Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ

Nucleic Acids Research

Volumn 43, Issue 22, 2015, Pages

  Mignardi, Marco ^a   Mezger, Anja ^a   Qian, Xiaoyan ^a   La Fleur, Linnea ^b   Botling, Johan ^b   Larsson, Chatarina ^b   Nilsson, Mats ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; MESSENGER RNA; MITOCHONDRIAL DNA; OLIGONUCLEOTIDE; DNA;

ACTB GENE; ARTICLE; CONTROLLED STUDY; EGFR GENE; GENE; GENE MUTATION; GENE SEQUENCE; GENETIC PROCEDURES; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN TISSUE; MUTATIONAL ANALYSIS; NUCLEIC ACID ANALYSIS; OLIGONUCLEOTIDE GAP FILL LIGATION; ONCOGENE K RAS; POINT MUTATION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; ANIMAL; CELL CULTURE; CELL LINE; CHEMISTRY; DNA MUTATIONAL ANALYSIS; MOUSE; PROCEDURES; TUMOR CELL LINE;

ANIMALS; CELL LINE; CELL LINE, TUMOR; CELLS, CULTURED; DNA MUTATIONAL ANALYSIS; DNA, MITOCHONDRIAL; DNA, NEOPLASM; HUMANS; MICE; OLIGONUCLEOTIDES; POINT MUTATION; RNA, MESSENGER;

EID: 84964461094     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv772     Document Type: Article

References (28)

1. Landegren, U., Kaiser, R., Sanders, J. and Hood, L. (1988) A ligase-mediated gene detection technique. Science, 241, 1077-1080.
2. Jackson, D. A., Symons, R. H. and Berg, P. (1972) Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A., 69, 2904-2909.
3. Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D. and Church, G. M. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728-1732.
4. Conze, T., Shetye, A., Tanaka, Y., Gu, J., Larsson, C., Goransson, J., Tavoosidana, G., Soderberg, O., Nilsson, M. and Landegren, U. (2009) Analysis of genes, transcripts, and proteins via DNA ligation. Annu. Rev. Anal. Chem., 2, 215-239.
5. Weiss, B. and Richardson, C. C. (1967) Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc. Natl. Acad. Sci. U. S. A., 57, 1021-1028.
6. Larsson, C., Koch, J., Nygren, A., Janssen, G., Raap, A. K., Landegren, U. and Nilsson, M. (2004) In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat. Methods, 1, 227-232.
7. Andersson, C., Henriksson, S., Magnusson, K. E., Nilsson, M. and Mirazimi, A. (2012) In situ rolling circle amplification detection of Crimean Congo hemorrhagic fever virus (CCHFV) complementary and viral RNA. Virology, 426, 87-92.
8. Shaposhnikov, S., Larsson, C., Henriksson, S., Collins, A. and Nilsson, M. (2006) Detection of Alu sequences and mtDNA in comets using padlock probes. Mutagenesis, 21, 243-247.
9. Larsson, C., Grundberg, I., Soderberg, O. and Nilsson, M. (2010) In situ detection and genotyping of individual mRNA molecules. Nat. Methods, 7, 395-397.
10. Hardenbol, P., Baner, J., Jain, M., Nilsson, M., Namsaraev, E. A., Karlin-Neumann, G. A., Fakhrai-Rad, H., Ronaghi, M., Willis, T. D., Landegren, U. et al. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol., 21, 673-678.
11. Porreca, G. J., Zhang, K., Li, J. B., Xie, B., Austin, D., Vassallo, S. L., LeProust, E. M., Peck, B. J., Emig, C. J., Dahl, F. et al. (2007) Multiplex amplification of large sets of human exons. Nat. Methods, 4, 931-936.
12. Lizardi, P. M., Huang, X., Zhu, Z., Bray-Ward, P., Thomas, D. C. and Ward, D. C. (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet., 19, 225-232.
13. Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wahlby, C. and Nilsson, M. (2013) In situ sequencing for RNA analysis in preserved tissue and cells. Nat. Methods, 10, 857-860.
14. Goto, Y., Nonaka, I. and Horai, S. (1990) A mutation in the tRNA (Leu) (UUR) gene associated with the MELAS subgroup of mitochondrial encephalomyopathies. Nature, 348, 651-653.
15. Botling, J., Edlund, K., Lohr, M., Hellwig, B., Holmberg, L., Lambe, M., Berglund, A., Ekman, S., Bergqvist, M., Ponten, F. et al. (2013) Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation. Clin. Cancer Res., 19, 194-204.
16. Carpenter, A. E., Jones, T. R., Lamprecht, M. R., Clarke, C., Kang, I. H., Friman, O., Guertin, D. A., Chang, J. H., Lindquist, R. A., Moffat, J. et al. (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100.
17. Szollosi, J., Lockett, S. J., Balazs, M. and Waldman, F. M. (1995) Autofluorescence correction for fluorescence in situ hybridization. Cytometry, 20, 356-361.
18. Luo, J., Bergstrom, D. E. and Barany, F. (1996) Improving the fidelity of Thermus thermophilus DNA ligase. Nucleic Acids Res., 24, 3071-3078.
19. Van Den Ouweland, J. M., Maechler, P., Wollheim, C. B., Attardi, G. and Maassen, J. A. (1999) Functional and morphological abnormalities of mitochondria harbouring the tRNA (Leu) (UUR) mutation in mitochondrial DNA derived from patients with maternally inherited diabetes and deafness (MIDD) and progressive kidney disease. Diabetologia, 42, 485-492.
20. Forbes, S. A., Beare, D., Gunasekaran, P., Leung, K., Bindal, N., Boutselakis, H., Ding, M., Bamford, S., Cole, C., Ward, S. et al. (2015) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res., 43, D805-D811.
21. Sharma, S. V., Bell, D. W., Settleman, J. and Haber, D. A. (2007) Epidermal growth factor receptor mutations in lung cancer. Nat. Rev. Cancer, 7, 169-181.
22. Hirsch, F. R., Janne, P. A., Eberhardt, W. E., Cappuzzo, F., Thatcher, N., Pirker, R., Choy, H., Kim, E. S., Paz-Ares, L., Gandara, D. R. et al. (2013) Epidermal growth factor receptor inhibition in lung cancer: status 2012. J. Thorac. Oncol., 8, 373-384.
23. Pritchard, C. E. and Southern, E. M. (1997) Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases. Nucleic Acids Res., 25, 3403-3407.
24. Khanna, M., Cao, W., Zirvi, M., Paty, P. and Barany, F. (1999) Ligase detection reaction for identification of low abundance mutations. Clin. Biochem., 32, 287-290.
25. Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
26. Wang, H., Mayhew, D., Chen, X., Johnston, M. and Mitra, R. D. (2012) 'Calling cards' for DNA-binding proteins in mammalian cells. Genetics, 190, 941-949.
27. Housby, J. N. and Southern, E. M. (1998) Fidelity of DNA ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides. Nucleic Acids Res., 26, 4259-4266.
28. Grundberg, I., Kiflemariam, S., Mignardi, M., Imgenberg-Kreuz, J., Edlund, K., Micke, P., Sundstrom, M., Sjoblom, T., Botling, J. and Nilsson, M. (2013) In situ mutation detection and visualization of intratumor heterogeneity for cancer research and diagnostics. Oncotarget, 4, 2407-2418.