Sequencing by hybridization is a class of methods for determining the order in which nucleotides occur on a strand of DNA. Typically used for looking for small changes relative to a known DNA sequence. [1] The binding of one strand of DNA to its complementary strand in the DNA double-helix (known as hybridization) is sensitive to even single-base mismatches when the hybrid region is short or if specialized mismatch detection proteins are present. This is exploited in a variety of ways, most notably via DNA chips or microarrays with thousands to billions of synthetic oligonucleotides found in a genome of interest plus many known variations or even all possible single-base variations. [2] [3]
The type of sequencing by hybridization described above has largely been displaced by other methods, including sequencing by synthesis, and sequencing by ligation (as well as pore-based methods). However hybridization of oligonucleotides is still used in some sequencing schemes, including hybridization-assisted pore-based sequencing, and reversible hybridization. [4]
Examples of commercial systems
- Affymetrix (true sequencing-by-hybridization)
- NABsys (Hybridization-assisted pore-based sequencing)
- Complete Genomics Inc. (reversible-hybridization of probes that call-out a single base with each hybridization)
See also
References
- ^ Drmanac, Radoje; Drmanac, Snezana; Chui, Gloria; Diaz, Robert; Hou, Aaron; Jin, Hui; Jin, Paul; Kwon, Sunhee; Lacy, Scott; Moeur, Bill; Shafto, Jay; Swanson, Don; Ukrainczyk, Tatjana; Xu, Chongjun; Little, Deane (2002). "Sequencing by Hybridization (SBH): Advantages, Achievements, and Opportunities". Chip Technology. Advances in Biochemical Engineering/Biotechnology. Vol. 77. pp. 75–101. doi: 10.1007/3-540-45713-5_5. ISBN 978-3-540-43215-9. ISSN 0724-6145. PMID 12227738. PDF
- ^ Preparata, FP; Upfal, E (2000). "Sequencing-by-hybridization at the information-theory bound: an optimal algorithm". J. Comput. Biol. 7 (3): 621–30. CiteSeerX 10.1.1.61.3325. doi: 10.1089/106652700750050970. PMID 11108482.
- ^ Hanna, GJ; et al. (July 2000). "Comparison of Sequencing by Hybridization and Cycle Sequencing for Genotyping of Human Immunodeficiency Virus Type 1 Reverse Transcriptase". J Clin Microbiol. 38 (7): 2715–2721. doi: 10.1128/JCM.38.7.2715-2721.2000. PMC 87006. PMID 10878069.
- ^ Church, George M. (January 2006). "Genomes for all". Scientific American. 294 (1): 46–54. Bibcode: 2006SciAm.294a..46C. doi: 10.1038/scientificamerican0106-46. PMID 16468433. S2CID 28769137.
Sequencing by hybridization is a class of methods for determining the order in which nucleotides occur on a strand of DNA. Typically used for looking for small changes relative to a known DNA sequence. [1] The binding of one strand of DNA to its complementary strand in the DNA double-helix (known as hybridization) is sensitive to even single-base mismatches when the hybrid region is short or if specialized mismatch detection proteins are present. This is exploited in a variety of ways, most notably via DNA chips or microarrays with thousands to billions of synthetic oligonucleotides found in a genome of interest plus many known variations or even all possible single-base variations. [2] [3]
The type of sequencing by hybridization described above has largely been displaced by other methods, including sequencing by synthesis, and sequencing by ligation (as well as pore-based methods). However hybridization of oligonucleotides is still used in some sequencing schemes, including hybridization-assisted pore-based sequencing, and reversible hybridization. [4]
Examples of commercial systems
- Affymetrix (true sequencing-by-hybridization)
- NABsys (Hybridization-assisted pore-based sequencing)
- Complete Genomics Inc. (reversible-hybridization of probes that call-out a single base with each hybridization)
See also
References
- ^ Drmanac, Radoje; Drmanac, Snezana; Chui, Gloria; Diaz, Robert; Hou, Aaron; Jin, Hui; Jin, Paul; Kwon, Sunhee; Lacy, Scott; Moeur, Bill; Shafto, Jay; Swanson, Don; Ukrainczyk, Tatjana; Xu, Chongjun; Little, Deane (2002). "Sequencing by Hybridization (SBH): Advantages, Achievements, and Opportunities". Chip Technology. Advances in Biochemical Engineering/Biotechnology. Vol. 77. pp. 75–101. doi: 10.1007/3-540-45713-5_5. ISBN 978-3-540-43215-9. ISSN 0724-6145. PMID 12227738. PDF
- ^ Preparata, FP; Upfal, E (2000). "Sequencing-by-hybridization at the information-theory bound: an optimal algorithm". J. Comput. Biol. 7 (3): 621–30. CiteSeerX 10.1.1.61.3325. doi: 10.1089/106652700750050970. PMID 11108482.
- ^ Hanna, GJ; et al. (July 2000). "Comparison of Sequencing by Hybridization and Cycle Sequencing for Genotyping of Human Immunodeficiency Virus Type 1 Reverse Transcriptase". J Clin Microbiol. 38 (7): 2715–2721. doi: 10.1128/JCM.38.7.2715-2721.2000. PMC 87006. PMID 10878069.
- ^ Church, George M. (January 2006). "Genomes for all". Scientific American. 294 (1): 46–54. Bibcode: 2006SciAm.294a..46C. doi: 10.1038/scientificamerican0106-46. PMID 16468433. S2CID 28769137.