Our Process

As a result of the genomic revolution, traditional medicine is evolving into personalized medicine, and as a result of Information Technology biology is evolving from a wet science to a dry science. DNA-SEQ is the world’s first genomic driven oncology pipeline, directed by precision crystallography, and powered by the most advanced IT resources in the world.

Genomics is still in its early stages and therefore parallels can be drawn with the development of computing. DNA can be thought of as basic machine code. It has no utility until programs are developed to give it meaning and structure.

Next Generation Sequencing (NGS) produces data and bioinformatics turns it into information; but that information only becomes potentially actionable when it is given structural context through crystallography. At DNA-SEQ we don’t just identify the mutation but can also predict the mutation’s resistance based on the context within the three dimensional structure.

The DNA-SEQ pipeline is a seamless network of collaborative alliances that enable us to combine clinical grade Next Generation Sequencing (NGS), bioinformatics, crystallography, and a comprehensive library of kinase inhibitors, and to tightly couple the process to the most advanced IT resources in the world including the San Diego Super Computing Center and D-Wave, the worlds first Quantum Computer company. The pipeline provides a new dimension to precision.

1. Data Gathering

  • Sample Preparation enables DNA to be extracted
  • DNA Sequencing translates the DNA to raw data
  • Bioinformatics analyses annotate the data transforming it into information

But the genomics data is still just the first level of information. It doesn’t mean anything without a context. Linear information is not actionable without meaning. By applying the information within a three dimensional structure we can discover the meaning of the information extracted from the cancer patient’s genomics.

2. Data Modeling

The crystallographic approach of Dr. Janusz M. Sowadski , the Founder and CEO of DNA-SEQ, required he design, in conjunction with the San Diego Super Computing Center, a methodology for three dimensional kinase modeling. That approach also required that Dr. Sowadski develop, in conjunction with XTAL BioStructures, the world’s most comprehensive kinase crystal structure library. These tools enable DNA-SEQ to derive context driven information from linear data and also to provide traditional data driven computational models to oncology.

Our precise crystal structure library enables DNA-SEQ to develop kinase inhibitors that precisely correlate the genomic content of the patient to the treatment proposed. Our methodology predicts the resistance in the crystal structure of the target as well as where the resistant mutation will appear. We can then select or design the drug that will overcome the resistance.

3. Data Search

DNA-SEQ has a data driven long-term genomics roadmap towards a future in which the possibility of 100% efficacy can be achieved through developing our understanding of kinase mutations as being part of a single vast data network on a cellular level. Our partnership with D-Wave, the first commercial quantum computing company, is a function of our commitment to that vision of the future. D-Wave presently has the only computational platform that is up to the big data challenge of precision crystallography.

At present, with D-Wave’s existing Artificial Intelligence capabilities, we are able to approach the challenges of genomics from the perspective of one interconnected network on a cellular level. Cells are networked, and if the signaling between these cells can be modeled, we can target mutations more precisely.

If we approach cancer on the 3 levels of a biological narrative; DNA, protein structure, and cellular communication, it can be reduced to a math problem. Our goal is for DNA-SEQ to provide the capabilities that can “solve for x” patient by patient, disease by disease.