RT Journal
A1 Gunderson, Kevin L.
A1 Huang, Xiaohua C.
A1 Morris, Macdonald S.
A1 Lipshutz, Robert J.
A1 Lockhart, David J.
A1 Chee, Mark S.
T1 Mutation Detection by Ligation to Complete n-mer DNA Arrays
JF Genome Research 
JO Genome Research 
YR 1998 
FD November 01 
VO 8 
IS 11 
SP 1142 
OP 1153 
DO 10.1101/gr.8.11.1142 
UL http://genome.cshlp.org/content/8/11/1142.abstract 
AB A new approach to comparative nucleic acid sequence analysis is described that uses the ligation of DNA targets to high-density arrays containing complete sets of covalently attached oligonucleotides of length eight and nine. The combination of enzymatic or chemical ligation with a directed comparative analysis avoids many of the intrinsic difficulties associated with hybridization-based de novo sequence reconstruction methods described previously. Double-stranded DNA targets were fragmented and labeled to produce quasirandom populations of 5′ termini suitable for ligation and detection on the arrays. Kilobase-size DNA targets were used to demonstrate that complete n-mer arrays can correctly verify known sequences and can determine the presence of sequence differences relative to a reference. By use of 9-mer arrays, sequences of 1.2-kb targets were verified with >99.9% accuracy. Mutations in target sequences were detected by directly comparing the intensity pattern obtained for an unknown with that obtained for a known reference sequence. For targets of moderate length (1.2 kb), 100% of the mutations in the queried sequences were detected with 9-mer arrays. For higher complexity targets (2.5 and 16.6 kb), a relatively high percentage of mutations (90% and 66%, respectively) were correctly identified with a low false-positive rate of <0.03 percent. The methods described provide a general approach to analyzing nucleic acid samples on the basis of the interpretation of sequence-specific patterns of hybridization and ligation on complete n-mer oligonucleotide arrays.