title: Decoding randomly ordered DNA arrays.
abstract: We have developed a simple and efficient algorithm to identify each member of a large collection of DNA-linked objects through the use of hybridization, and have applied it to the manufacture of randomly assembled arrays of beads in wells. Once the algorithm has been used to determine the identity of each bead, the microarray can be used in a wide variety of applications, including single nucleotide polymorphism genotyping and gene expression profiling. The algorithm requires only a few labels and several sequential hybridizations to identify thousands of different DNA sequences with great accuracy. We have decoded tens of thousands of arrays, each with 1520 sequences represented at approximately 30-fold redundancy by up to approximately 50,000 beads, with a median error rate of <1 x 10(-4) per bead. The approach makes use of error checking codes and provides, for the first time, a direct functional quality control of every element of each array that is manufactured. The algorithm can be applied to any spatially fixed collection of objects or molecules that are associated with specific DNA sequences.
authors.affiliation: Illumina, Inc., San Diego, California 92121, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.forename: Semyon
authors.initials: S
authors.lastname: Kruglyak
authors.forename: Michael S
authors.initials: MS
authors.lastname: Graige
authors.forename: Francisco
authors.initials: F
authors.lastname: Garcia
authors.forename: Bahram G
authors.initials: BG
authors.lastname: Kermani
authors.forename: Chanfeng
authors.initials: C
authors.lastname: Zhao
authors.forename: Diping
authors.initials: D
authors.lastname: Che
authors.forename: Todd
authors.initials: T
authors.lastname: Dickinson
authors.forename: Eliza
authors.initials: E
authors.lastname: Wickham
authors.forename: Jim
authors.initials: J
authors.lastname: Bierle
authors.forename: Dennis
authors.initials: D
authors.lastname: Doucet
authors.forename: Monika
authors.initials: M
authors.lastname: Milewski
authors.forename: Robert
authors.initials: R
authors.lastname: Yang
authors.forename: Chris
authors.initials: C
authors.lastname: Siegmund
authors.forename: Juergen
authors.initials: J
authors.lastname: Haas
authors.forename: Lixin
authors.initials: L
authors.lastname: Zhou
authors.forename: Arnold
authors.initials: A
authors.lastname: Oliphant
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.forename: Steven
authors.initials: S
authors.lastname: Barnard
authors.forename: Mark S
authors.initials: MS
authors.lastname: Chee
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000639:trends; D011897:Random Allocation; D012107:Research Design; D017422:Sequence Analysis, DNA / Q000379:methods*; D012822:Silicon Dioxide / Q000737:chemistry
chemical_list: D012822:Silicon Dioxide