Whole genome amplification as a method for analysis of single cells
Abstract
Analysis of the genetic material of single cells is a very urgent task for such fields of science as oncology, forensic medicine, preimplantation genetic diagnosis. Whole genome amplification is an indispensable stage in the study of single cells. Among methods of whole genome amplification, methods based on thermocycling and isothermal methods are distinguished. Each of the methods of whole genome amplification should ensure the maximum possible representation and proportionality of all parts of the investigated genome, and also have a minimal bias, that is, it is most accurate to represent the primary DNA sequence in products of whole genome amplification. These characteristics can be influenced by the types of primers, polymerases used in the methods of whole genome amplification, as well as the initial quality and quantity of the DNA being studied. Therefore, depending on the protocol used, the quality of the amplification may vary significantly, which should undoubtedly be taken into account when choosing the method of whole genome amplification in accordance with the intended purpose of the study.
About the Authors
A. A. Tveleneva
Research Centre for Medical Genetics
Russian Federation
Russian Federation
E. V. Musatova
Research Centre for Medical Genetics
Russian Federation
Russian Federation
N. V. Shilova
Research Centre for Medical Genetics
Russian Federation
Russian Federation
References
1. Nelson D.L., Ledbetter S.A., Corbo L., et al. Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources // Proc Natl Acad Sci U S A, Vol. 86, No. 17, 1989. pp. 6686-90.
2. Korenberg J.R., Rykowski M.C. Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands // Cell, Vol. 53, No. 3, 1998. pp. 391-400.
3. Ludecke H.J., Senger G., Claussen U., Horsthemke B. Cloning defined regions of the human genome by microdissection of banded chromosomes and enzymatic amplification // Nature, Vol. 338, No. 6213, 1989. pp. 348-350.
4. Zhang L., Cui X., Schmitt K., Hubert R., Navidi W., Arnheim N. 85. Zhang L, Cui X, SWhole genome amplification from a single cell: implications for genetic analysis // Proc Natl Acad Sci USA, Vol. 89, No. 13, 1992. pp. 5847-5851.
5. Dietmaier W., Hartmann A., Wallinger S., Heinmоller E., Kerner T., Endl E., Jauch K.W., Hofstаdter F., Ruschoff J. Multiple mutation analyses in single tumor cells with improved whole genome amplification // Am J Patho, Vol. 154, No. 1, 1999. pp. 83-95.
6. Telenius H., Carter N., Bebb C.E., Nordenskjоld M., Ponder B.A., Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer // Genomics, Vol. 13, No. 3. pp. 718-725.
7. Kittler R., Stoneking M., Kayser M. A whole genome amplification method to generate long fragments from low quantities of genomic DNA // Anal. Biochem, Vol. 300, No. 2, 2002. pp. 237-244.
8. Bonnette M.D., Pavlova V.R., Rodier D.N., Thompson L.P., Boone E.L., Brown K.L., Meyer K.M., Trevino M.B., Champagne J.R., Cruz T.D. dcDegenerate oligonucleotide primed-PCR for multilocus, genome-wide analysis from limited quantities of DNA // Diagn Mol Pathol, Vol. 18, No. 3, 2009. pp. 165-175.
9. 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, Vol. 338, No. 6114, 2012. pp. 1622-1626.
10. Dean F.B., Hosono S., Fang L., Wu X., Faruqi A.F., Bray-Ward P., Sun Z., Zong Q., Du Y., Du J., Driscoll M., Song W., Kingsmore S.F., Egholm M., Lasken R.S. Comprehensive human genome amplification using multiple displacement amplification // Proc Natl Acad Sci U S A, Vol. 99, No. 8, 2002. pp. 5261-5266.
11. Spits C., Le Caignec C., De Rycke M., Van Haute L., Van Steirteghem A., Liebaers I., Sermon K. Whole-genome multiple displacement amplification from single cells // Proc Natl Acad Sci USA, Vol. 1, No. 4, 2006. pp. 1965-1970.
12. Zheng Y.M., Wang N., Li L., Jin F. Whole genome amplification in preimplantation genetic diagnosis // J Zhejiang Univ Sci В, Vol. 12, No. 1. pp. 1-11.
13. Cheung V.G., Nelson S.F. Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA // Proc Natl Acad Sci USA, Vol. 93, No. 25, 1996. pp. 14676-14679.
14. Lledо B., Ten J, Galаn FM, Bernabeu R. Preimplantation genetic diagnosis of Marfan syndrome using multiple displacement amplification // Fertil Steril, Vol. 86, No. 4, 2006. pp. 945-955.
15. Sabina J., Leamon J.H. Bias in Whole Genome Amplification: Causes and Considerations // Methods Mol Biol, Vol. 1347, 2015. pp. 15-41.
16. Pirker C., Raidl M., Steiner E., Elbling L., Holzmann K., Spiegl-Kreinecker S., Aubele M., Grasl-Kraupp B., Marosi C., Micksche M., Berger W. Whole genome amplification for CGH analysis: Linker-adapter PCR as the method of choice for difficult and limited samples. // Cytometry A, Vol. 61, No. 1, 2004. pp. 26-34.
17. Borgstrоm E., Paterlini M., Mold J.E., Frisen J., Lundeberg J. Comparison of whole genome amplification techniques for human single cell exome sequencing // PLoS One, Vol. 12, No. 2, 2017. P. e0171566.
18. Huang L., Ma F., Chapman A., Lu S., Xie X.S. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. // Annu Rev Genomics Hum Genet, No. 16, 2015. pp. 79-102.
Review
For citations:
Tveleneva A.A., Musatova E.V., Shilova N.V. Whole genome amplification as a method for analysis of single cells. Medical Genetics. 2017;16(11):3-6. (In Russ.)
Views:
1133
Email this article 