메뉴 건너뛰기




Volumn 4, Issue 1, 2015, Pages

Using optical mapping data for the improvement of vertebrate genome assemblies

Author keywords

Genome assembly; Genome Reference Consortium; Optical mapping; Reference genomes; Rmap

Indexed keywords

GENE AMPLIFICATION; GENE SEQUENCE; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; HYBRIDIZATION; MOLECULAR CLONING; NONHUMAN; OPTICAL MAPPING; PRIORITY JOURNAL; REVIEW; VERTEBRATE; ANIMAL; GENETICS; GENOMICS; PROCEDURES; RESTRICTION MAPPING; SEQUENCE ANALYSIS;

EID: 84945498007     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/s13742-015-0052-y     Document Type: Review
Times cited : (45)

References (27)
  • 1
    • 0027485082 scopus 로고
    • Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping
    • 8211116
    • Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 1993, 262:110-114. 10.1126/science.8211116, 8211116.
    • (1993) Science , vol.262 , pp. 110-114
    • Schwartz, D.C.1    Li, X.2    Hernandez, L.I.3    Ramnarain, S.P.4    Huff, E.J.5    Wang, Y.K.6
  • 2
    • 84873595859 scopus 로고    scopus 로고
    • Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)
    • 23263233
    • Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 2013, 31:135-141. 10.1038/nbt.2478, 23263233.
    • (2013) Nat Biotechnol , vol.31 , pp. 135-141
    • Dong, Y.1    Xie, M.2    Jiang, Y.3    Xiao, N.4    Du, X.5    Zhang, W.6
  • 5
    • 84945498158 scopus 로고    scopus 로고
    • Accessed 17 Dec 2014.
    • Genome Reference Consortium. http://genomereference.org (2014). Accessed 17 Dec 2014..
    • (2014)
  • 6
    • 0033804974 scopus 로고    scopus 로고
    • Optical mapping of BAC clones from the human Y chromosome DAZ locus
    • 10984460
    • Giacalone J, Delobette S, Gibaja V, Ni L, Skiadas Y, Qi R, et al. Optical mapping of BAC clones from the human Y chromosome DAZ locus. Genome Res 2000, 10:1421-1429. 10.1101/gr.112100, 10984460.
    • (2000) Genome Res , vol.10 , pp. 1421-1429
    • Giacalone, J.1    Delobette, S.2    Gibaja, V.3    Ni, L.4    Skiadas, Y.5    Qi, R.6
  • 7
    • 84880943505 scopus 로고    scopus 로고
    • Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy
    • 23428595
    • Levy-Sakin M, Ebenstein Y. Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy. Curr Opin Biotechnol 2013, 24:690-698. 10.1016/j.copbio.2013.01.009, 23428595.
    • (2013) Curr Opin Biotechnol , vol.24 , pp. 690-698
    • Levy-Sakin, M.1    Ebenstein, Y.2
  • 8
    • 43049143055 scopus 로고    scopus 로고
    • Mapping and sequencing of structural variation from eight human genomes
    • 18451855
    • Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, et al. Mapping and sequencing of structural variation from eight human genomes. Nature 2008, 453:56-64. 10.1038/nature06862, 18451855.
    • (2008) Nature , vol.453 , pp. 56-64
    • Kidd, J.M.1    Cooper, G.M.2    Donahue, W.F.3    Hayden, H.S.4    Sampas, N.5    Graves, T.6
  • 9
    • 66249148986 scopus 로고    scopus 로고
    • Lineage-specific biology revealed by a finished genome assembly of the mouse
    • 19468303
    • Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, et al. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 2009, 7:e1000112. 10.1371/journal.pbio.1000112, 19468303.
    • (2009) PLoS Biol , vol.7
    • Church, D.M.1    Goodstadt, L.2    Hillier, L.W.3    Zody, M.C.4    Goldstein, S.5    She, X.6
  • 11
    • 81455140597 scopus 로고    scopus 로고
    • Optically mapping multiple bacterial genomes simultaneously in a single run
    • 22132087
    • Riley MC, Lee JE, Lesho E, Kirkup BC. Optically mapping multiple bacterial genomes simultaneously in a single run. PLoS One 2011, 6:e27085. 10.1371/journal.pone.0027085, 22132087.
    • (2011) PLoS One , vol.6
    • Riley, M.C.1    Lee, J.E.2    Lesho, E.3    Kirkup, B.C.4
  • 12
    • 84945497469 scopus 로고    scopus 로고
    • Accessed 17 Dec 2014
    • OpGen. http://www.opgen.com (2015). Accessed 17 Dec 2014..
    • (2015)
  • 13
    • 78649341898 scopus 로고    scopus 로고
    • Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes
    • 20699272
    • Das SK, Austin MD, Akana MC, Deshpande P, Cao H, Xiao M. Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. Nucleic Acids Res 2010, 38:e177. 10.1093/nar/gkq673, 20699272.
    • (2010) Nucleic Acids Res , vol.38
    • Das, S.K.1    Austin, M.D.2    Akana, M.C.3    Deshpande, P.4    Cao, H.5    Xiao, M.6
  • 14
    • 84945498218 scopus 로고    scopus 로고
    • Accessed 17 Dec 2014.
    • BioNano Genomics. http://www.bionanogenomics.com (2013). Accessed 17 Dec 2014..
    • (2013)
  • 15
    • 84863847010 scopus 로고    scopus 로고
    • Multicolor super-resolution DNA imaging for genetic analysis
    • 22698062
    • Baday M, Cravens A, Hastie A, Kim H, Kudeki DE, Kwok PY, et al. Multicolor super-resolution DNA imaging for genetic analysis. Nano Lett 2012, 12:3861-3866. 10.1021/nl302069q, 22698062.
    • (2012) Nano Lett , vol.12 , pp. 3861-3866
    • Baday, M.1    Cravens, A.2    Hastie, A.3    Kim, H.4    Kudeki, D.E.5    Kwok, P.Y.6
  • 16
    • 84864883566 scopus 로고    scopus 로고
    • Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
    • 22797562
    • Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 2012, 30:771-776. 10.1038/nbt.2303, 22797562.
    • (2012) Nat Biotechnol , vol.30 , pp. 771-776
    • Lam, E.T.1    Hastie, A.2    Lin, C.3    Ehrlich, D.4    Das, S.K.5    Austin, M.D.6
  • 17
    • 84902080336 scopus 로고    scopus 로고
    • Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome
    • 24885025
    • O'Bleness M, Searles VB, Dickens CM, Astling D, Albracht D, Mak AC, et al. Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome. BMC Genomics 2014, 15:387. 10.1186/1471-2164-15-387, 24885025.
    • (2014) BMC Genomics , vol.15 , pp. 387
    • O'Bleness, M.1    Searles, V.B.2    Dickens, C.M.3    Astling, D.4    Albracht, D.5    Mak, A.C.6
  • 18
    • 84876087138 scopus 로고    scopus 로고
    • Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing
    • 23590730
    • van Heesch S, Kloosterman WP, Lansu N, Ruzius FP, Levandowsky E, Lee CC, et al. Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing. BMC Genomics 2013, 14:257. 10.1186/1471-2164-14-257, 23590730.
    • (2013) BMC Genomics , vol.14 , pp. 257
    • van Heesch, S.1    Kloosterman, W.P.2    Lansu, N.3    Ruzius, F.P.4    Levandowsky, E.5    Lee, C.C.6
  • 19
    • 84991528460 scopus 로고    scopus 로고
    • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
    • 23870653
    • Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2013, 2:10. 10.1186/2047-217X-2-10, 23870653.
    • (2013) Gigascience , vol.2 , pp. 10
    • Bradnam, K.R.1    Fass, J.N.2    Alexandrov, A.3    Baranay, P.4    Bechner, M.5    Birol, I.6
  • 20
    • 84945497902 scopus 로고    scopus 로고
    • Germinate & Grow: A de Bruijn assembly algorithm for optical maps
    • Accessed 17 Dec 2014.
    • Goldstein S, Schwartz DW. Germinate & Grow: A de Bruijn assembly algorithm for optical maps. F1000Posters. 2011. http://f1000.com/posters/browse/summary/1047. Accessed 17 Dec 2014..
    • (2011) F1000Posters
    • Goldstein, S.1    Schwartz, D.W.2
  • 21
    • 84921918950 scopus 로고    scopus 로고
    • High-coverage sequencing and annotated assemblies of the budgerigar genome
    • 25061512
    • Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience 2014, 3:11. 10.1186/2047-217X-3-11, 25061512.
    • (2014) Gigascience , vol.3 , pp. 11
    • Ganapathy, G.1    Howard, J.T.2    Ward, J.M.3    Li, J.4    Li, B.5    Li, Y.6
  • 22
    • 84875737598 scopus 로고    scopus 로고
    • Using population admixture to help complete maps of the human genome
    • 23435088
    • Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, et al. Using population admixture to help complete maps of the human genome. Nat Genet 2013, 45:406-414. 10.1038/ng.2565, 23435088.
    • (2013) Nat Genet , vol.45 , pp. 406-414
    • Genovese, G.1    Handsaker, R.E.2    Li, H.3    Altemose, N.4    Lindgren, A.M.5    Chambert, K.6
  • 23
    • 84883786102 scopus 로고    scopus 로고
    • Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes
    • 23932108
    • Genovese G, Handsaker RE, Li H, Kenny EE, McCarroll SA. Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes. Am J Hum Genet 2013, 93:411-421. 10.1016/j.ajhg.2013.07.002, 23932108.
    • (2013) Am J Hum Genet , vol.93 , pp. 411-421
    • Genovese, G.1    Handsaker, R.E.2    Li, H.3    Kenny, E.E.4    McCarroll, S.A.5
  • 24
    • 84876798186 scopus 로고    scopus 로고
    • The zebrafish reference genome sequence and its relationship to the human genome
    • 23594743
    • Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013, 496:498-503. 10.1038/nature12111, 23594743.
    • (2013) Nature , vol.496 , pp. 498-503
    • Howe, K.1    Clark, M.D.2    Torroja, C.F.3    Torrance, J.4    Berthelot, C.5    Muffato, M.6
  • 25
    • 84945497536 scopus 로고    scopus 로고
    • Accessed 17 Dec 2014.
    • gEVAL - The Genome Evaluation Browser. http://geval.sanger.ac.uk (2014). Accessed 17 Dec 2014..
    • (2014)
  • 27
    • 84355166513 scopus 로고    scopus 로고
    • The Medicago genome provides insight into the evolution of rhizobial symbioses
    • 22089132
    • Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480:520-524. 10.1038/480162a, 22089132.
    • (2011) Nature , vol.480 , pp. 520-524
    • Young, N.D.1    Debelle, F.2    Oldroyd, G.E.3    Geurts, R.4    Cannon, S.B.5    Udvardi, M.K.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.