Sequencing by hybridization
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. The binding of one strand of DNA to its complementary strand in the DNA double-helix (aka 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 notable 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.
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.
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)
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- Preparata FP, Upfal E. Sequencing-by-hybridization at the information-theory bound: an optimal algorithm. J Comput Biol. 2000;7(3-4):621-30. PMID 11108482
- Drmanac R et al. Sequencing by hybridization (SBH): advantages, achievements, and opportunities. Adv Biochem Eng Biotechnol. 2002;77:75-101. PMID 12227738
- 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. 2000 July; 38(7): 2715–2721. PMID 10878069.
- Church, George M. Genomes for all. Scientific American. 2006 Jan;294(1):52. doi:10.1038/scientificamerican0106-46 PMID 16468433