Genomic Analysis for Cancer

Recruiting at 9 trial locations

Overseen By Clinical Trials Office

Age: Any Age

Sex: Any

Trial Phase: Academic

Sponsor: Rutgers, The State University of New Jersey

Disqualifiers: Performance score < 30, Life expectancy < 3 months

No Placebo Group All trial participants will receive the active study treatment (no placebo)

Approved in 1 Jurisdiction This treatment is already approved in other countries

Compensation: Varies

Number of Visits: 3

1100 Participants Needed

Trial Summary

What is the purpose of this trial?

This research trial studies the use of targeted genomic analysis of blood and tissue samples from patients with cancer. Genomic sequencing is a laboratory method that is used to determine the entire genetic makeup of a specific organism or cell type. Genomic sequencing can be used to find changes in areas of the genome that may be important in the development of cancer. It may also help doctors improve ways to diagnose and treat patients with rare cancers with poor prognosis or lack of effective therapy.

Will I have to stop taking my current medications?

The trial information does not specify whether you need to stop taking your current medications. It's best to discuss this with the trial coordinators or your doctor.

What data supports the effectiveness of the treatment Targeted Genomic Analysis, FoundationOne CDx, Comprehensive Genomic Profiling?

The FoundationOne CDx test is FDA-approved and helps identify patients with cancer who may benefit from specific drug therapies by analyzing genetic changes in tumors. Studies show that using genomic profiling like FoundationOne CDx can improve treatment decisions and outcomes for some cancer patients by matching them to targeted therapies based on their tumor's genetic makeup. ^{1 2 3 4 5}

Is genomic analysis for cancer safe for humans?

The safety of genomic analysis for cancer, including tests like FoundationOne CDx, is generally supported by its FDA approval, which indicates it has met safety standards for use in humans. ^{1 6 7 8 9}

How does this treatment differ from other cancer treatments?

This treatment is unique because it uses genomic analysis to understand the specific genetic changes in cancer cells, allowing for a more personalized approach to treatment. Unlike traditional methods that categorize tumors broadly, this approach can identify specific gene expression patterns, potentially leading to more targeted and effective therapies. ^{10 11 12 13 14}

Research Team

Shridar Ganesan

Principal Investigator

Rutgers Cancer Institute of New Jersey

Eligibility Criteria

This trial is for patients with rare or hard-to-treat cancers who have a Karnofsky/Lansky score of at least 30, indicating they can care for themselves. They must have confirmed cancer diagnosis, available tumor tissue samples, and consent to participate. Those with life expectancy under 3 months or very poor physical condition (score below 30) cannot join.

Inclusion Criteria

My tumor tissue samples are available for testing.

I have a rare or hard-to-treat cancer confirmed by biopsy and reviewed by the study's lead researcher.

I can care for myself but may need occasional help.

Exclusion Criteria

Life expectancy < 3 months

I am unable to care for myself and spend all day in bed.

Timeline

Screening

Participants are screened for eligibility to participate in the trial

2-4 weeks

Genomic Analysis

Previously collected tissue samples are analyzed for the presence of mutations via next generation sequencing. Patients may also undergo collection of blood samples for analysis of circulating cell-free DNA and circulating tumor cells.

Not specified

Follow-up

Participants are monitored for clinical outcomes and safety after genomic analysis

Up to 15 years

Every 3 months for 2 years, then every 6 months for 15 years

Treatment Details

Interventions

• Targeted Genomic Analysis

Trial Overview The study is examining the use of targeted genomic analysis on blood and tissue from cancer patients to identify genetic changes that could be important in cancer development. This may help improve diagnosis and treatment options for those with rare cancers that respond poorly to standard therapies.

Participant Groups

Group I: Ancillary-Correlative (genomic analysis) Experimental Treatment 2 Interventions

Previously collected tissue samples are analyzed for the presence of mutations via next generation sequencing. Patients may also undergo collection of blood samples for analysis of circulating cell-free DNA and circulating tumor cells.

Who Is Running the Clinical Trial?

Rutgers, The State University of New Jersey

Lead Sponsor

Trials

471

Recruited

81,700+

National Cancer Institute (NCI)

Collaborator

Trials

14,080

Recruited

41,180,000+

Rutgers Cancer Institute of New Jersey

Collaborator

Trials

72

Recruited

22,200+

Findings from Research

In a study of 43 Japanese patients with advanced solid tumors, the FoundationOne CDx test successfully identified actionable gene mutations in 96% of cases, indicating its potential clinical utility in guiding treatment decisions.

Despite the high detection rate of mutations, only 15% of patients received treatments corresponding to their identified mutations, primarily due to disease progression and reduced performance status, highlighting challenges in translating genomic findings into clinical action.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

[Clinical Utility of Comprehensive Genome Profiling Using FoundationOne CDx in Japanese Population(PROFILE-F Study)]. Kumaki, Y., Takahashi, K., Mitsumura, T., et al.[2020]

In the MOSCATO 01 trial involving 1,035 adult patients with advanced cancers, high-throughput genomic analyses identified actionable molecular alterations in 411 patients, leading to targeted therapies for 199 of them.

Approximately 33% of patients receiving matched therapy experienced a progression-free survival (PFS) that was more than 1.3 times longer than their previous treatment, indicating that genomic profiling can potentially improve outcomes for some patients, although only 7% of those screened benefited from this approach.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

High-Throughput Genomics and Clinical Outcome in Hard-to-Treat Advanced Cancers: Results of the MOSCATO 01 Trial. Massard, C., Michiels, S., Ferté, C., et al.[2022]

In a study of 109,695 patients with solid tumors, FoundationOneCDx identified clinically significant genomic alterations in about 51.2% of tumor profiles, which can guide treatment decisions for various cancer therapies.

The test revealed that 89.2% of solid tumor profiles contained genomic results that could potentially inform the selection of immunotherapy and targeted therapy clinical trials, highlighting its utility in personalized cancer treatment.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Insights of Clinical Significance From 109 695 Solid Tumor Tissue-Based Comprehensive Genomic Profiles. Heilmann, AM., Riess, JW., McLaughlin-Drubin, M., et al.[2023]

The FDA has approved F1CDx, a comprehensive diagnostic test that identifies genetic changes and genomic signatures in solid tumors, allowing for personalized treatment options.

This test can match patients with five common types of advanced cancer to one of 17 targeted therapies, enhancing the potential for effective treatment based on individual tumor characteristics.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

First Comprehensive Companion Diagnostic OK'd. [2019]

FoundationOne®CDx (F1CDx) is an FDA-approved diagnostic test that uses next-generation sequencing to analyze 324 cancer genes, helping identify patients who may benefit from 28 specific cancer therapies.

The extensive analytical and clinical validation of F1CDx, based on over 30,000 test results, demonstrates its high sensitivity and reliability, ensuring accurate matching of patients with solid tumors to appropriate targeted therapies or immunotherapies.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors. Milbury, CA., Creeden, J., Yip, WK., et al.[2022]

In a study analyzing 500 patient samples using advanced genomic techniques, combining tumor and normal tissue data significantly improved mutation identification and reduced false positives, leading to better matching of patients to targeted cancer therapies.

The integration of DNA-seq, RNA-seq, and immunotherapy biomarkers allowed 76.8% of patients to be matched to relevant clinical trials, demonstrating that comprehensive molecular profiling is more effective than using tumor-only DNA testing.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Integrated genomic profiling expands clinical options for patients with cancer. Beaubier, N., Bontrager, M., Huether, R., et al.[2022]

Acquire is a comprehensive, web-based system designed to enhance the management and workflow of cancer biobanks, facilitating better integration with genomic sequencing and patient-derived xenografts.

The system includes features for real-time reporting, specimen tracking, quality control, and resource allocation, which are crucial for supporting effective cancer treatment based on actionable genetic mutations.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Acquire: an open-source comprehensive cancer biobanking system. Dowst, H., Pew, B., Watkins, C., et al.[2018]

Genetic drift is a significant issue in cancer cell lines, with studies showing that 4.5%-6.1% of the genome can change between isogenic cell lines, which can affect the reproducibility of research results.

To address this problem, the study emphasizes the importance of molecular profiling of cell lines and introduces the CCLid web application, which helps researchers screen the genomic profiles of their cell lines against a comprehensive dataset of 1,497 unique cell lines.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Assessment of Genetic Drift in Large Pharmacogenomic Studies. Quevedo, R., Smirnov, P., Tkachuk, D., et al.[2021]

A comprehensive genomic profiling study analyzed 18,004 unique adult cancers, revealing significant insights into tumor subtypes, including rare cancers, and highlighting the presence of treatment-refractory samples in breast and lung cancers.

The dataset identified novel and known druggable kinase fusions and enriched alterations like NOTCH1 in adenoid cystic carcinomas and SMAD4 in colon cancer, suggesting new therapeutic targets and opportunities for expanding the use of existing targeted therapies.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis. Hartmaier, RJ., Albacker, LA., Chmielecki, J., et al.[2018]

DNA microarray technology allows for the rapid assessment of gene expression across thousands of genes, providing insights into the genetic and epigenetic changes that lead to cancer development.

This technology can help classify tumors more precisely, study drug sensitivity and resistance, and identify biological markers, ultimately aiding in the development of targeted cancer therapies.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

[Differential gene expression analysis by DNA microarrays technology and its application in molecular oncology]. Frolov, AE., Godwin, AK., Favorova, OO.[2015]

The cDNA microarray technique allows researchers to analyze the expression of thousands of human genes simultaneously, leveraging over 1,000,000 human expressed sequence tag (EST) sequences available in public databases.

This technology has significant potential in cancer research, enabling genome-wide expression profiling that can lead to better understanding and treatment of cancer, as discussed in the review of existing literature and future applications.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Expression profiling in cancer using cDNA microarrays. Khan, J., Saal, LH., Bittner, ML., et al.[2005]

The cDNA project aims to create a comprehensive database of gene expression profiles across different human cells, which helps identify which genes are active and their levels of activity at any given time.

By analyzing gene expression in various cell types, including liver and lung cells, researchers can classify genes as either housekeeper genes or those specific to certain cell functions, providing insights into the unique characteristics of each cell type.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

[Body mapping of human genes]. Okubo, K.[2011]

Global gene expression analyses, particularly through microarray technology, enable researchers to classify cancer types, predict outcomes, and assess responses to therapies based on tumor sample profiles.

These analyses not only help in understanding the molecular mechanisms of tumor development but also pave the way for personalized treatment strategies by predicting how individual patients will respond to specific drugs.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Gene expression profiling as a tool for basic analysis and clinical application of human cancer. García-Escudero, R., Paramio, JM.[2008]

High-throughput tools for analyzing cancer genomes have enabled comprehensive identification of somatic alterations, leading to the discovery of new potential therapeutic targets.

The complexity of these genomic alterations necessitates the development of advanced analytical methods and frameworks to effectively study the functions of the identified genes in cancer.

NCBI (Pubmed)

pubmed.ncbi.nlm.nih.gov

Making sense of cancer genomic data. Chin, L., Hahn, WC., Getz, G., et al.[2023]

References

1. Japan pubmed.ncbi.nlm.nih.gov

[Clinical Utility of Comprehensive Genome Profiling Using FoundationOne CDx in Japanese Population(PROFILE-F Study)]. [2020]

2. United States pubmed.ncbi.nlm.nih.gov

High-Throughput Genomics and Clinical Outcome in Hard-to-Treat Advanced Cancers: Results of the MOSCATO 01 Trial. [2022]

3. England pubmed.ncbi.nlm.nih.gov

Insights of Clinical Significance From 109 695 Solid Tumor Tissue-Based Comprehensive Genomic Profiles. [2023]

4. United States pubmed.ncbi.nlm.nih.gov

First Comprehensive Companion Diagnostic OK'd. [2019]

5. United States pubmed.ncbi.nlm.nih.gov

Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors. [2022]

6. United States pubmed.ncbi.nlm.nih.gov

Integrated genomic profiling expands clinical options for patients with cancer. [2022]

7. England pubmed.ncbi.nlm.nih.gov

Acquire: an open-source comprehensive cancer biobanking system. [2018]

8. United States pubmed.ncbi.nlm.nih.gov

Assessment of Genetic Drift in Large Pharmacogenomic Studies. [2021]

9. United States pubmed.ncbi.nlm.nih.gov

High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis. [2018]

10. Russia (Federation) pubmed.ncbi.nlm.nih.gov

[Differential gene expression analysis by DNA microarrays technology and its application in molecular oncology]. [2015]

11. Germany pubmed.ncbi.nlm.nih.gov

Expression profiling in cancer using cDNA microarrays. [2005]

12. Japan pubmed.ncbi.nlm.nih.gov

[Body mapping of human genes]. [2011]

13. United States pubmed.ncbi.nlm.nih.gov

Gene expression profiling as a tool for basic analysis and clinical application of human cancer. [2008]

14. United States pubmed.ncbi.nlm.nih.gov

Making sense of cancer genomic data. [2023]