PolyomX aims
to collect comprehensive molecular and clinical data from patients
undergoing cancer treatment. Currently 6 cancers are being studied
including: breast, lung, lymphoma, gastrointestinal and certain leukemia.
After a patient has been diagnosed and appropriate consent has been given, a
detailed patient history is collected and electronically archived with
the PolyomX database. Later, tumor biopsy samples are collected and snap
frozen within 20 minutes of surgery. Patients are also
asked to contribute blood and urine samples for later analysis. Tumor
samples are subsequently analyzed via DNA microarray (genomic) and 2D gel
(proteomic) analysis. Blood samples are used to identify single nucleotide
polymorphisms (SNPs), while urine samples are used to look for unusual
concentrations of metabolites. These data are also entered into the PolyomX
database and sorted in a variety of ways. On average, comprehensive
polyomic data from 15 tumor samples is collected and entered into the
PolyomX database every week. This data is subsequently “enriched” with
knowledge or facts acquired from dozens of bioinformatics databases located
around the world. The enriched data is then analyzed using advanced pattern
recognition techniques and sophisticated data mining methods to look for
molecular patterns or epidemiological trends that might identify the cause,
consequences and treatment options of a given cancer. In this way, a
detailed picture of several common cancers and their many causes and
consequences will be obtained. The hope is that this PolyomX database and
the associated software will help drug companies discover new drug targets
or treatments. It is also expected that the PolyomX software will
ultimately assist doctors and patients in treating and coping with cancer in
the not-too-distant future.
Genomics is the comprehensive, high-throughput study of the genome – the complete complement of all genes in a cell, tissue or organism.
Proteomics is the comprehensive, high-throughput study of the proteome – the complete complement of all the proteins in a cell, tissue or organism
Metabonomics is the comprehensive, high-throughput study of the metabonome – the complete complement of all the small molecule metabolites used or produced by a cell, tissue or organism.
Bioinformatics is a branch of information science that is dedicated to the storage, management and analysis of genomic, proteomic and metabonomic data.
Polyomics is the combination of genomics, proteomics, metabonomics and bioinformatics. It is the comprehensive, system-wide study of all the components and interactions of a cell, tissue or organism.
PolyomX is looking for contributors, collaborators and partners of all kinds.
1) If you are a cancer patient and you are interested in being involved
in this study, please let your GP or oncologist know about your interest and
tell them about this web site.
2) If you are a prospective student, post-doctoral fellow or research associate and are interested in pursuing a career in
- Genomics, proteomics or metabonomics, please contact Dr. Sambasivarao Damaraju
- Informatics, please contact Dr. Russ Greiner
- Microarray, please contact Dr. Kathryn Graham
3) If you are a scientist or a not-for-profit research institute and you are interested in contributing samples or in collaborating, please contact Kathryn Calder.
4) If you are interested in supporting this research through a personal financial contribution, or if you are an organization and you would like to support this work or to highlight it in brochures or presentations, or if you are a company and you would like to get involved in PolyomX through an industrial sponsorship, we welcome your inquires. Please contact Dr. Carol Cass.
5) Join the PolyomX mailing list. This list server will inform you of the latest developments at PolyomX and keep you informed about any breakthroughs in patient care and treatment.
How are patient
records handled? – Patient confidentiality is our highest priority. PolyomX
has made every effort to ensure the patient records and patient samples are
fully anonymized using
protocols approved by the CCI and University of
Alberta Ethics review boards. Blood, urine and tumor samples are numbered
and only information about the date of collection, tumor type, gender and
age of the patient are retained. A master list linking patient histories to
each samples is kept in a separate, secure site. Several levels of data encryption and data
security are attached to the electronic PolyomX database so that only those
with appropriate clearance will be able to access a limited subset of data.
The PolyomX database and its security software has also been the subject of
an independent computer security audit.
9. How do patients become involved in the PolyomX program?
When a patient is booked
for surgery to have cancerous tissue removed, the surgeon will ask if he or
she would allow a sample of tissue to be entered into the PolyomX tumor
bank.
Patients will be given an informed consent form which describes
the purpose of the project, what patients can expect to happen if they
participate, any potential risks and benefits of taking part, and who to
contact with questions or concerns. It is stressed that taking part in PolyomX is voluntary, and that their decision will not impact their care in
any way. If a patient agrees to take part and signs the consent form,
arrangements are made to retrieve and store their samples. Sometimes tissue
is removed for testing before it is known that a patient has cancer. When
this happens, many hospitals keep the extra tissue aside. In cases like
this, tissue will not be entered into the PolyomX database until patients
have given informed consent. If a patient decides not to give consent, his
or her sample will be discarded. (Two extra tubes of blood (about 15 mls)
are drawn with routine blood work and stored in the lab. During surgery, once
the tumor is removed and the pathologist has taken the necessary samples for
tests, an extra portion will be frozen in liquid nitrogen and transferred to
the Cross Cancer Institute.)
10. Who decides what research is done on the tissue samples?
PolyomX has ethical and administrative approval to establish and maintain a bank of tissue, blood, and urine samples. In the future, when researchers wish to use these samples, they must first receive approval from their institution's ethics committee. This is a group of people from different but relevant professional backgrounds who review a research protocol and ensure that it does not violate the rights and safety of study subjects. In addition, the PolyomX director and core members will review each protocol to ensure the research is consistent with the program's mission and standards.
11. What if a patient changes his or her mind?
No problem. Participation
in PolyomX is entirely voluntary. If a patient decides to withdraw, he or
she just calls Kathryn Calder, the Clinical Research Nurse for PolyomX, and
informs her of this decision. The patient's sample will be discarded. Every
year, a newsletter will be sent to patients, updating them on PolyomX's
current research. If patients feel uncomfortable with any of the protocols
and chose to withdraw, they may contact the research nurse and their samples
will be discarded. No record of these samples will be kept. Patient can be
assured of complete anonymity.
12. What if a patient only wants to participate in part of the project?
No problem. the PolyomX bank includes tumor tissue, blood and urine. Patients may contribute any or all of these. In the consent, patients can indicate whether they would like their samples to be used for cancer research only, or if they consent for researchers studying other health problems (like diabetes or asthma) to access their samples.