Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping

作者：Ambroise Jerome^*; Deccache Yann; Irenge Leonid; Savov Encho; Robert Annie; Gala Jean Luc

来源：Bioinformatics, 2014, 30(24): 3590-3597.

DOI：10.1093/bioinformatics/btu516

Motivation: Pyrosequencing is a cost-effective DNA sequencing technology that has many applications, including rapid genotyping of a broad spectrum of bacteria. When molecular typing requires to genotype multiple DNA stretches, several pyrosequencing primers could be used simultaneously but this would create overlapping primer-specific signals, which are visually uninterpretable. Accordingly, the objective was to develop a new method for signal processing (AdvISER-M-PYRO) to automatically analyze and interpret multiplex pyrosequencing signals. In parallel, the nucleotide dispensation order was improved by developing the SENATOR (%26apos;SElecting the Nucleotide dispensATion Order%26apos;) algorithm. %26lt;br%26gt;Results: In this proof-of-concept study, quintuplex pyrosequencing was applied on eight bacterial DNA and targeted genetic alterations underlying resistance to beta-lactam antibiotics. Using SENATOR-driven dispensation order, all genetic variants (31 of 31; 100%) were correctly identified with AdvISER-M-PYRO. Among nine expected negative results, there was only one false positive that was tagged with an %26apos;unsafe%26apos; label. %26lt;br%26gt;Availability and implementation: SENATOR and AdvISER-M-PYRO are implemented in the AdvISER-M-PYRO R package (http://sites.uclouvain. be/md-ctma/index.php/softwares) and can be used to improve the dispensation order and to analyze multiplex pyrosequencing signals generated in a broad range of typing applications.

• 出版日期2014-12-15
• 单位中国人民解放军军事医学科学院