title: Sequencing by hybridization (SBH): advantages, achievements, and opportunities.
abstract: Efficient DNA sequencing of the genomes of individual species and organisms is a critical task for the advancement of biological sciences, medicine and agriculture. Advances in modern sequencing methods are needed to meet the challenge of sequencing such megabase to gigabase quantities of DNA. Two possible strategies for DNA sequencing exist: direct methods, in which each base position in the DNA chain is determined individually (e.g., gel sequencing or pyrosequencing), and indirect methods, in which the DNA sequence is assembled based on experimental determination of oligonucleotide content of the DNA chain. One promising indirect method is sequencing by hybridization (SBH), in which sets of oligonucleotides are hybridized under conditions that allow detection of complementary sequences in the target nucleic acid. The unprecedented sequence search parallelism of the SBH method has allowed development of high-throughput, low-cost, miniaturized sequencing processes on arrays of DNA samples or probes. Newly developed SBH methods use DNA ligation to combine relatively small sets of short probes to score potentially tens of millions of longer oligonucleotide sequences in a target DNA. Such combinatorial approaches allow analysis of DNA samples of up to several kilobases (several times longer than allowed by current direct methods) for a variety of DNA sequence analysis applications, including de novo sequencing, resequencing, mutation/SNP discovery and genotyping, and expression monitoring. Future advances in biochemistry and implementation of detection methods that allow single-molecule sensitivity may provide the necessary miniaturization, specificity, and multiplexing efficiency to allow routine whole genome analysis in a single solution-based hybridization experiment.
authors.affiliation: Callida Genomics, Sunnyvale, CA 94085, USA. rade@sbh.com
authors.forename: Radoje
authors.initials: R
authors.lastname: Drmanac
authors.forename: Snezana
authors.initials: S
authors.lastname: Drmanac
authors.forename: Gloria
authors.initials: G
authors.lastname: Chui
authors.forename: Robert
authors.initials: R
authors.lastname: Diaz
authors.forename: Aaron
authors.initials: A
authors.lastname: Hou
authors.forename: Hui
authors.initials: H
authors.lastname: Jin
authors.forename: Paul
authors.initials: P
authors.lastname: Jin
authors.forename: Sunhee
authors.initials: S
authors.lastname: Kwon
authors.forename: Scott
authors.initials: S
authors.lastname: Lacy
authors.forename: Bill
authors.initials: B
authors.lastname: Moeur
authors.forename: Jay
authors.initials: J
authors.lastname: Shafto
authors.forename: Don
authors.initials: D
authors.lastname: Swanson
authors.forename: Tatjana
authors.initials: T
authors.lastname: Ukrainczyk
authors.forename: Chongjun
authors.initials: C
authors.lastname: Xu
authors.forename: Deane
authors.initials: D
authors.lastname: Little
mesh_terms: D001483:Base Sequence; D011088:DNA Ligases / Q000737:chemistry / Q000235:genetics; D004258:DNA Polymerase III / Q000737:chemistry / Q000235:genetics; D015342:DNA Probes / Q000737:chemistry* / Q000235:genetics*; D004867:Equipment Design; D006801:Humans; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods* / Q000639:trends; D011786:Quality Control; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*
chemical_list: D015342:DNA Probes; C065639:DNA polymerase A; D004258:DNA Polymerase III; D011088:DNA Ligases