Breast TumorNCT01247480
Analysis of Prognostic and Predictive Genomic Signatures Using Archival Paraffin-embedded Tumor Specimens in Breast Cancer
An observational study of Breast Tumor, run by National University Hospital, Singapore at 1 site in Singapore.
Trial summary
Major Aims of study: 1. To create a gene expression-based prognostic device that complements or exceeds the prognostic utility of conventional biomarkers of breast cancer outcome. 2. Read more about this study
- Who is it for?
- Any age, women only
- Conditions the study is for
- Breast Tumor
- How many people
- Not given
- Where
- 1 siteSingapore
- Study dates
- Sep 2010to Dec 2014
- Phase
- Observational
- Are there results?
- None posted in the registry
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages Any age
- Women only
- No healthy volunteers
- Child, Adult, Older adult
Study population: 800 breast cancer patients who fulfill the eligibility criteria will be selected from the NUH breast cancer registry (400 for training, 400 for validation).
Who may be able to join
- Eligible patients should have at least 5 years' follow-up at NUH and have an available archival paraffin-embedded tumor block stored at the Department of Pathology, NUH
Who cannot join
- Non breast cancer patients
Trial locations and contacts
1 site in 1 country.
About this study
Major Aims of study:
- To create a gene expression-based prognostic device that complements or exceeds the prognostic utility of conventional biomarkers of breast cancer outcome.
- To identify one or more clinical subgroups of patients for which the prognostic device outperforms, or substantially adds to, the prognostic performance of conventional markers that currently determine therapeutic strategies.
Read more
Sub-Aims of study:
- Assess the prognostic value of the multiple gene expression signatures, alone and in combination, using a large cohort of breast cancer patients for which pathology, treatment and outcome is available. A "training" and "testing" design is proposed.
- Evaluate the utility of a prognostic device that measures gene expression levels from formalin-fixed paraffin-embedded specimens (FFPEs) of primary resected tumors. The investigators will utilize the Affymetrix Quantigene 2.0 Assay and/or the Illumina BeadXpress VeraCode DASL Gene Expression Assay (FDA-approved IVDMIA.)
- For specific clinical subgroups of patients/tumors, the investigators will mathematically identify additive or synergistic prognostic relationships between genes and gene signatures that, in combination, will yield maximal risk prediction (distant metastases-free survival) for patients.
- Compare the prognostic utility of the investigators device to that of the conventional prognostic variables that are currently used to determine therapeutic strategy.
- Incorporate the prognostic signatures into a practical prognosis algorithm that seeks to include conventional measures of outcome such as tumor size, histologic grade, nodal status, patient age, or Nottingham index, etc.
The investigators hypothesize that adequate quality and quantity of tumor RNA may be extracted from archival paraffin-embedded tumor specimens for gene expression profiling, and that archival tumor-derived genomic signatures may be used as prognosticators or predictors in breast cancer.
Read the detailed description
800 breast cancer patients who fulfill the eligibiltiy criteria will be selected from the NUH breast cancer registry (400 for training, 400 for validation). Eligible patients should have at least 5 years' follow-up at NUH and have an available archival paraffin-embedded tumor block stored at the Department of Pathology, NUH. 8-10 ten-micron sections from each tumor block will be cut and RNA extracted from the sections. RNA will then be profiled using high-throughput gene expression platforms (Illumina Veracode assay, Affymetrix Quantigene assay). Raw gene expression data will be applied in the following signatures previously generated by the Genome Institute of Singapore:
- 32-gene p53 Pathway Signature
- 5-gene Genetic Grade Signature
- 33-gene TuM1 Signature
- 10-gene ER Signature (Miller \& Tan, et. al., unpublished)
- 6-gene 3-Ratio Predictor (Miller \& Karuturi, et. al., unpublished)
- 5-gene HER2 Amplicon Predictor (Miller \& Karuturi, et. al., unpublished)
- 7-gene Basal-Luminal Discriminator (Miller, unpublished)
The prognostic and/or predictive abilities of these signatures will be compared with conventional clinical prognosticators and predictors with the goal of developing archival tumor-derived genomic tests for breast cancer management in the future.
The archival paraffin-embedded tumor blocks are left-over samples after clinical use. They are not samples that have been consented for research purpose. We are requesting for waiver of consent as this is a minimal risk study. We will ensure that sufficient tissue be left behind for future routine diagnostic purposes. Sections taken from each tumor will be coded with no patient identifiers to protect the privacy and confidentiality of the participants.
The results generated from the tumor samples in this study will not impact on the clinical management of the patients.
- Conditions
- Breast Tumor
- Medical subject headings
- Breast Neoplasms
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
| Study group | Role | What they receive |
|---|---|---|
| Breast cancer patients | Not described |
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted24 Nov 2010 (estimated)
- Study startSep 2010
- Primary completionDec 2014 (estimated)
- Study completionDec 2014
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Publications (2)Papers the sponsor has linked to this study.
- Other trials for Breast TumorStudies of the same condition, open and under way.
- More trials run by National University Hospital, SingaporeThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Observational model
- Cohort
- Time perspective
- Retrospective
Sponsor and investigators
- Lead sponsor
- National University Hospital, Singapore
- Sponsor type
- University, hospital or other
- Investigators
- Soo Chin Lee, MBBS, MRCP, Principal investigator, National University Hospital, Singapore
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT01247480
- Sponsor's protocol ID
- BR05/22/10
- Status last verified
- Jan 2014
- First submitted
- 31 Aug 2010
- Last updated
- 22 Jan 2014
- Results posted
- No
- Data monitoring committee
- No
Publications
Slodkowska EA, Ross JS. MammaPrint 70-gene signature: another milestone in personalized medical care for breast cancer patients. Expert Rev Mol Diagn. 2009 Jul;9(5):417-22. doi: 10.1586/erm.09.32.
PubMed 19580427Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D, Foekens JA. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet. 2005 Feb 19-25;365(9460):671-9. doi: 10.1016/S0140-6736(05)17947-1.
PubMed 15721472
Study at a glance
From the registry record, last updated by the sponsor on 22 Jan 2014. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Analysis of Prognostic and Predictive Genomic Signatures Using Archival Paraffin-embedded Tumor Specimens in Breast Cancer
- ClinicalTrials.gov ID
- NCT01247480
- Acronym / sponsor ID
- BR05/22/10
- Conditions
- Breast Tumor
- Study type
- Observational
- Recruitment status
- Unknown status
- Lead sponsor
- National University Hospital, SingaporeUniversity, hospital or other
- Study start
- Sep 2010
- Primary completion
- Dec 2014 (estimated)
- Study completion
- Dec 2014
- First posted
- 24 Nov 2010 (estimated)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
Major Aims of study:
- To create a gene expression-based prognostic device that complements or exceeds the prognostic utility of conventional biomarkers of breast cancer outcome.
- To identify one or more clinical subgroups of patients for which the prognostic device outperforms, or substantially adds to, the prognostic performance of conventional markers that currently determine therapeutic strategies.
Sub-Aims of study:
- Assess the prognostic value of the multiple gene expression signatures, alone and in combination, using a large cohort of breast cancer patients for which pathology, treatment and outcome is available. A "training" and "testing" design is proposed.
- Evaluate the utility of a prognostic device that measures gene expression levels from formalin-fixed paraffin-embedded specimens (FFPEs) of primary resected tumors. The investigators will utilize the Affymetrix Quantigene 2.0 Assay and/or the Illumina BeadXpress VeraCode DASL Gene Expression Assay (FDA-approved IVDMIA.)
- For specific clinical subgroups of patients/tumors, the investigators will mathematically identify additive or synergistic prognostic relationships between genes and gene signatures that, in combination, will yield maximal risk prediction (distant metastases-free survival) for patients.
- Compare the prognostic utility of the investigators device to that of the conventional prognostic variables that are currently used to determine therapeutic strategy.
- Incorporate the prognostic signatures into a practical prognosis algorithm that seeks to include conventional measures of outcome such as tumor size, histologic grade, nodal status, patient age, or Nottingham index, etc.
The investigators hypothesize that adequate quality and quantity of tumor RNA may be extracted from archival paraffin-embedded tumor specimens for gene expression profiling, and that archival tumor-derived genomic signatures may be used as prognosticators or predictors in breast cancer.
Detailed description
800 breast cancer patients who fulfill the eligibiltiy criteria will be selected from the NUH breast cancer registry (400 for training, 400 for validation). Eligible patients should have at least 5 years' follow-up at NUH and have an available archival paraffin-embedded tumor block stored at the Department of Pathology, NUH. 8-10 ten-micron sections from each tumor block will be cut and RNA extracted from the sections. RNA will then be profiled using high-throughput gene expression platforms (Illumina Veracode assay, Affymetrix Quantigene assay). Raw gene expression data will be applied in the following signatures previously generated by the Genome Institute of Singapore:
- 32-gene p53 Pathway Signature
- 5-gene Genetic Grade Signature
- 33-gene TuM1 Signature
- 10-gene ER Signature (Miller \& Tan, et. al., unpublished)
- 6-gene 3-Ratio Predictor (Miller \& Karuturi, et. al., unpublished)
- 5-gene HER2 Amplicon Predictor (Miller \& Karuturi, et. al., unpublished)
- 7-gene Basal-Luminal Discriminator (Miller, unpublished)
The prognostic and/or predictive abilities of these signatures will be compared with conventional clinical prognosticators and predictors with the goal of developing archival tumor-derived genomic tests for breast cancer management in the future.
The archival paraffin-embedded tumor blocks are left-over samples after clinical use. They are not samples that have been consented for research purpose. We are requesting for waiver of consent as this is a minimal risk study. We will ensure that sufficient tissue be left behind for future routine diagnostic purposes. Sections taken from each tumor will be coded with no patient identifiers to protect the privacy and confidentiality of the participants.
The results generated from the tumor samples in this study will not impact on the clinical management of the patients.
Study design
- Observational model
- Cohort
- Time perspective
- Retrospective
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| Breast cancer patients | – | – |
Who may qualify
- Sex
- Female only
- Healthy volunteers
- Not accepted
- Age groups
- Child, Adult, Older adult
- Study population
- 800 breast cancer patients who fulfill the eligibility criteria will be selected from the NUH breast cancer registry (400 for training, 400 for validation).
Key inclusion criteria (1 listed)
- Eligible patients should have at least 5 years' follow-up at NUH and have an available archival paraffin-embedded tumor block stored at the Department of Pathology, NUH
Key exclusion criteria (1 listed)
- Non breast cancer patients
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Primary outcome
Not reported in the source record.
Results and safety
Results are not available in the source record.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 22 Jan 2014.
- Background: PubMed 19580427Slodkowska EA, Ross JS. MammaPrint 70-gene signature: another milestone in personalized medical care for breast cancer patients. Expert Rev Mol Diagn. 2009 Jul;9(5):417-22. doi: 10.1586/erm.09.32.
- Background: PubMed 15721472Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D, Foekens JA. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet. 2005 Feb 19-25;365(9460):671-9. doi: 10.1016/S0140-6736(05)17947-1.
Related trials for Breast Tumor
Active, not recruiting
Streamlined Geriatric and Oncological Evaluation Based On IC Technology
Breast Cancer, Comorbidities and Coexisting Conditions
RecruitingPhase 2
Gene Signatures to Guide HR+MBC Therapy in a Diverse Cohort
Invasive Mammary Carcinoma, Metastatic Breast Cancer
Not yet recruitingObservational study
Comparison of Reliability, Time Cost, and Participant Comfort of Lymphedema Assessments in Upper Extremity
Lymphedema, Upper Extremity Lymphedema
RecruitingPhase 3
A Study of Camrelizumab Plus Chemotherapy in Combination With or Without Famitinib as Neoadjuvant Therapy in Participants With Triple Negative Breast Cancer (BCTOP-T-N01)
TNBC - Triple-Negative Breast Cancer
RecruitingPhase 3
Testing Whether Hormone Therapy With Ribociclib is as Effective as Chemotherapy Followed by Hormone Therapy With Ribociclib for the Treatment of High Anatomic Stage Breast Cancer With Low Recurrence Risk, The RxFINE-Low Trial
Anatomic Stage II Breast Cancer AJCC v8, Anatomic Stage IIIA Breast Cancer AJCC v8
Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part. This study is not recruiting at the moment.
Soo Chin Lee, MBBS, MRCP principal investigator
National University Hospital, Singapore
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Breast Tumor, run by National University Hospital, Singapore at 1 site in Singapore.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 1 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: status not confirmed, as of the sponsor's last update on 22 Jan 2014. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in Singapore. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
Results are not available in the source record.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
Where can I read the original study information?
On the ClinicalTrials.gov record for NCT01247480, which also lists 2 linked publications.
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 22 Jan 2014.