Sequencing by hybridization explained

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

• Sequencing by ligation

Notes and References

1. Book: 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. Chip Technology . Sequencing by Hybridization (SBH): Advantages, Achievements, and Opportunities. Advances in Biochemical Engineering/Biotechnology . 77. 2002. 75–101. 0724-6145. 10.1007/3-540-45713-5_5. 12227738 . 978-3-540-43215-9 . PDF
2. Preparata . FP. Upfal . E . Sequencing-by-hybridization at the information-theory bound: an optimal algorithm. J. Comput. Biol.. 2000. 7. 3. 621–30. 11108482 . 10.1089/106652700750050970. 10.1.1.61.3325.
3. Hanna . GJ . et al. Comparison of Sequencing by Hybridization and Cycle Sequencing for Genotyping of Human Immunodeficiency Virus Type 1 Reverse Transcriptase. J Clin Microbiol. July 2000. 38. 7. 2715–2721. 10.1128/JCM.38.7.2715-2721.2000 . 10878069. 87006.
4. Church. George M. . Genomes for all.. Scientific American. January 2006. 294. 1. 46–54 . 10.1038/scientificamerican0106-46. 16468433. 2006SciAm.294a..46C . 28769137 .