At DNA Genotek, we recently learned the details of study being conducted by Generation Scotland called The Scottish Family Health Study. We wanted to share some of this information with you here on The Genetic Link.
Study overview
Generation Scotland is creating an ethically sound, family and population-based resource to identify the genetic basis of common complex diseases. The Generation Scotland Scottish Family Health Study is a large-scale, long-term project, which aims to find out more about common illnesses, such as heart disease and stroke. It is known that heredity plays a role in these diseases. By collecting medical and genetic information from families, and by following their health over the coming years, Generation Scotland hopes to find out which lifestyle and inherited factors are connected with higher or lower risk of these illnesses.
Main challenges
The Generation Scotland Scottish Family Health Study aims to collect phenotype information and blood for biochemical analysis and DNA isolation from 25,000 people living in Scotland. As the name suggests, the Scottish Family Health Study is based on families, so they need at least one sibling and preferably other family members (aged 18 or over) as well. The inclusion of as many family members as possible, especially from large families, will increase the power of the study. However, for a variety of reasons, not all participants can make a clinic appointment. Collecting DNA samples from relatives who live in geographically dispersed locations may not be possible within a clinic setting. Others may be inconvenienced by a visit to the clinic. To overcome this barrier to compliance and to maximize the number of study participants, Oragene•DNA kits are mailed to such participants, with instructions for self-collection.
To read the full case study on this study and how Oragene•DNA helped overcome their recruitment challenge, please click here.
I hope you enjoyed learning more about this study. Be sure to subscribe to The Genetic Link so you don't miss any of our articles.
Beckman Coulter Genomics has developed a new version of their DNAdvance System specifically for use with DNA Genotek’s Oragene•DNA samples.
DNAdvance SP, from Beckman Coulter Genomics, is an extraction kit for the isolation and purification of DNA from saliva samples collected with Oragene•DNA Self Collection Kits. The high throughput genomic DNA (gDNA) isolation reagent system enables the purification of high quality DNA from saliva samples, making it ideal for genotyping applications (SNP, fragment analysis), sequencing and qPCR. The system provides researchers and laboratories with an optimized and robust solution for DNA extraction and purification from saliva collected with Oragene•DNA kits.
Bassam El-Fahmawi, product manager, strategic marketing with Beckman Coulter Genomics stated: “We chose to develop DNAdvance SP for Oragene•DNA samples because more and more of our customers are using this proven, non-invasive collection method. Customers will see the benefits of our collaboration in the consistent, high quality results delivered by the system.”
Cindy Maccullough, vice president marketing at DNA Genotek commented: “The development of the DNAdvance SP System is a clear sign of the growing interest in non-invasive DNA sample collection in the scientific community. There is an increasing demand for automated extractions from our customer base, and the DNAdvance SP System provides a streamlined extraction process that delivers predictable, quality yields for Oragene•DNA.”
The DNAdvance SP product is available from Beckman Coulter Genomics. For more information, you can contact Beckman Coulter here.
A few weeks ago, I posted an article about best practices for long term storage of unpurified Oragene•DNA samples on The Genetic Link. The response to the article was positive so I'm following up with today's story about long term storage of DNA purified from Oragene•DNA samples.
The preservation and storage of DNA is an important consideration for molecular epidemiology and population studies. As the makers of the Oragene•DNA family of products, we have prepared these recommendations for the long-term storage of DNA purified from saliva samples collected with Oragene•DNA to help our customers achieve optimal results.
Preventing DNA Degradation
There are three major causes of DNA degradation in a purified sample (ref. 1). Samples may be accidentally contaminated by bacteria, but storage at 4°C or lower will minimize bacterial metabolism and the release of nucleases. DNases may be inadvertently introduced from the skin, but this can be minimized by wearing gloves when handling samples. Repeated cycles of freezing and thawing may also contribute to DNA degradation. This may be minimized by splitting the purified DNA into multiple aliquots and thawing one at a time.
There are two major causes of degradation of purified DNA:
- Acid hydrolysis - due to storage in a solution with no buffering capacity, explained in "Comparison of TE and water" section
- Nuclease activity - DNases may come from the skin of the person handling the sample, contaminated labware or bacterial contamination of the purified sample. Use of gloves can minimize contamination from the person and use of nuclease-free labware and working in a clean environment can prevent both nuclease and bacterial contamination. Additionally, inclusion of a metal ion-chelating agent, such as EDTA, in the storage buffer can effectively inhibit the activity of any DNases present in the sample.
Comparison of TE and water
Kasper and Lenz (ref. 2) performed an 8-year study of DNA stored in water or Buffer AE (10 mM TrisHCl; 0.5 mM EDTA, pH 9.0). DNA stored in Buffer AE at -20°C or 2-8°C showed no degradation by gel electrophoresis and amplified well in a PCR assay. DNA in water remained intact when stored at -20°C but samples were degraded when stored at 2-8°C and performed poorly in a PCR assay. Pure water lacks buffering capacity and an acidic pH may lead to DNA hydrolysis.
Biobank recommendations
An EU workshop on Biobanks (ref. 3) recommends freezing DNA samples to prevent bacterial contamination and to minimize evaporation of the sample. Tris-EDTA (TE) buffer contains sufficient buffering capacity to prevent acid hydrolysis of DNA. Similarly, the UK Biobank (ref. 4) recommends the storage of DNA in a nuclease-inhibiting environment at a temperature of -20°C, since no significant increase in stability is observed at temperatures below -20°C.
References
-
O'Brien, D. (2002). High-throughput DNA purification. Modern Drug Discovery. 5(3), 25-26.
-
Kasper, Y. et Lenz, C. (2004). Stable 8-year storage of DNA purified with the QIAamp DNA Blood Mini Kit. QIAGEN News. 2004 e10.
-
Biobanks for health: Optimising the use of European biobanks and health registries for research relevant to public health and combating disease. Report and recommendations from an EU workshop held at Voksenåsen Hotel, Oslo. January 28-31, 2003.
-
Sample handling and storage: Subgroup protocol and recommendations. Version 1.0. UK Biobank. July 7, 2004
We hope these best practices will help you optimize the long term storage of all your purified Oragene•DNA samples. If you like this article, be sure to let us know by leaving a comment.
Today, DNA Genotek announced our involvement in a significant pilot project with the UK's largest bone marrow registry, the Anthony Nolan Trust. The details of this exciting project follow:
DNA Genotek, a leading provider of products for biological sample collection, stabilization and preparation, today announced that The Anthony Nolan Trust, the UK's largest bone marrow donor registry, has selected Oragene•DNA for a pilot project aimed at increasing donor recruitment. Bone marrow donor registries, also known as HLA registries, use HLA DNA testing to match leukemia patients with prospective donors. The pilot project will determine if donor recruitment can be increased significantly with the use of non-invasive, saliva-based DNA collection compared to blood collection.
The Anthony Nolan Trust has traditionally required all registry participants to have a blood sample collected either at their doctor's office or by phlebotomists at recruitment clinics. Under this pilot project, the potential donor provides a saliva sample without any assistance (for example, at home) and mails the sample back through the regular postal system, thereby facilitating and dramatically reducing the cost of the entire process. DNA samples collected with Oragene•DNA are easier, safer, and faster to collect than other methods and remain stable at ambient temperature for transport and storage prior to being analyzed at the lab.
There are currently over 400,000 people included in The Anthony Nolan Trust's registry, but many more participants are needed. 70% of patients needing a transplant cannot find a compatible match from within their families and rely on registries to find an unrelated donor for life-saving procedures. Through using Oragene•DNA, The Anthony Nolan Trust expects an increase in donor recruitment and therefore the likelihood of matches between those patients needing bone marrow transplants and potential donors held in their database.
Ailsa Ogilvie, director of operations at The Anthony Nolan Trust stated: "We have historically recruited new people to our register using blood samples, but our early laboratory results confirm that Oragene•DNA provides the high quality DNA that we need. We are optimistic that this pilot project will simplify the recruitment process and ultimately increase the number of people willing to join our register. Following the successful completion of this pilot phase, we hope to switch completely to using saliva samples to recruit new donors to our register via Oragene•DNA from late 2010."
"By streamlining the sample collection and transportation procedures, Oragene•DNA enables The Anthony Nolan Trust to focus on its primary goal of increasing donor recruitment", said Ian Curry, president and CEO, DNA Genotek, Inc. "Oragene•DNA provides a reliable, cost-effective, and scalable method that is ideal for bone marrow donor registries worldwide. Our product is easy to use, safe to transport through the mail and remains stable at ambient temperature for long periods of time. What we learn from this pilot project will help chart the future for The Anthony Nolan Trust and we are certainly proud to be part of this effort."
Note: The pilot project referenced in this press release is currently available in limited areas in the United Kingdom. It is not expected to be available nationally until the summer of 2010.
Learn more at the European Immunogenetics and Histocompatibility Conference (EFI) in Florence, Italy May 17th when Alasdair J. McWhinnie of the Anthony Nolan Trust will present a session titled: "Saliva specimens collected with Oragene are a reliable alternative to blood and buccal swabs for large scale DNA extraction and HLA typing of recruits for hematopoietic stem cell donor registries." Register here.
The Genetic Link welcomes guest blog authors. Our first guest submission is from Rachel Dvoskin, Ph.D., with the University of Florida. We thank Rachel for her submission and welcome her as a guest author. I hope you enjoy this article.
At the department of Anthropology and Genetics Institute at the University of Florida, we study genetic variation in modern human populations to answer diverse questions ranging from the route early humans took when they first migrated out of Africa to the underlying causes of racial differences in susceptibility to complex diseases. To explore these varied aspects of human evolutionary history, we spend a lot of time figuring out how to collect DNA from a large number of volunteers. With today's genetic technology, all that's necessary is to obtain a small blood or saliva sample from each of our participants -- a task relatively easy to do in concept but quite a bit more challenging in practice.
When doing this kind of research -- whether at home or abroad -- we come up against a bunch of potential hurdles. Language and cultural barriers can make it difficult to explain what we are doing and what we are hoping to gain from our participants. As a blond, female, American anthropologist who could hardly say hello in Arabic, Dr. Connie Mulligan never expected collecting DNA samples to be as easy as it was in the remote corners of the Middle Eastern country of Yemen. The Oragene•DNA saliva collection kits are non-invasive, simple to use, and even include illustrated instructions right on the package, making their use completely self-explanatory. We had no problem collecting saliva samples from hundreds of Yemeni participants, including many women garbed in the full abaya.
Furthermore, the lack of need for freezing or refrigeration allowed us to travel around the country without worrying about storage conditions. The disks are small and self-contained, and we did not have to carry any separate buffers or processing equipment. The saliva collectors made it possible to obtain large volumes of high-quality DNA. This DNA is used to answer questions about the movement of early humans out of Arabia. We will soon be able to thank our Yemeni study participants by telling them something new about their country's role in the peopling of the world.
We are now gearing up to do a study here in our own backyard in Florida. In collaboration with cultural anthropologists, we are studying how genetic factors and the social environment interact to influence a person's susceptibility to hypertension. Because we are interested in racial disparities in health in the U.S., we chose to conduct our community-based study in Tallahassee, a city with a long history of racial tension and civil rights activism. Given the potential for misuse of genetic information and the rare but horrific cases of unethical medical experimentation on oppressed minorities, it is understandable that people would be fearful or reluctant to participate in a study of this kind. We expect, however, that the non-threatening nature of the Oragene•DNA saliva collection kits will put people at ease and increase participation.
We value highly this simple, non-invasive technique because unlike many studies in which researchers opportunistically collect samples from people who are already being treated in a hospital or clinic, we are instead approaching regular people in their homes -- trying to get a representative sample of all types of people within a community. We think that the more benign and user-friendly the collection techniques, the more useful they will be for our research and for future work with minority groups and previously unsampled populations. This includes people in regions where lab or storage facilities are scarce as well as populations that have been overlooked or underrepresented in medical and health research.
Did you like this guest authored article? Leave a comment and let us know.
This morning, Clinical Reference Laboratory (CRL) announced that it has completed validation testing of DNA Genotek's Oragene•DNA saliva collection kits and will adopt Oragene•DNA for use with its molecular diagnostic services.
CRL is a CLIA-certified molecular diagnostics services provider based in Lenexa, Kansas offering a wide assortment of molecular diagnostic services including gene expression profiling, microarrays, CNV/SNP typing, pathogen detection, infectious disease testing, pharmacogenetic testing, sample banking, assays for personalized medicine and custom diagnostics. CRL also operates a global clinical trials division.
"Working with DNA Genotek and utilizing its products enhances CRL's menu of high quality molecular services through saliva-based DNA tests", said CRL Executive Director of Molecular Diagnostics, Dr. Heather Newkirk. "Offering services integrating the Oragene•DNA product allows us to provide our clients with a state of the art solution for extraction and genotyping DNA from saliva. We are impressed with the quality and quantity of DNA we obtain using Oragene•DNA."
"CRL joins a growing list of genomic service providers and technology vendors that have validated Oragene•DNA with their products and/or service offerings," said Ian Curry, president and CEO, DNA Genotek, Inc. "Adding CRL to our program gives our customers increased access to an approved service provider that can reliably process samples collected with our products. Our customers can benefit from CRL's offerings for saliva-based DNA extraction, analysis and testing."
Everyone at DNA Genotek welcomes CRL to the DNA Genotek Partner Program.
For the second year in a row, DNA Genotek will be collecting DNA samples onsite at the National Walk for Epilepsy on March 27th, 2010 in Washington, DC. Our participation in this event supports the efforts of the Columbia University Family Studies in Epilepsy Program and their study which is designed to identify genes that play a role in causing epilepsy.
The National Walk for Epilepsy is the largest of its kind nationally that is dedicated to increasing awareness of epilepsy and raising funds to support epilepsy programs, education, advocacy and research. The venue attracts more than 8,000 participants who are personally invested in helping find a cure for the condition and presents an excellent opportunity for Columbia University to accelerate its research by providing access to significant numbers of candidates who satisfy donor profile requirements.
This scale of onsite DNA collection would not be possible without our Oragene•DNA self collection kit. Oragene•DNA enables easy and non-invasive self-collection of saliva samples from large numbers of people and delivers high quality DNA. The samples remain stable at room temperature for 5 years enabling our customers to collect hundreds or even thousands of samples at an event like this and not have to worry about the storage temperature or degradation in quality of the sample.
This event is part of our DNA Genotek Helping Hands Program which is designed to assist organizations that are innovators in disease research, disease prevention and treatment. Within this program, we apply our technology and expertise to accelerate DNA sample collection or treatment and prevention of disease. The goal of the program is to help our customers' research and advance the fight against disease across the globe.
This year, I will personally be on-site for this collection event and I couldn't be more excited. As the event unfolds, I will update you on the status of the collection, tell you what I experienced and share what I learned.
We're hoping for a record turn out at the ‘Give a Spit' booth and you can help. You can join the hundreds of families that participate in this research program and make a critical contribution to understanding the causes of certain seizure types. Families and scientists, working together, can find the causes of epilepsy and improve treatment.
So if you happen to be in the Washington, DC area on March 27th, drop by the National Walk for Epilepsy and come to the ‘Give a Spit' booth. You can find us on Jefferson Street (between 12th and 14th).
To learn more about the Family Studies in Epilepsy at Columbia University, visit their Web site.
Recent statistics suggest cancer mortality rates are declining due to better prevention, early detection methods and improved treatments, yet so much remains to be done. With cutting-edge research continually pushing the boundaries of science and discovery, it is not surprising that an increasing number of cancer researchers are turning to the newest tool in the DNA collection toolbox - DNA from saliva.
Saliva has traditionally been overlooked as a source of DNA for cancer research but Oragene•DNA has changed that. What makes saliva-based DNA collection with Oragene•DNA so important to cancer research? Saliva provides a non-invasive means of collecting high quality and quantity DNA that is stable at room temperature, which makes samples easy to collect, store and ship. With geographically dispersed subjects, scientists can even mail Oragene•DNA kits to participants, who follow the directions, and return the saliva samples to the laboratory for analysis using standard mail service. Cancer research groups around the world are now focusing on the potential of this common bodily fluid for detecting the genetic link to the disease and studying genes without the need for a blood draw.
Now that researchers trust that DNA from saliva using Oragene is equivalent to DNA from blood, the door is open to populations they would normally not have access to. Collecting blood is very invasive and not a practical procedure for children or individuals that can't give blood for religious or medical reasons or for those who do not have access to a collection center. Compliance rates improve with saliva resulting in the collection of more samples.
Breast cancer researchers at the University of Arkansas for Medical Sciences (UAMS) are hoping to answer some important questions with DNA from saliva. They are building a repository aimed at studying breast cancer risk and treatment. Their goal is to collect 40,000 samples over a five year period. They want to learn why one individual is affected by breast cancer but another is not. Or why two women with the same disease respond differently to the same treatment. What inherited factors contribute to the disease? What environmental factors contribute to breast cancer? How do inherited and environmental factors interact to cause the disease?
The researchers decided to use Oragene•DNA because saliva-based collection offered them a non-invasive, easy-to-use and reliable method to collect the large number of DNA samples they need. The kit stabilizes DNA at room temperature until it can be analyzed, which eliminates storage and logistical issues. In addition, Oragene•DNA provides the high quality, high quantity DNA required for establishing the bio-repository. The reliability and ease-of-use also enabled on site event-based collections bolstering the donor group by thousands in a single day.
In another example, researchers at Inserm (I'Institut national de la santé et de la recherché medicale) in France are conducting a study on thyroid cancer using Oragene•DNA. The primary goal of the project is to better understand the risk factors associated with the development of thyroid cancer. The project will establish a DNA bank to permit future studies of candidate genes linked with thyroid cancer and to study gene-environment interactions. The team evaluated the possibility of collecting blood samples, buccal swabs or Oragene•DNA. After evaluating all options, they decided to use Oragene•DNA as it was the only method that allowed them to overcome their main challenge of maximizing compliance rates for geographically dispersed participants.
So, is saliva-based DNA collection the newest tool in the fight against cancer? Enabled by Oragene•DNA, the answer is a definitive ‘yes'. Cancer research with saliva DNA has definitely come of age.
Do you have thoughts you'd like to share on this topic? Leave a comment and let us know what you think. Don't forget, The Genetic Link has subscription options; you can follow by email or RSS feed.
This morning, BioServe Biotechnologies announced that they have completed validation testing of the Oragene•DNA saliva collection kits and have joined DNA Genotek's Partner Program. Now, BioServe can offer customers a comprehensive testing platform for extraction and genetic analysis for Oragene•DNA samples. BioServe has validated Oragene•DNA kits for use within its DNA extraction and genotyping service, including sample quantification and normalization; whole genome amplification; multiplex-based genotyping, expression analysis and sample archiving.
"Validating Oragene•DNA kits for use with our genomic services is consistent with our goal of providing customers the highest quality and most economical services," said Rama Modali, president, BioServe. "Partnering with DNA Genotek, we can now offer our customers a best-in-class solution for processing Oragene•DNA samples including extraction and genotyping from saliva, which is in keeping with the high standards customers expect from BioServe."
"DNA Genotek's Partner Program is designed to facilitate the development of strong collaborations between the customers who use our technologies and our global partners. BioServe Biotechnologies has fully met all the program criteria and has proven expertise in working with our products," said Ian Curry, president and CEO, DNA Genotek, Inc. "We look forward to further developing this relationship with BioServe and providing our customers with another validated option for processing the DNA samples collected with Oragene•DNA."
Everyone at DNA Genotek welcomes BioServe to the DNA Genotek Partner Program.
Every day, it seems, scientists learn something new about how our genes work. One fascinating area of research involves understanding the role of our genes in the initiation, progression and treatment of diseases; such as cancer. Understanding cancer on a molecular and genetic level makes for good science and good medicine. We understand that all cancers are not created equally. From the moment you are conceived, your genes may increase your susceptibility to developing certain cancers or, later on, your environmental exposures or other factors may cause changes in your genes that cause cancer to develop. Cancer is not one disease, but many, adding to the complexity and breadth of studies.
Research is the best way to fully understand the mechanics of this disease and ultimately develop better strategies to combat it. Scientists and clinicians alike are constantly working to learn more about the role of genetics in cancers so they can improve treatment options and health outcomes for patients. The study of genes and cancer all share a fundamental requirement - they all need DNA.
The collection and analysis of DNA from blood and tissue have long been considered the golden standards in cancer research studies. Obtaining high quality genomic DNA is critical for studies that aim to evaluate the role of genetic factors in cancer. However, cancer research studies often require very large numbers of samples from a dispersed population and non-invasive methods for DNA collection. Saliva samples, which are painless for the donor and relatively easily collected, are quickly becoming the preferred choice.
Oragene•DNA is the product of choice for many cancer researchers who require a safer, simpler mechanism for collecting genetic samples than the traditional method of blood collection. This method of DNA collection is highly desirable in certain patient groups (e.g., children, those fearful of venipuncture, geographically dispersed study populations, or as a back up source of DNA in studies that collect blood).
Oragene•DNA kits are being used today in a wide variety of cancer studies including those investigating candidate genes and inherited risk family studies. Oragene•DNA is well suited for cancer research applications including:
Genetic Research: to identify genetic targets for therapy or diagnostics;
Genetic Screening: to help determine who is at high risk of developing cancer and who would have the better prognosis;
Pharmacogenomics: to determine the influence of genetics on treatment choice and disease prognosis.
One example of the type of cancer research that is benefiting from non-invasive DNA sample collection is breast cancer. One such research study was published in 2009: Christine B. Ambrosone, Gregory L. Ciupak, Elisa V. Bandera, et al., "Conducting Molecular Epidemiological Research in the Age of HIPAA: A Multi-Institutional Case-Control Study of Breast Cancer in African-American and European-American Women," Journal of Oncology, vol. 2009, Article ID 871250, 15 pages, 2009. doi:10.1155/2009/871250.
The authors of this research conducted a case-control study with the goal of recruiting 1200 African American and 1200 European American women with breast cancer and an equal number of controls in order to evaluate numerous risk factors for early/aggressive breast cancer and to evaluate the distribution of these risk factors within and across racial/ethnic groups. They initially collected blood samples which were processed and stored in the laboratory at the Mount Sinai School of Medicine. In 2007, to reduce costs and to facilitate participation, they transitioned to collection of saliva using Oragene•DNA kits for DNA extraction. The authors state: "These collection kits yield large quantities of high quality DNA, comparable to that obtained from whole blood."
If you'd like more details on how the researchers benefitted from non-invasive DNA collection in this breast cancer research study, download the full copy here.
At DNA Genotek, we're committed to creating educational resources for researchers involved in cancer genetics and to facilitate the sharing of best practices for DNA collection. If you have information to share or would like to contribute to this blog, please send us your suggestions and ideas.
We'll be posting more articles on saliva DNA collection methods for cancer research in the coming weeks. Don't forget, The Genetic Link has subscription options; you can follow by email or RSS feed.