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Table 3 Comparison of available technologies for identification of microbial sequences in human tissues

From: Identification of microbial DNA in human cancer

(A) Genomic DNA-based platform vs. RNA-based platform
Platform Principle for Analysis Advantages Disadvantages References
RNA-based Extraction of sequences from expression library data sets Detection of actively expressed microbial genes regardless of DNA copy number No detection of non-transcribed microbial genes Computational Subtraction [14, 16]
   Tags can be generated as long as genes are transcripted Can miss detection if low microbial load DTS [17, 21]
   Tag numbers are not limited by the genome size Subject to sequencing errors or tag site polymorphisms matching microbial sequences Viral Detection DNA Microarray [8]
     RDA [13]
Genomic DNA-based Extraction of sequences from genomic library data sets Detection of microbial DNA regardless of expression status of the genes No detection of non-reverse transcribed RNA DK-MICROBE
   Potential to detect latent microbial genomic fragments which have been integrated into human genome Can miss detection if low microbial load Computational Subtraction [15]
   Utilization of clinical samples not suitable for RNA extraction including paraffin-embedded fixed tissue Subject to sequencing errors or tag site polymorphisms matching microbial sequences  
(B) Tag-based vs. array hybridization
Platform Principle for Analysis Advantages Disadvantages References
Array hybridization Cross hybridization to homologous sequences of microorganisms on microarray Currently lower cost Array designed to target limited number of candidate microbes Viral Detection DNA Microarray [811]
   Method is highly versatile and generally high throughput Risk of unspecific binding  
Tag-based Fractional representations through extraction of sequences from specific locations in microbial genomes Sequence based non biased result Limited by sequencing costs DK-MICROBE
   Greater chance to identify rare microbial associations Subject to sequencing errors, tag site polymorphisms Computational Subtraction [1416]
   No physical generation of organism-specific array   DTS [17, 21]
   Results can be utilized and referenced for additional human genome analyses   
  1. A. Advantages and disadvantages of using genomic DNA- versus RNA-based platforms. B. Advantages and disadvantages of using tag-based versus array hybridization platforms. Abbreviations: DTS, digital transcript subtraction; RDA, representational difference analysis.