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243 Novel and Improved Methods to Measure Cancer Epigenetic Biomarkers

Number of anticipated awards: 3-6
(Fast-Track proposals will be accepted.)
Budget (total costs): Phase I: $150,000;
Phase II: $1,000,000

The deadline for receipt of all contract proposals submitted in response to this solicitation is: 5:00 p.m. Eastern Standard Time Monday, November 5, 2007

Epigenetic markers, especially DNA methylation, have shown promise for early detection of cancerous lesions. However, it is unlikely that any single epigenetic marker has sufficient sensitivity and specificity to accurately and reliably detect early cancers or to predict cancer risk. Also, methods used to measure DNA methylation and other epigenetic markers need to be improved to increase specificity, sensitivity, reproducibility, and throughput. For example, most methods to measure CpG methylation at specific sites require bisufite treatment, which is time consuming, can result in incomplete conversion of cytosines to uracils, and can cause fluctuations in methylation measurements, thus decreasing accuracy. Assays, methods and arrays or chips need to be developed to integrate and improve the use of DNA methylation as a non-invasive approach for early cancer detection and risk prediction.

Project goals:

The purpose of this initiative is to solicit small businesses to develop innovative and improved assays, methods, or chips for detecting CpG methylation status for early cancer detection and risk assessment. This SBIR contract solicitation encourages: (1) development of new methods for methylation detection that do not require bisulfite treatment; (2) development of methods that substantially increase the conversion rate of cytosine to uracil by bisulfite treatment; (3) development of a chip for detection of methylation biomarkers; and (4) development of more sensitive techniques that allow for DNA methylation to be measured in small volumes of bodily fluids such as sera or sputum. Most current methods require large volumes, making them unsuitable for use with these bodily fluids and hence for use in early cancer detection.

Phase I activities and expected deliverables:

Develop innovative and improved methylation detection methods that do not require bisulfate treatment, or that substantially increase the conversion rate of cytosine to uracil by bisulfate treatment, to allow for the quantitative measurement of CpG methylation and/or an increase in analytical sensitivity:

  • Demonstrate proof of principle for the development of chips.
  • Demonstrate feasibility by testing a panel of 5 to 10 genes.
  • Test the usefulness of these methods using DNA extracted from cell lines or clinical samples.

Phase II activities and expected deliverables:

Refine and analytically validate the assays, methods, or chips to test accuracy.

  • Use these assays, methods, or chips to test the methylation status for more than 30 genes.
  • Validate the sensitivities and specificities of the assays and methods using appropriate clinical samples.
  • Plan the next step for commercialization of the assays, methods, and chips for detecting epigenetic biomarkers.

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