Genome-wide copy number analysis of single cells

Nature Protocols

Volumn 7, Issue 6, 2012, Pages 1024-1041

  Baslan, Timour ^a,b   Kendall, Jude ^a   Rodgers, Linda ^a   Cox, Hilary ^a   Riggs, Mike ^a   Stepansky, Asya ^a   Troge, Jennifer ^a   Ravi, Kandasamy ^a   Esposito, Diane ^a   Lakshmi, B ^c   Wigler, Michael ^a   Navin, Nicholas ^d   Hicks, James ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b STONY BROOK UNIVERSITY   (United States)

^c ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^d UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL NUCLEUS; COPY NUMBER VARIATION; DNA CONTENT; DNA LIBRARY; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; GENE AMPLIFICATION; GENOME ANALYSIS; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEUS SEQUENCING; WHOLE GENOME AMPLIFICATION;

ALGORITHMS; CELL NUCLEUS; DNA COPY NUMBER VARIATIONS; FLOW CYTOMETRY; GENETIC HETEROGENEITY; GENETIC TECHNIQUES; HUMANS; SINGLE-CELL ANALYSIS;

EID: 84861033754     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2012.039     Document Type: Article

References (30)

1. Beckmann, J. S., Estivill, X. Antonarakis, S. E. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat. Rev. Genet. 8, 639-646 (2007).
2. Hasin, Y. et al. High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet. 4, e1000249 (2008).
3. Perry, G. H. et al. Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39, 1256-1260 (2007).
4. Speliotes, E. K. et al. Association analyses of 249, 796 individuals reveal 18 new loci associated with body mass index. Nat. Genet. 42, 937-948 (2010).
5. Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007).
6. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
7. Bignell, G. R. et al. Signatures of mutation and selection in the cancer genome. Nature 463, 893-898 (2010).
8. Russnes, H. G. et al. Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci. Transl. Med. 2, 38ra47 (2010).
9. Shiu, K. K., Natrajan, R., Geyer, F. C., Ashworth, A. Reis-Filho, J. S. DNA amplifications in breast cancer: genotypic-phenotypic correlations. Future Oncol. 6, 967-984 (2010).
10. Shinawi, M. Cheung, S. W. The array CGH and its clinical applications. Drug Discov. Today 13, 760-770 (2008).
11. Santarius, T., Shipley, J., Brewer, D., Stratton, M. R. Cooper, C. S. A census of amplified and overexpressed human cancer genes. Nat. Rev. Cancer 10, 59-64 (2010).
12. Pinkel, D. Albertson, D. G. Array comparative genomic hybridization and its applications in cancer. Nat. Genet. 37 (suppl.): S11-17 (2005).
13. Praulich, I. et al. Clonal heterogeneity in childhood myelodysplastic syndromes-challenge for the detection of chromosomal imbalances by array-CGH. Genes Chromosomes Cancer 49, 885-900 (2010).
14. Metzker, M. L. Sequencing technologies-the next generation. Nat. Rev. Genet. 11, 31-46 (2010).
15. Mardis, E. R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133-141 (2008).
16. Meyerson, M., Gabriel, S. Getz, G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11, 685-696 (2010).
17. Chiang, D. Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103 (2009).
18. Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet. 41, 1061-1067 (2009).
19. Shah, S. P. et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461, 809-813 (2009).
20. Ding, L. et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464, 999-1005 (2010).
21. Campbell, P. J. et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467, 1109-1113 (2010).
22. Yachida, S. et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467, 1114-1117 (2010).
23. Anderson, K. et al. Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature 469, 356-361 (2011).
24. Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 90-94 (2011).
25. Langmead, B., Trapnell, C., Pop, M. Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
26. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 15, 2078-2079 (2009).
27. Venkatraman, E. S. Olshen, A. B. A faster cicular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657-63 (2007).
28. Wersto, R. P. et al. Doublet discrimination in DNA cell-cycle analysis. Cytometry 46, 296-306 (2001).
29. Nagata, S., Nagase, H., Kawane, K., Mukae, N. Fukuyama, H. Degradation of chromosomal DNA during apoptosis. Cell Death Differ 10, 108-116 (2003).
30. Stephans, P. J. et al. Massive genomic rearragement acquired in a single catastrophic event during cancer development. Cell 144, 27-40 (2011).