SBIR-STTR Award

Cancers develop from the life-long accumulation of critical somatic mutations due to DNA-damaging agents that lead to cells transforming into tumor-forming cells. These low-level tumor-associated somatic DNA mutations can have profound implications for development of metastasis, prognosis, choice of treatment, follow-up or early cancer detection. Unless they are effectively detected, these low-level mutations can misinform patient management decisions or become missed opportunities for personalized medicine. Widely-used technologies such as sequencing are not sensitive enough to detect these mutations when they are at very low percentages compared to normal DNA. Likewise the next generation sequencing technologies (NGS) are promising technology advances that can effectively detect prevalent somatic mutations in targeted gene panels; however due to the limited quantity of DNA in most patient samples and the abundance of normal DNA when analyzing blood, NGS 'loses steam' and its integration with clinical practice is problematic. For mutations at an abundance of ~2-5% or below, NGS generates false positives ('noise') independent of sequencing depth; yet these are often the clinically relevant mutations causing resistance to drug treatments. Commercial sample preparation kits for targeted re-sequencing of cancer gene panels have emerged1-3, however they are uniformly unable to detect mutations below a 2% abundance level. Thus, while targeted re-sequencing provides an opportunity for integration of NGS with clinical oncology, the technology is ineffective in detecting DNA mutations in heterogeneous cancers or in circulating DNA. We intend to use COLD-PCR, a new method that enriches unknown mutation-containing sequences over wild-type, normal alleles during PCR amplification. We have been able to show sequencing of mutations down to 0.02% abundance. However in its current form this method only can be used with single amplicon per reaction, limiting its efficient combination with NGS. In this project we propose a simple and powerful modification that enables COLD-PCR to be applied on hundreds or thousands of DNA targets in a single reaction, thus enabling mutation enrichment in cancer- specific gene panels prior to NGS. This would convert the rare mutations to high abundance mutations, overcoming the 'noise' and avoid the costly need for repeated sequence reads during NGS. This method, known as temperature-tolerant-COLD-PCR (TT-COLD-PCR), will be developed into kits for cancer-specific gene panels, to magnify rare mutations in multiple DNA targets thus enabling expanded application of targeted re-sequencing for heterogeneous cancers or circulating DNA. This project meets one of the stated aims of the NCI to support the development of new methods of diagnosis for the detection, discovery and validation of biomarkers for cancer detection, diagnosis and prognosis.

Public Health Relevance Statement:


Public Health Relevance:
The selection of the best available cancer treatment is, in many instances, dependent on the genetic profile of the patient's cancer cells. This can be difficult to determine when there is limited availability of tumor DNA, as when analyzing blood, when obscured by far more abundant healthy cell DNA and when many DNA targets need to be analyzed. This project aims to develop a multiplexed DNA analysis technique that enriches low abundance cancer mutations in clinical specimens such as blood to improve cancer treatment selection.

Project Terms:
2,6-Diaminopurine; Alleles; base; Biological Markers; Blood; cancer cell; Cancer Detection; cancer diagnosis; cancer therapy; Cell Line; cell transformation; Cells; Clinical; Clinical Oncology; clinical practice; clinically relevant; Collaborations; Colonic Neoplasms; Detection; Development; Diagnosis; Dideoxy Chain Termination DNA Sequencing; Disease; DNA; DNA analysis; DNA Damage; DNA Fingerprinting; Drug resistance; Early Diagnosis; Epidermal Growth Factor Receptor; Exons; follow-up; Gene Mutation; Gene Targeting; Genes; genetic profiling; Genomics; Heterogeneity; improved; Inosine; Ions; KRAS2 gene; Lead; Licensing; Life; Liquid substance; Lung Neoplasms; Malignant Neoplasms; Marketing; Medicine; meetings; Methods; Modification; mutant; Mutation; Neoplasm Metastasis; next generation sequencing; Noise; novel strategies; Nucleotides; Oncogenes; outcome forecast; Patients; Phase; Positioning Attribute; Preparation; Process; public health relevance; Radio; Reaction; Reading; research study; Resistance development; Sampling; Screening for cancer; Small Business Technology Transfer Research; Somatic Mutation; Specimen; Steam; Tail; Techniques; Technology; Temperature; therapy resistant; Time; TP53 gene; Tube; tumor; Validation

Low-level, tumor-associated somatic DNA mutations can have profound implications for development of metastasis, prognosis, choice of treatment, follow-up or early cancer detection. Unless they are effectively detected, these low-level mutations can misinform patient management decisions or become missed opportunities for personalized medicine. Widely-used technologies such as sequencing are not sensitive enough to detect these mutations when they are at very low percentages compared to normal DNA. Likewise the next generation sequencing technologies (NGS) are promising technology advances that can effectively detect prevalent somatic mutations in targeted gene panels; however due to the limited quantity of DNA in most patient samples and the abundance of normal DNA when analyzing blood, NGS 'loses steam' and its integration with clinical practice is problematic. For mutations at an abundance of ~2-5% or below, NGS generates false positives (`noise') independent of sequencing depth; yet these are often the clinically relevant mutations causing resistance to drug treatments. Commercial sample preparation kits for targeted re-sequencing of cancer gene panels have emerged, however they are uniformly unable to detect mutations below a 2% abundance level. Thus, while targeted re-sequencing provides an opportunity for integration of NGS with clinical oncology, the technology is ineffective in detecting DNA mutations in circulating DNA, urine, or heterogeneous cancers. We intend to use COLD-PCR, a recently developed method that enriches unknown mutation-containing sequences over wild-type, normal alleles during PCR amplification. In previous work we showed COLD-PCR- NGS-based sequencing for mutations down to 0.02% abundance. However, COLD-PCR was only applicable with a single amplicon per reaction, limiting its efficient combination with NGS. This STTR proposes a simple and powerful modification that enables COLD-PCR to be applied to hundreds or thousands of DNA targets in a single reaction, thus enabling mutation enrichment in disease- specific gene panels prior to NGS. The new approach, temperature-tolerant-COLD-PCR (TT-COLD-PCR) converts the rare mutations to high abundance mutations, overcoming the `noise' and avoiding the costly need for repeated sequence reads during NGS. In Phase I we obtained proof of principle for TT-COLD-PCR. In Phase II, TT-COLD-PCR will be developed into kits for cancer-specific gene panels, to magnify rare mutations in multiple DNA targets thus enabling expanded application of targeted re-sequencing for heterogeneous cancers or circulating DNA. This project meets one of the aims of the NCI to support the development of new methods of diagnosis for the detection, discovery and validation of biomarkers for cancer detection, diagnosis and prognosis.

Public Health Relevance Statement:


Public Health Relevance:
Screening of patients' tumors for genetic alterations over many genes in a minimally- invasive, rapid and cost-effective manner is a significant challenge that must be fulfilled in order to realize the promise of individualized cancer treatment. Although major advances have been made, there is still a significant gap in technology that prevents molecular profiling from repeated blood collections (`liquid biopsies'). This STTR project provides an answer to this challenge by employing a new technology, TT-COLD-PCR in combination with Next Generation Sequencing. This novel approach overcomes technical limitations and enables reliable mutation screening in multiple genes simultaneously, in bodily fluids or surgical cancer samples from individual patients. In view of the fundamental role of mutations in causing cancer and modulating tumor response to drug treatment, this project has significant implications for public health.

Project Terms:
Alleles; base; Base Sequence; Biological Markers; Biopsy; Blood; Cancer Detection; cancer diagnosis; Cancer Etiology; cancer therapy; circulating DNA; Clinical; Clinical Oncology; clinical practice; clinically relevant; clinically significant; Collection; Colon; cost; cost effective; design; Detection; Development; Diagnosis; Disease; DNA; DNA Sequence Alteration; Drug resistance; Engineering; follow-up; Future; Gene Targeting; Genes; Genetic Fingerprintings; Genomic DNA; Genotype; Heterogeneity; individual patient; Licensing; Liquid substance; Malignant Neoplasms; meetings; melting; Methods; minimally invasive; Modification; Molecular Profiling; Mutation; mutation screening; Neoplasm Metastasis; new technology; next generation sequencing; Noise; novel strategies; Nucleotides; Oncogenes; Operative Surgical Procedures; outcome forecast; Patients; personalized medicine; Pharmacotherapy; Phase; Plasma; Positioning Attribute; Preparation; prevent; Process; public health medicine (field); public health relevance; Reaction; Reading; Relative (related person); Reproducibility; response; Role; Sampling; screening; Screening for cancer; Sensitivity and Specificity; Small Business Technology Transfer Research; Somatic Mutation; Steam; Technology; Temperature; Testing; Time; treatment choice; Tube; tumor; Urine; Validation; Work