Genomic Analysis for Cancer

Recruiting at 10 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

What You Need to Know Before You Apply

What is the purpose of this trial?

This trial focuses on using genomic analysis to better understand and treat rare cancers. Researchers aim to identify genetic changes in cancer cells from blood and tissue samples that could lead to more effective diagnosis and treatment options. The trial seeks participants diagnosed with a rare cancer that does not respond well to standard treatments. Those with previously collected tissue samples available for testing might be a good fit for this study. As a Phase 2 trial, this research measures the treatment's effectiveness in an initial, smaller group, offering a chance to contribute to groundbreaking advancements in cancer care.

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 prior data suggests that targeted genomic analysis is safe for cancer patients?

Research has shown that targeted genomic analysis is already used in medicine, particularly with a method called FoundationOne CDx. The FDA has approved this method for various solid tumors, confirming its safety in analyzing tissue samples.

The process examines the genes in a person’s tumor to identify significant changes. These changes can help doctors understand the cancer better and determine the most effective treatment. The analysis itself is well-tolerated, as it involves only the study of samples and does not cause harm.

In summary, targeted genomic analysis is considered safe for individuals based on current studies and its FDA-approved status for similar applications. ^{1 2 3 4 5}

Why are researchers excited about this trial?

Researchers are excited about targeted genomic analysis for cancer because it offers a personalized approach to treatment. Unlike traditional chemotherapy or radiation, which attack cancer cells but also affect healthy cells, genomic analysis identifies specific genetic mutations in a person's cancer. This allows doctors to tailor treatments that directly target those mutations, potentially leading to more effective and less harmful therapies. Additionally, analyzing circulating cell-free DNA and tumor cells from blood samples can offer a non-invasive way to monitor the cancer's progress and response to treatment, giving patients and doctors real-time insights without the need for repeated biopsies.

What evidence suggests that targeted genomic analysis is effective for cancer?

Research shows that analyzing the genes of cancer cells can help doctors treat cancer more effectively. Comprehensive genomic profiling (CGP) examines many genes simultaneously to identify changes that might cause cancer to grow. Studies have shown that this method can help predict how well patients might respond to certain cancer treatments. For example, in soft tissue sarcoma, next-generation sequencing has been helpful in planning treatments. Similarly, in early-stage triple-negative breast cancer, genomic testing can predict treatment effectiveness. This trial involves genomic analysis, where previously collected tissue samples undergo next-generation sequencing to identify mutations. By understanding the genetic details of a tumor, doctors can make better decisions about which treatments are likely to be most effective. ^{1 6 7 8 9}

Who Is on the Research Team?

Shridar Ganesan

Principal Investigator

Rutgers Cancer Institute of New Jersey

Are You a Good Fit for This Trial?

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 for a Trial Participant

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

What Are the Treatments Tested in This Trial?

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.

How Is the Trial Designed?

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+

Published Research Related to This Trial

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]

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]

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 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]

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]

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]

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]

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]

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]

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]

Citations

1. foundationmedicine.com foundationmedicine.com/test/foundationone-cdx

FoundationOne CDx | Foundation ... FoundationOne CDx is the first FDA-approved tissue-based broad companion diagnostic (CDx) that is clinically and analytically validated for all solid tumors.

2. pubmed.ncbi.nlm.nih.gov pubmed.ncbi.nlm.nih.gov/40701291/

Cost-Effectiveness Analysis of Comprehensive Genomic ... Using real-world evidence, this study compared the cost-effectiveness of comprehensive genomic profiling (CGP) versus small panel (SP) testing ...

3. pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov/articles/PMC10670373/

Genomic Profiling and Clinical Outcomes of Targeted ... In this review, we focus on the clinical utility of next-generation sequencing (NGS) to inform therapeutics in soft tissue sarcoma (STS).

4. foundationmedicine.com foundationmedicine.com/resource/why-comprehensive-genomic-profiling

Why Comprehensive Genomic Profiling? Comprehensive genomic profiling (CGP) can analyze a broad panel of genes to detect the four main classes of genomic alterations known to drive cancer growth.

5. sciencedirect.com sciencedirect.com/science/article/pii/S0960977625000426

Comprehensive genomic profiling can predict response to ... This study suggests that comprehensive CDx testing can be explored as a prognostic tool in early-stage TNBC to predict responses to NACT and disease ...

6. accessdata.fda.gov accessdata.fda.gov/cdrh_docs/pdf17/P170019S014C.pdf

FoundationOne®CDx Technical Information FoundationOne®CDx (F1CDx) is a qualitative next-generation sequencing based in vitro diagnostic test that uses targeted high throughput hybridization-based ...

7. foundationmedicine.com foundationmedicine.com/patient

Cancer Genomic Testing to Inform Treatment Foundation Medicine uses comprehensive genomic profiling, a type of biomarker testing, that looks at more genes to find information in your tumor's DNA.

8. pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov/articles/PMC8926248/

Clinical and analytical validation of FoundationOne®CDx, a ... F1CDx utilizes next-generation sequencing (NGS)-based comprehensive genomic profiling (CGP) technology to examine 324 cancer genes in solid ...

9. blueshieldca.com blueshieldca.com/content/dam/bsca/en/provider/docs/medical-policies/Comprehensive-Genomic-Profiling-Targeted-Cancer-Therapies.pdf

Comprehensive-Genomic-Profiling-Targeted-Cancer- ... Comprehensive genomic profiling offers the potential to evaluate a large number of genetic markers at a single time to identify cancer ...