RT Journal
A1 Gunderson, Kevin L.
A1 Kruglyak, Semyon
A1 Graige, Michael S.
A1 Garcia, Francisco
A1 Kermani, Bahram G.
A1 Zhao, Chanfeng
A1 Che, Diping
A1 Dickinson, Todd
A1 Wickham, Eliza
A1 Bierle, Jim
A1 Doucet, Dennis
A1 Milewski, Monika
A1 Yang, Robert
A1 Siegmund, Chris
A1 Haas, Juergen
A1 Zhou, Lixin
A1 Oliphant, Arnold
A1 Fan, Jian-Bing
A1 Barnard, Steven
A1 Chee, Mark S.
T1 Decoding Randomly Ordered DNA Arrays
JF Genome Research 
JO Genome Research 
YR 2004 
FD May 01 
VO 14 
IS 5 
SP 870 
OP 877 
DO 10.1101/gr.2255804 
UL http://genome.cshlp.org/content/14/5/870.abstract 
AB 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 ∼30-fold redundancy by up to ∼50,000 beads, with a median error rate of <1 × 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.