利用全基因组独特序列进行单核苷酸多态性定位

Single nucleotide polymorphism mapping using genome-wide unique sequences.

作者信息

Chen Leslie Y Y, Lu Szu-Hsien, Shih Edward S C, Hwang Ming-Jing

机构信息

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

出版信息

Genome Res. 2002 Jul;12(7):1106-11. doi: 10.1101/gr.224502.

DOI:10.1101/gr.224502

PMID:12097348

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC186620/

Abstract

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.

摘要

随着越来越多的基因组DNA被测序以表征人类遗传变异，对一种非常快速且准确的方法来在基因组上定位这些DNA序列的需求很高。我们开发了一种不需要序列比对的新映射方法。在这种方法中，我们首先鉴定出在人类基因组中独一无二的15bp长的DNA片段，然后用它们来定位单核苷酸多态性（SNP）序列。通过使用四台配备AMD K7（1GHz）处理器的台式个人计算机，我们的新方法在20小时内映射了超过160万个SNP序列，并且与基于比对的方法得到的映射结果非常吻合。