The chemistry of next-generation sequencing

References

Sanger, F., Nicklen, F. & Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463–5467 (1977).

Article
CAS
PubMed
PubMed Central

Google Scholar

Tsien, R. Y., Ross, P., Fahnestock, M. & Johnston, A. DNA sequencing. Patent WO9106678A1 (1990).

Ronaghi, M., Uhlén, M. & Nyrén, P. A sequencing method based on real-time pyrophosphate. Science 281, 363–365 (1998).

Article
CAS
PubMed

Google Scholar

International Human Genome Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

Article

Google Scholar

Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).

Article
CAS
PubMed

Google Scholar

Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

Article
CAS
PubMed

Google Scholar

Johnson, G. D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007).

Article
CAS
PubMed

Google Scholar

Gupta, N. & Verma, V. K. Next-generation sequencing and its application: empowering in public health beyond reality. In Microbial Technology for the Welfare of Society: Microorganisms for Sustainability (ed. Arora, P.) Vol. 17 (Springer, 2019).

Willson, J. Sequencing — the next generation. Nature Milestones S7 (2021).

Burgess, D. The dawn of personal genomes. Nature Milestones S9 (2021).

Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008).

Article
CAS
PubMed
PubMed Central

Google Scholar

Wang, J. et al. The diploid genome sequence of an Asian individual. Nature 456, 60–66 (2008).

Article
CAS
PubMed
PubMed Central

Google Scholar

Furey, W. S. et al. Use of fluorescence resonance energy transfer to investigate the conformation of DNA substrates bound to the Klenow fragment. Biochemistry 37, 2979–2990 (1998).

Article
CAS
PubMed

Google Scholar

Canard, B. & Sarfati, R. S. DNA polymerase fluorescent substrates with reversible 3′-tags. Gene 148, 1–6 (1994).

Article
CAS
PubMed

Google Scholar

Welch, M. B. et al. Syntheses of nucleosides designed for combinatorial DNA sequencing. Chem. Eur. J. 5, 951–960 (1999).

Article
CAS

Google Scholar

Metzker, M. L. et al. Termination of DNA synthesis by novel 3′-modified deoxyribonucleoside 5′-triphosphates. Nucleic Acids Res. 22, 4259–4267 (1994).

Article
CAS
PubMed
PubMed Central

Google Scholar

Turcatti, G., Romieu, A., Fedurco, M. & Tairi, A.-P. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res. 36, e25 (2008).

Article
PubMed
PubMed Central

Google Scholar

Staudinger, H. & Meyer, J. Über neue organische phosphorverbindungen III. Phosphinmethylenderivate und phosphinimine. Helv. Chim. Acta 2, 635 (1919).

Article
CAS

Google Scholar

Balasubramanian, S. Sequencing nucleic acids: from chemistry to medicine. Chem. Commun. 47, 7281–7286 (2011).

Article
CAS

Google Scholar

Barnes, C., Balasubramanian, S., Liu, X., Swerdlow, H. & Milton, J. Labelled nucleotides. US patent 7,057,026 B2 (2002).

Sarfati, S. R. et al. Synthesis of fluorescent or biotinylated nucleoside compounds. Tetrahedron 43, 3491–3497 (1987).

Article
CAS

Google Scholar

Rosenblum, B. B. et al. New dye-labeled terminators for improved DNA sequencing patterns. Nucleic Acids Res. 25, 4500–4504 (1997).

Article
CAS
PubMed
PubMed Central

Google Scholar

Kiefer, J. R., Mao, C., Braman, J. C. & Beese, L. S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391, 304–307 (1998).

Article
CAS
PubMed

Google Scholar

Smith, G. P., Bailey, D. M. D., Sanches, R. M., Swerdlow, H. & Earnshaw, D. J. Modified polymerases for improved incorporation of nucleotide analogues. Patent WO 2005/024010 A1 (2003).

Ost, T. W. B., Smith, G. P., Balasubramanian, S., Rigatti, R. & Sanches, R. M. Improved polymerases. Patent WO 2006/120433 A1 (2006).

Smith, G. P., Bailey, D. M. D., Sanches-Kuiper, R. M., Swerdlow, H. & Earnshaw, D. J. Modified polymerases for improved incorporation of nucleotide analogues. US patent 8,852,910 B2 (2003).

Smith, M. et al. Modified molecular arrays. Patent WO 2005/065814 A1 (2005).

Kawashima, E., Farinelli, L. & Mayer, P. Method of nucleic acid amplification by extension of immobilized primers. Patent WO 9844151 (1998).

Mayer, P. Isothermal amplification of nucleic acids on a solid support. Patent WO 02/46456 (2001).

Robinson, R. A synthesis of tropinone. J. Chem. Soc. 111, 762–768 (1917).

Rodriguez, A. R. et al. Total synthesis of cyercene A and the biomimetic synthesis of (±)-9,10-deoxytridachione and (±)-ocellapyrone. Tetrahedron 63, 4500–4509 (2007).

Article
CAS

Google Scholar

Wuts, P. G. M. & Greene, T. W. Greene’s Protective Groups in Organic Synthesis 4th edn (John Wiley & Sons, 2006).

Baran, P. S., Maimone, T. J. & Richter, J. M. Total synthesis of marine natural products without using protecting groups. Nature 446, 404–408 (2007).

Article
CAS
PubMed

Google Scholar

Trost, B. M. The atom economy—a search for synthetic efficiency. Science 254, 1471–1477 (1991).

Article
CAS
PubMed

Google Scholar

Koboldt, D. C., Meltz Steinberg, K., Larson, D. E., Wilson, R. K. & Mardis, E. R. The next-generation sequencing revolution and its impact on genomics. Cell 155, 27–38 (2013).

Article
CAS
PubMed
PubMed Central

Google Scholar

Rodriguez, R. et al. Small molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat. Chem. Biol. 8, 301–310 (2012).

Article
CAS
PubMed
PubMed Central

Google Scholar

Rodriguez, R. & Miller, K. M. Unravelling the genomic targets of small molecules using high-throughput sequencing. Nat. Rev. Genet. 15, 783–796 (2014).

Article
CAS
PubMed

Google Scholar

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621–628 (2008).

Article
CAS
PubMed

Google Scholar

Ståhl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78–82 (2016).

Article
PubMed

Google Scholar

Shendure, J. et al. DNA sequencing at 40: past, present and future. Nature 550, 346–353 (2017).

Article

Google Scholar

Newby, G. A. et al. Base editing of haematopoietic stem cells rescues sickle cell disease in mice. Nature 595, 295–302 (2021).

Article
CAS
PubMed
PubMed Central

Google Scholar

Zhu, N. et al. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733 (2020).