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Next Generation Sequencing Pathogen Discovery

 

Discover pathogens in diverse samples
 
Next generation sequencing (NGS) is a cutting-edge technology that sequences large quantities of DNA and RNA from biological samples and converts it into digital data. The typical size of a single raw sequencing file reaches up to several gigabytes.

I have developed a computational workflow which efficiently identifies viruses and micro-organisms from NGS data. The workflow is very powerful as it reveals what organisms are present in samples (eg. blood, body fluid, tissues, food, water, soil, meat, etc). The workflow can be used to quantitatively measure the activities (gene expression) of organisms, when RNA sequencing data (RNA-seq) is used. The workflow is suitable for detecting DNA/RNA viruses, bacteria, and fungi.

The workflow can be used as a diagnostic tool by identifying pathogens present in hosts (human, animals, plants), and it is suitable for investigating host-pathogen interactions. Profiling of the complex biodiversity in environmental, agricultural and industrial samples is also possible. It can also be used as a quality control measure in NGS experiments themselves, by identifying laboratory contaminants associated with commercial laboratory kits.
 
How the technology works

The workflow compares NGS data to over 9,000 reference genomes simultaneously, to determine what species are present in samples. Sequences aligned to organisms can be identified, visualised, quantified, and annotated. The locations of viral integrations into host genomes can be pinpointed.

 
Features of the technology
 
  1. Identifying over 9,000 species in a single run.
     
  2. Detecting organisms in the hosts without prior knowledge.
     
  3. Hosts could be human, animals, plants, insects, microorganisms (as long as their genomes are available).
     
  4. Flexible as it is made of modules. It is easy to upgrade the genome library and change outdated software in the workflow.
     
  5. More time-efficient and cost-effective in terms of turnaround and labour in near future when NGS becomes less expensive in comparison to the traditional laboratory based methods.

What we can do with the technolgy
 
  1. Profiling organisms in patients for diagnostics (cancer, infectious diseases, gut/oral/skin microbiota, food poisoning)
     
  2. Profiling pathogens in animals, insects, and crops for infectious agents and pathogens jumping around different host species.
     
  3. Detection of unwanted micro-organisms in diary, meat, food products for quality control.
     
  4. Profiling dynamics of micro-organisms in fermentation process (wine making, brewing, bioethanol production)
     
  5. Landscaping biodiversity in natural environments (soils, water) and bioremediation process (sludge, biofilms, polluted water).
     
  6. Data mining in the public NGS data bases such as National centre for biotechnology information (NCBI), European molecular biology laboratory (EMBL), The cancer genome atlas (TCGA),     International cancer genome consortium (ICGC).
     
  7. Detection of laboratory contaminants using negative 'blank' controls for next generation sequencing.
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