Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Ning, Luwen ^a   Li, Zhoufang ^a   Wang, Guan ^b   Hu, Wen ^b,c   Hou, Qingming ^b   Tong, Yin ^a   Zhang, Meng ^a   Chen, Yao ^a   Qin, Li ^c   Chen, Xiaoping ^c   Man, Heng Ye ^b   Liu, Pinghua ^b   He, Jiankui ^a  

^a SOUTHERN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b USA   (United States)

^c GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; COPY NUMBER VARIATION; DNA BASE COMPOSITION; GENE DOSAGE; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; POLYMERASE CHAIN REACTION; PROCEDURES; PYRAMIDAL NERVE CELL; RAT; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SINGLE CELL ANALYSIS;

ANIMALS; BASE COMPOSITION; DNA COPY NUMBER VARIATIONS; GENE DOSAGE; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POLYMERASE CHAIN REACTION; PYRAMIDAL CELLS; RATS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SINGLE-CELL ANALYSIS;

EID: 84934980871     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep11415     Document Type: Article

References (40)

1. Wang, J., Fan, H. C., Behr, B. & Quake, S. R. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150, 402-412 (2012).
2. McConnell, M. J. et al. Mosaic copy number variation in human neurons. Science 342, 632-637 (2013).
3. Ramskold, D. et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nature biotechnology 30, 777-782 (2012).
4. Yan, L. et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nature structural & molecular biology 20, 1131-1139 (2013).
5. Hou, Y. et al. Single-Cell Exome Sequencing and Monoclonal Evolution of a< i> JAK2< i>-Negative Myeloproliferative Neoplasm. Cell 148, 873-885 (2012).
6. Gole, J. et al. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol 31, 1126-32 (2013).
7. Cai, X. et al. Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. Cell Rep 8, 1280-9 (2014).
8. Gole, J. et al. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nature biotechnology 31, 1126-1132 (2013).
9. Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 90-94 (2011).
10. Zong, C., Lu, S., Chapman, A. R. & Xie, X. S. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338, 1622-1626 (2012).
11. de Bourcy, C. F. et al. A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods. PloS one 9, e105585 (2014).
12. Williams, R. W. & Herrup, K. The control of neuron number. Annual review of neuroscience 11, 423-453 (1988).
13. Azevedo, F. A. et al. Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. Journal of Comparative Neurology 513, 532-541 (2009).
14. Muotri, A. R. & Gage, F. H. Generation of neuronal variability and complexity. Nature 441, 1087-1093 (2006).
15. Zhang, D. et al. Na, K-ATPase activity regulates AMPA receptor turnover through proteasome-mediated proteolysis. The Journal of Neuroscience 29, 4498-4511 (2009).
16. Hou, Q., Gilbert, J. & Man, H.-Y. Homeostatic regulation of AMPA receptor trafficking and degradation by light-controlled single-synaptic activation. Neuron 72, 806-818 (2011).
17. Campbell, K. H., Alberio, R., Denning, C. & Lee, J.-H. Somatic cell nuclear transplantation. (Cell Biology: A Laboratory Handbook, 3rd edn. New York: Academic Press, 2006).
18. Nawy, T. Single-cell sequencing. Nature methods 11, 18-18, doi: 10.1038/nmeth.2771 (2014).
19. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-359 (2012).
20. Ning, L. et al. Current challenges in the bioinformatics of single cell genomics. Frontiers in oncology 4, doi: 10.3389 (2014).
21. Ni, X. et al. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proceedings of the National Academy of Sciences 110, 21083-21088 (2013).
22. Navin, N. E. Cancer genomics: one cell at a time. Genome Biol 15, 452 (2014).
23. Yu, Z., Lu, S. & Huang, Y. Microfluidic whole genome amplification device for single cell sequencing. Anal Chem 86, 9386-90 (2014).
24. Hou, Y. et al. Genome analyses of single human oocytes. Cell 155, 1492-506 (2013).
25. Benjamini, Y. & Speed, T. P. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic acids research, doi: 10.1093/nar/gks001 (2012).
26. Yilmaz, S., Allgaier, M. & Hugenholtz, P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7, 943-4 (2010).
27. Ellegaard, K. M., Klasson, L. & Andersson, S. G. Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations. PLoS One 8, e82319 (2013).
28. Rodrigue, S. et al. Whole genome amplification and de novo assembly of single bacterial cells. PLoS One 4, e6864 (2009).
29. Baslan, T. et al. Genome-wide copy number analysis of single cells. Nature protocols 7, 1024-1041 (2012).
30. Affymetrix. Median of the absolute values of all pairwise differences and quality control on Affymetrix genome-wide human SNP array 6.0. Affymetrix White Paper (2008). http://media.affymetrix.com/support/technical/whitepapers/mapd-snp6-whitepaper. pdf.
31. Yim, S. H. et al. Copy number variations in East-Asian population and their evolutionary and functional implications. Hum Mol Genet 19, 1001-8 (2010).
32. Rehen, S. K. et al. Constitutional aneuploidy in the normal human brain. The Journal of neuroscience 25, 2176-2180 (2005).
33. Westra, J. W. et al. Neuronal DNA content variation (DCV) with regional and individual differences in the human brain. Journal of Comparative Neurology 518, 3981-4000 (2010).
34. Singer, T., McConnell, M. J., Marchetto, M. C., Coufal, N. G. & Gage, F. H. LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes? Trends in neurosciences 33, 345-354 (2010).
35. Evrony, G. D. et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151, 483-496 (2012).
36. Hou, Y. et al. Genome analyses of single human oocytes. Cell 155, 1492-1506 (2013).
37. Harris, T. D. et al. Single-molecule DNA sequencing of a viral genome. Science 320, 106-109 (2008).
38. Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
39. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
40. Venkatraman, E. & Olshen, A. B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657-663 (2007).