Genome-Informed Awareness System to Examine Cancer-Derived Raw HTS Outputs Using Electronic-Probe Diagnostic Nucleic-acid Analysis (EDNA)

About 606,880 Americans were expected to die of cancer in 2019, which translates to about 1,660 deaths per day, and more than 1.7 million new cancer cases were expected to be diagnosed in 2019. There is a need for novel diagnostic alternatives to rapidly identify, characterize, and contextualize cancer and associated infectious diseases.

Purpose. In general, to deliver a genome-informed detection system able to examine raw High Throughput Sequencing (HTS) outputs and to detect early cancer development in patients. To analyze metagenomic datasets, our research group has developed a bioinformatic pipeline that uses electronic probes (e-probes) of genetic signatures of targeted pathogens and other taxonomically related species, allowing for their rapid identification in minutes.

 

Expected outcome. This project will result in a unique set of breast cancer-specific sequences (e-probes) designed for searches of unassembled, unchecked raw base call read sequence data (i.e. Illumina or MinION) with a low limit of detection and high specificity.

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Brief Description of Potential Work

Generating essential data to validate EDNA-BC to rapidly identify and monitor the genetic signatures of targeted associated cancer genes and/or pathogens in metagenomic datasets.

 

No bioinformatic experience is needed because the EDNA technology is unique, new, and training will be provided.

 

Network Mentor: Dr. Francisco Ochoa Corona