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Published online before print June 18, 2002, 10.1101/gr.224502. Article published online before print in June 2002
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Vol. 12, Issue 7, 1106-1111, July 2002

METHODS
Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences

Leslie Y.Y. Chen, Szu-Hsien Lu, Edward S.C. Shih, and Ming-Jing Hwang1

Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan

As more and more genomic DNAs are sequenced to characterize human genetic variations, the demand for a very fast and accurate method to genomically position these DNA sequences is high. We have developed a new mapping method that does not require sequence alignment. In this method, we first identified DNA fragments of 15 bp in length that are unique in the human genome and then used them to position single nucleotide polymorphism (SNP) sequences. By use of four desktop personal computers with AMD K7 (1 GHz) processors, our new method mapped more than 1.6 million SNP sequences in 20 hr and achieved a very good agreement with mapping results from alignment-based methods.

1 Corresponding author.

12:1106-1111 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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