman, L.2    Cox, A.3    Aloise, R.4    Fisher, M.5    Grainger, R.M.6
  • 26
    • 78650837422 scopus 로고    scopus 로고
    • The secreted integrin ligand nephronectin is necessary for forelimb formation in Xenopus tropicalis
    • 10.1016/j.ydbio.2010.10.015, 3021715, 20977901
    • Abu-Daya A, Nishimoto S, Fairclough L, Mohun TJ, Logan MP, Zimmerman LB. The secreted integrin ligand nephronectin is necessary for forelimb formation in Xenopus tropicalis. Dev Biol 2011, 349:204-212. 10.1016/j.ydbio.2010.10.015, 3021715, 20977901.
    • (2011) Dev Biol , vol.349 , pp. 204-212
    • Abu-Daya, A.1    Nishimoto, S.2    Fairclough, L.3    Mohun, T.J.4    Logan, M.P.5    Zimmerman, L.B.6
  • 27
    • 70350622304 scopus 로고    scopus 로고
    • Absence of heartbeat in the Xenopus tropicalis mutation muzak is caused by a nonsense mutation in cardiac myosin myh6
    • 10.1016/j.ydbio.2009.09.019, 2786259, 19769958
    • Abu-Daya A, Sater AK, Wells DE, Mohun TJ, Zimmerman LB. Absence of heartbeat in the Xenopus tropicalis mutation muzak is caused by a nonsense mutation in cardiac myosin myh6. Dev Biol 2009, 336:20-29. 10.1016/j.ydbio.2009.09.019, 2786259, 19769958.
    • (2009) Dev Biol , vol.336 , pp. 20-29
    • Abu-Daya, A.1    Sater, A.K.2    Wells, D.E.3    Mohun, T.J.4    Zimmerman, L.B.5
  • 28
    • 77954557597 scopus 로고    scopus 로고
    • Paralysis and delayed Z-disc formation in the Xenopus tropicalis unc45b mutant dicky ticker
    • 10.1186/1471-213X-10-75, 2919470, 20637071
    • Geach TJ, Zimmerman LB. Paralysis and delayed Z-disc formation in the Xenopus tropicalis unc45b mutant dicky ticker. BMC Dev Biol 2010, 10:75. 10.1186/1471-213X-10-75, 2919470, 20637071.
    • (2010) BMC Dev Biol , vol.10 , pp. 75
    • Geach, T.J.1    Zimmerman, L.B.2
  • 29
    • 77956302465 scopus 로고    scopus 로고
    • Focal adhesion kinase is essential for cardiac looping and multichamber heart formation
    • 10.1002/dvg.20650, 20572259
    • Doherty JT, Conlon FL, Mack CP, Taylor JM. Focal adhesion kinase is essential for cardiac looping and multichamber heart formation. Genesis 2010, 48:492-504. 10.1002/dvg.20650, 20572259.
    • (2010) Genesis , vol.48 , pp. 492-504
    • Doherty, J.T.1    Conlon, F.L.2    Mack, C.P.3    Taylor, J.M.4
  • 30
    • 79959732147 scopus 로고    scopus 로고
    • Early cardiac morphogenesis defects caused by loss of embryonic macrophage function in Xenopus
    • 10.1016/j.mod.2011.04.002, 3157588, 21515365
    • Smith SJ, Mohun TJ. Early cardiac morphogenesis defects caused by loss of embryonic macrophage function in Xenopus. Mech Dev 2011, 128:303-315. 10.1016/j.mod.2011.04.002, 3157588, 21515365.
    • (2011) Mech Dev , vol.128 , pp. 303-315
    • Smith, S.J.1    Mohun, T.J.2
  • 31
    • 70450203075 scopus 로고    scopus 로고
    • The miR-30 miRNA family regulates Xenopus pronephros development and targets the transcription factor Xlim1/Lhx1
    • 10.1242/dev.037432, 2778741, 19906860
    • Agrawal R, Tran U, Wessely O. The miR-30 miRNA family regulates Xenopus pronephros development and targets the transcription factor Xlim1/Lhx1. Development 2009, 136:3927-3936. 10.1242/dev.037432, 2778741, 19906860.
    • (2009) Development , vol.136 , pp. 3927-3936
    • Agrawal, R.1    Tran, U.2    Wessely, O.3
  • 33
    • 52649159125 scopus 로고    scopus 로고
    • Role of VEGF-D and VEGFR-3 in developmental lymphangiogenesis, a chemicogenetic study in Xenopus tadpoles
    • 10.1182/blood-2007-08-106302, 18474726
    • Ny A, Koch M, Vandevelde W, Schneider M, Fischer C, Diez-Juan A, Neven E, Geudens I, Maity S, Moons L, et al. Role of VEGF-D and VEGFR-3 in developmental lymphangiogenesis, a chemicogenetic study in Xenopus tadpoles. Blood 2008, 112:1740-1749. 10.1182/blood-2007-08-106302, 18474726.
    • (2008) Blood , vol.112 , pp. 1740-1749
    • Ny, A.1    Koch, M.2    Vandevelde, W.3    Schneider, M.4    Fischer, C.5    Diez-Juan, A.6    Neven, E.7    Geudens, I.8    Maity, S.9    Moons, L.10
  • 34
    • 76949102244 scopus 로고    scopus 로고
    • Lymph heart musculature is under distinct developmental control from lymphatic endothelium
    • 10.1016/j.ydbio.2010.01.002, 2845526, 20067786
    • Peyrot SM, Martin BL, Harland RM. Lymph heart musculature is under distinct developmental control from lymphatic endothelium. Dev Biol 2010, 339:429-438. 10.1016/j.ydbio.2010.01.002, 2845526, 20067786.
    • (2010) Dev Biol , vol.339 , pp. 429-438
    • Peyrot, S.M.1    Martin, B.L.2    Harland, R.M.3
  • 36
    • 0033215449 scopus 로고    scopus 로고
    • Synergism between Pax-8 and lim-1 in embryonic kidney development
    • 10.1006/dbio.1999.9414, 10491256
    • Carroll TJ, Vize PD. Synergism between Pax-8 and lim-1 in embryonic kidney development. Dev Biol 1999, 214:46-59. 10.1006/dbio.1999.9414, 10491256.
    • (1999) Dev Biol , vol.214 , pp. 46-59
    • Carroll, T.J.1    Vize, P.D.2
  • 37
    • 3042543035 scopus 로고    scopus 로고
    • Proximo-distal specialization of epithelial transport processes within the Xenopus pronephric kidney tubules
    • 10.1016/j.ydbio.2004.03.036, 15223337
    • Zhou X, Vize PD. Proximo-distal specialization of epithelial transport processes within the Xenopus pronephric kidney tubules. Dev Biol 2004, 271:322-338. 10.1016/j.ydbio.2004.03.036, 15223337.
    • (2004) Dev Biol , vol.271 , pp. 322-338
    • Zhou, X.1    Vize, P.D.2
  • 38
    • 0028783517 scopus 로고
    • Development of the Xenopus pronephric system
    • 10.1006/dbio.1995.1302, 7556934
    • Vize PD, Jones EA, Pfister R. Development of the Xenopus pronephric system. Dev Biol 1995, 171:531-540. 10.1006/dbio.1995.1302, 7556934.
    • (1995) Dev Biol , vol.171 , pp. 531-540
    • Vize, P.D.1    Jones, E.A.2    Pfister, R.3
  • 41
    • 84860720930 scopus 로고    scopus 로고
    • High prevalence of respiratory ciliary dysfunction in congenital heart disease patients with heterotaxy
    • 10.1161/CIRCULATIONAHA.111.079780, 22499950
    • Nakhleh N, Francis R, Giese RA, Tian X, Li Y, Zariwala MA, Yagi H, Khalifa O, Kureshi S, Chatterjee B, et al. High prevalence of respiratory ciliary dysfunction in congenital heart disease patients with heterotaxy. Circulation 2012, 125:2232-2242. 10.1161/CIRCULATIONAHA.111.079780, 22499950.
    • (2012) Circulation , vol.125 , pp. 2232-2242
    • Nakhleh, N.1    Francis, R.2    Giese, R.A.3    Tian, X.4    Li, Y.5    Zariwala, M.A.6    Yagi, H.7    Khalifa, O.8    Kureshi, S.9    Chatterjee, B.10
  • 42
    • 84883412952 scopus 로고    scopus 로고
    • Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton
    • Salmon A, Udall JA, Jeddeloh JA, Wendel J. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton. G3 (Bethesda) 2012, 2:921-930.
    • (2012) G3 (Bethesda) , vol.2 , pp. 921-930
    • Salmon, A.1    Udall, J.A.2    Jeddeloh, J.A.3    Wendel, J.4
  • 43
    • 77954223026 scopus 로고    scopus 로고
    • Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing
    • 10.1101/gr.102921.109, 2892099, 20472684
    • Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C, Gibbs R, Zhang K, Chen R. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res 2010, 20:981-988. 10.1101/gr.102921.109, 2892099, 20472684.
    • (2010) Genome Res , vol.20 , pp. 981-988
    • Wang, H.1    Chattopadhyay, A.2    Li, Z.3    Daines, B.4    Li, Y.5    Gao, C.6    Gibbs, R.7    Zhang, K.8    Chen, R.9
  • 45
    • 79960698975 scopus 로고    scopus 로고
    • Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
    • 10.1016/j.ygeno.2011.05.009, 21651976
    • Kong Y. Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 2011, 98:152-153. 10.1016/j.ygeno.2011.05.009, 21651976.
    • (2011) Genomics , vol.98 , pp. 152-153
    • Kong, Y.1
  • 46
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • 10.1093/bioinformatics/btp324, 2705234, 19451168
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 48
    • 0033953635 scopus 로고    scopus 로고
    • An economic method for the fluorescent labeling of PCR fragments
    • 10.1038/72708, 10657137
    • Schuelke M. An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 2000, 18:233-234. 10.1038/72708, 10657137.
    • (2000) Nat Biotechnol , vol.18 , pp. 233-234
    • Schuelke, M.1
  • 49
    • 0026285616 scopus 로고
    • In situ hybridization: an improved whole-mount method for Xenopus embryos
    • Harland RM. In situ hybridization: an improved whole-mount method for Xenopus embryos. Methods Cell Biol 1991, 36:685-695.
    • (1991) Methods Cell Biol , vol.36 , pp. 685-695
    • Harland, R.M.1
  • 51
    • 84868570270 scopus 로고    scopus 로고
    • Series: Methods in Molecular Biology: 2nd edition. Edited by Stefan Hoppler and Peter D Vize, In Xenopus Protocols: Post-Genomic Approaches
    • del Viso F, Khokha M, In Xenopus Protocols: Post-Genomic Approaches Generating Diploid Embryos from Xenopus tropicalis 2012, 33-41. Series: Methods in Molecular Biology: 2nd edition. Edited by Stefan Hoppler and Peter D Vize, In Xenopus Protocols: Post-Genomic Approaches.
    • (2012) Generating Diploid Embryos from Xenopus tropicalis , pp. 33-41
    • del Viso, F.1    Khokha, M.2


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