基于微阵列的病原体诊断检测的寡核苷酸指纹识别

Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays.

作者信息

Tembe Waibhav, Zavaljevski Nela, Bode Elizabeth, Chase Catherine, Geyer Jeanne, Wasieloski Leonard, Benson Gary, Reifman Jaques

机构信息

Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD Boston, MA, USA.

出版信息

Bioinformatics. 2007 Jan 1;23(1):5-13. doi: 10.1093/bioinformatics/btl549. Epub 2006 Oct 26.

DOI:10.1093/bioinformatics/btl549

PMID:17068088

Abstract

MOTIVATION

Advances in DNA microarray technology and computational methods have unlocked new opportunities to identify 'DNA fingerprints', i.e. oligonucleotide sequences that uniquely identify a specific genome. We present an integrated approach for the computational identification of DNA fingerprints for design of microarray-based pathogen diagnostic assays. We provide a quantifiable definition of a DNA fingerprint stated both from a computational as well as an experimental point of view, and the analytical proof that all in silico fingerprints satisfying the stated definition are found using our approach.

RESULTS

The presented computational approach is implemented in an integrated high-performance computing (HPC) software tool for oligonucleotide fingerprint identification termed TOFI. We employed TOFI to identify in silico DNA fingerprints for several bacteria and plasmid sequences, which were then experimentally evaluated as potential probes for microarray-based diagnostic assays. Results and analysis of approximately 150 in silico DNA fingerprints for Yersinia pestis and 250 fingerprints for Francisella tularensis are presented.

AVAILABILITY

The implemented algorithm is available upon request.

摘要

动机

DNA微阵列技术和计算方法的进步为识别“DNA指纹”带来了新机遇，即能唯一识别特定基因组的寡核苷酸序列。我们提出一种综合方法，用于基于微阵列的病原体诊断检测设计中DNA指纹的计算识别。我们从计算和实验角度给出了DNA指纹的可量化定义，并给出分析证明，即使用我们的方法可找到所有满足所述定义的计算机模拟指纹。