Sequence-based characterization of structural variation in the mouse genome

Nature

Volumn 477, Issue 7364, 2011, Pages 326-329

  Yalcin, Binnaz ^a   Wong, Kim ^b   Agam, Avigail ^a,c   Goodson, Martin ^a   Keane, Thomas M ^b   Gan, Xiangchao ^a   Nellåker, Christoffer ^c   Goodstadt, Leo ^a   Nicod, Jérôme ^a   Bhomra, Amarjit ^a   Hernandez Pliego, Polinka ^a   Whitley, Helen ^a   Cleak, James ^a   Dutton, Rebekah ^a   Janowitz, Deborah ^a,d   Mott, Richard ^a   Adams, David J ^b   Flint, Jonathan ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ABUNDANCE; EXPERIMENTAL STUDY; GENE EXPRESSION; GENOME; IMMUNOASSAY; PHENOTYPE; RODENT;

ARTICLE; EXON; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; MOUSE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS;

MAMMALIA;

EID: 80052851948     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature10432     Document Type: Article

References (30)

1. Mills, R. E. et al. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65 (2011).
2. Quinlan, A. R. et al. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res. 20, 623-635 (2010).
3. Zhang,F.,Gu,W.,Hurles,M.E.&Lupski, J.R.Copynumber variationinhumanhealth, disease, and evolution. Annu. Rev. Genomics Hum. Genet. 10, 451-481 (2009).
4. Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2010).
5. Stranger, B. E. et al. Population genomics of humangene expression.Nature Genet. 39, 1217-1224 (2007).
6. Agam, A. et al. Elusive copy number variation in the mouse genome. PLoS ONE 5, e12839 (2010).
7. Cahan, P., Li, Y., Izumi, M.& Graubert, T. A. The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nature Genet. 41, 430-437 (2009).
8. Henrichsen, C. N. et al. Segmental copy number variation shapes tissue transcriptomes. Nature Genet. 41, 424-429 (2009).
9. Schadt, E. E. et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genet. 37, 710-717 (2005). (Pubitemid 41754887)
10. Zhang, F. et al. The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans.Nature Genet. 41, 849-853 (2009).
11. Ma, J. L., Kim, E. M., Haber, J. E.& Lee, S. E. Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double-strand breaks lacking overlapping end sequences. Mol. Cell. Biol. 23, 8820-8828 (2003). (Pubitemid 37433382)
12. Stankiewicz, P. & Lupski, J. R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437-455 (2010).
13. Stankiewicz, P. & Lupski, J. R. Genomearchitecture, rearrangements and genomic disorders. Trends Genet. 18, 74-82 (2002).
14. Hastings, P. J., Ira, G. & Lupski, J. R. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 5, e1000327 (2009).
15. Huang, G. J. et al. High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues. Genome Res. 19, 1133-1140 (2009).
16. Yalcin, B., Flint, J. & Mott, R. Using progenitor strain information to identify quantitative trait nucleotides in outbred mice. Genetics 171, 673-681 (2005). (Pubitemid 43156455)
17. Valdar, W. et al. Genome-wide genetic association of complex traits in heterogeneous stock mice. Nature Genet. 38, 879-887 (2006). (Pubitemid 44141655)
18. Keane, T. M. et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature doi:10.1038/nature10413 (this issue).
19. Yalcin, B. et al. Commercially available outbred mice for genome-wide association studies. PLoS Genet. 6, e1001085 (2010).
20. Best, S., Le Tissier, P., Towers, G. & Stoye, J. P. Positional cloning of the mouse retrovirus restriction gene Fv1. Nature 382, 826-829 (1996). (Pubitemid 26299569)
21. Boyden, L. M. et al. Skint1, the prototype of a newly identified immunoglobulin superfamily gene cluster, positively selects epidermal cd T cells. Nature Genet. 40, 656-662 (2008). (Pubitemid 351601202)
22. Nelson, T. M., Munger, S. D. & Boughter, J. D. Jr. Haplotypes at the Tas2r locus on distal chromosome 6 vary with quinine taste sensitivity in inbred mice.BMCGenet. 6, 32 (2005).
23. Persson, K., Heby, O. & Berger, F. G. The functional intronless S-adenosylmethionine decarboxylase gene of the mouse (Amd-2) is linked to the ornithine decarboxylase gene (Odc) on chromosome12 and is present in distantly related species of the genus Mus. Mamm. Genome 10, 784-788 (1999). (Pubitemid 29390554)
24. Wu, B. et al. Mutations in sterol O-acyltransferase 1 (Soat1) result in hair interior defects in AKR/J mice. J. Invest. Dermatol. 130, 2666-2668 (2010).
25. Tareen, S. U., Sawyer, S. L., Malik, H. S.&Emerman, M.An expanded clade of rodent Trim5 genes. Virology 385, 473-483 (2009).
26. Taylor, K. et al. Defensin-related peptide 1 (Defr1) is allelic to Defb8 and chemoattracts immature DC and CD41 T cells independently of CCR6. Eur. J. Immunol. 39, 1353-1360 (2009).
27. Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871 (2009).
28. Chen, K. et al. BreakDancer: an algorithmfor high-resolution mapping of genomic structural variation. Nature Methods 6, 677-681 (2009).
29. Simpson, J. T., McIntyre, R. E., Adams, D. J. & Durbin, R. Copy number variant detection in inbred strains from short read sequence data. Bioinformatics 26, 565-567 (2010).
30. Manske, H. M. & Kwiatkowski, D. P. LookSeq: a browser-based viewer for deep sequencing data. Genome Res. 19, 2125-2132 (2009).