DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

Nature Methods

Volumn 9, Issue 11, 2012, Pages 1107-1112

  Falconer, Ester ^a   Hills, Mark ^a   Naumann, Ulrike ^a   Poon, Steven S S ^a   Chavez, Elizabeth A ^a   Sanders, Ashley D ^a   Zhao, Yongjun ^b   Hirst, Martin ^b,c   Lansdorp, Peter M ^a,c,d  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b BRITISH COLUMBIA CANCER AGENCY   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^d UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; DNA FRAGMENT;

ANIMAL CELL; ARTICLE; DNA SEQUENCE; DNA TEMPLATE; EMBRYONIC STEM CELL; FEMALE; GENE MAPPING; GENE REARRANGEMENT; GENOME ANALYSIS; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; SINGLE CELL ANALYSIS; SISTER CHROMATID EXCHANGE;

ANIMALS; CELLS, CULTURED; GENOMICS; MICE; SEQUENCE ANALYSIS, DNA; SISTER CHROMATID EXCHANGE; TEMPLATES, GENETIC;

MURINAE;

EID: 84869096434     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2206     Document Type: Article

References (34)

1. Bishop, A.J. & Schiestl, R.H. Homologous recombination and its role in carcinogenesis. J. Biomed. Biotechnol. 2, 75-85 (2002). (Pubitemid 44204493)
2. Greaves, M. & Maley, C.C. Clonal evolution in cancer. Nature 481, 306-313 (2012).
3. Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 90-94 (2011).
4. Aguilera, A. & Gomez-Gonzalez, B. Genome instability: a mechanistic view of its causes and consequences. Nat. Rev. Genet. 9, 204-217 (2008). (Pubitemid 351271797)
5. Wilson, D.M. III. & Thompson, L.H. Molecular mechanisms of sister-chromatid exchange. Mutat. Res. 616, 11-23 (2007). (Pubitemid 46198860)
6. Wu, L. Role of the BLM helicase in replication fork management. DNA Repair (Amst.) 6, 936-944 (2007). (Pubitemid 46880474)
7. Kato, H. Spontaneous sister chromatid exchanges detected by a BUdR-labelling method. Nature 251, 70-72 (1974).
8. Allen, J.W. & Latt, S.A. Analysis of sister chromatid exchange formation in vivo in mouse spermatogonia as a new test system for environmental mutagens. Nature 260, 449-451 (1976).
9. Falconer, E. et al. Identification of sister chromatids by DNA template strand sequences. Nature 463, 93-97 (2010).
10. Sakaue-Sawano, A. et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132, 487-498 (2008). (Pubitemid 351191996)
11. Vassilev, L.T. et al. Selective small-molecule inhibitor reveals critical mitotic functions of human CDK1. Proc. Natl. Acad. Sci. USA 103, 10660-10665 (2006). (Pubitemid 44078033)
12. Helleday, T. Pathways for mitotic homologous recombination in mammalian cells. Mutat. Res. 532, 103-115 (2003). (Pubitemid 37487849)
13. Yang, H., Chen, X. & Wong, W.H. Completely phased genome sequencing through chromosome sorting. Proc. Natl. Acad. Sci. USA 108, 12-17 (2011).
14. Fan, H.C., Wang, J., Potanina, A. & Quake, S.R. Whole-genome molecular haplotyping of single cells. Nat. Biotechnol. 29, 51-57 (2011).
15. Tateishi, S. et al. Enhanced genomic instability and defective postreplication repair in RAD18 knockout mouse embryonic stem cells. Mol. Cell. Biol. 23, 474-481 (2003). (Pubitemid 36050542)
16. Jaco, I., Canela, A., Vera, E. & Blasco, M.A. Centromere mitotic recombination in mammalian cells. J. Cell Biol. 181, 885-892 (2008). (Pubitemid 351846822)
17. Trask, B.J. et al. Studies of metaphase and interphase chromosomes using fluorescence in situ hybridization. Cold Spring Harb. Symp. Quant. Biol. 58, 767-775 (1993). (Pubitemid 24219539)
18. Rebuzzini, P. et al. Karyotype analysis of the euploid cell population of a mouse embryonic stem cell line revealed a high incidence of chromosome abnormalities that varied during culture. Cytogenet. Genome Res. 121, 18-24 (2008). (Pubitemid 351820626)
19. Liang, Q., Conte, N., Skarnes, W.C. & Bradley, A. Extensive genomic copy number variation in embryonic stem cells. Proc. Natl. Acad. Sci. USA 105, 17453-17456 (2008).
20. Kalisky, T. & Quake, S.R. Single-cell genomics. Nat. Methods 8, 311-314 (2011).
21. Cox, A. et al. A new standard genetic map for the laboratory mouse. Genetics 182, 1335-1344 (2009).
22. Armakolas, A. & Klar, A.J. Cell type regulates selective segregation of mouse chromosome 7 DNA strands in mitosis. Science 311, 1146-1149 (2006).
23. Rocheteau, P., Gayraud-Morel, B., Siegl-Cachedenier, I., Blasco, M.A. & Tajbakhsh, S. A subpopulation of adult skeletal muscle stem cells retains all template DNA strands after cell division. Cell 148, 112-125 (2012).
24. Cairns, J. Somatic stem cells and the kinetics of mutagenesis and carcinogenesis. Proc. Natl. Acad. Sci. USA 99, 10567-10570 (2002).
25. Lansdorp, P.M. Immortal strands? Give me a break. Cell 129, 1244-1247 (2007). (Pubitemid 46962099)
26. Kloosterman, W.P. et al. Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum. Mol. Genet. 20, 1916-1924 (2011).
27. Stephens, P.J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27-40 (2011).
28. Campbell, P.J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40, 722-729 (2008). (Pubitemid 351748860)
29. Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007). (Pubitemid 47614521)
30. Szymczak, A.L. et al. Correction of multi-gene deficiency in vivo using a single 'self-cleaving' 2A peptide-based retroviral vector. Nat. Biotechnol. 22, 589-594 (2004). (Pubitemid 38585911)
31. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
32. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
33. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
34. Bezrookove, V. et al. Premature chromosome condensation revisited: a novel chemical approach permits efficient cytogenetic analysis of cancers. Genes Chromosom. Cancer 38, 177-186 (2003). (Pubitemid 37093435)