I'm always fascinated to learn more about how our customers use our products. What diseases are they studying? What geographic areas are they targeting? What are they hoping to achieve? It's these questions and more that make every day interesting at DNA Genotek. I recently had the privilege to learn more about how one of our customers is using our product and I wanted to share that knowledge with you.
The South African Tuberculosis Vaccine Initiative (SATVI) of the University of Cape Town is a new customer who has tried the Oragene•DNA Self Collection Kits for the first time. SATVI's aim is to develop novel tuberculosis vaccination strategies. Their focus is on the clinical side of tuberculosis vaccine development. They therefore embark on clinical, epidemiological, immunological and genetic research to answer critical questions in TB vaccinology.
A large focus of SATVI's research is aimed at identifying host correlates of protection against TB, following BCG vaccination. These studies include looking at genetic differences between infants who are either protected or not protected against TB, following BCG vaccination. They are also interested in determining if there is a genetic disposition to susceptibility to TB by recruiting parents of both the protected and unprotected infants. They are collecting DNA from both infants and their parents, and will conduct target gene and whole genome screening to delineate polymorphisms that associate with protection. Over the course of the 4 year study, approximately 6000 samples will be collected.
SATVI's project is not without its challenges. Maximizing compliance of potential study participants is a major challenge faced by the SATVI researchers. In order to maximize the number of study participants, the researchers identify potential participants through procedures in place either at clinics or home visits. Subsequently, an appointment is scheduled with the whole family where the DNA samples are collected for isolation.
The study was begun with blood collection for DNA isolation of the participants. However, the researchers encountered misbleeds and study withdrawals from some participants, mostly because of concerns or fear of blood collection methods. A large percentage of the potential study participants are children so the researchers felt a non-invasive method of DNA collection would be very beneficial.
Recently the SATVI researchers decided to use Oragene•DNA for the sample collection because it offered them a non-invasive, easy to use and reliable method to collect samples. In addition, the Oragene•DNA kits were cheaper, less invasive and thus more appropriate for collecting from both children and adults in clinic environments and home settings.
The researchers were able to achieve an outstanding 95% compliance rate with the non-invasive saliva collection method available with the Oragene•DNA kits. Overall, participant drop out has been reduced with the non-invasive collection process. In addition, they are achieving very high quantity of DNA with an average of 200ng/ul of DNA from adult saliva and 90ng/ul from infants. The quality is also very high with an A260/280 of 1.7-1.9. Oragene•DNA has performed reliably on their downstream processes - generating equivalent results to the blood kits used previously.
Overall, the use of Oragene•DNA kits has resulted in cost savings. The Oragene•DNA kits were less expensive than the isolation kits used to isolate DNA from blood. SATVI was also able to eliminate the cost of re-collecting blood for phlebotomies that failed on the first attempt.
"We believe the Oragene•DNA system is the most practical for collecting DNA in this environment. The Oragene•DNA kits are cheaper, less invasive and thus more appropriate in our setting," said Muki S. Shey, PhD Student, South African TB Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine (IIDMM), University of Cape Town. "Donors who have provided blood samples for other studies and who have now used the Oragene•DNA kits say they much prefer the non-invasive method of collection with Oragene. We would definitely recommend the kit to anyone who wants an easy and reliable method of collecting samples for DNA isolation."
SATVI's successful use of Oragene•DNA to study TB opens up a new opportunity for all infectious diseases researchers who would traditionally rely on blood collection methods.
Did this article interest you? Leave a comment and let us know what you think.
Photo credit: (top photo) Muki Shey, second photo (Fabio Julies).
If you've been following our blog or our newsletter, you're probably aware that DNA Genotek has experienced significant growth in our partner program. We've added partners across all categories: genomics service providers, diagnostic service providers and technology vendors.
One of the newest partners to complete this validation process is Precision Biomarker Resources. Precision Biomarker provides automated, high-throughput microarray services to expedite the biologic investigations of pharmaceutical, biotechnology and academic researchers. Their services include: nucleic acid isolation, SNP genotyping, expression profiling, qPCR protocol design and processing, and custom bioinformatic analysis. Precision Biomarker Resources serves as a Genomics Service Provider for investigators working with DNA Genotek’s Oragene•DNA sample collection system.
Precison Biomarker is also the first partner to provide a special offer to Oragene•DNA customers to help them celebrate their successful completion of the partner program requirements. I'm pleased to share this news with you and pass along information about this limited time promotion.
From now until September 30th, 2010, Precision Biomarker Resources will include free DNA isolation from your Oragene•DNA samples as part of any whole genome genotyping project performed by Precision Biomarker Resources and using the Affymetrix SNP Array 5.0 or SNP Array 6.0 microarrays. A minimum of 30 samples must be submitted to qualify. Samples and a purchase order for the accompanying genotyping service must be received by Precision Biomarker Resources before September 30th, 2010.
To schedule your experiment now, please call Precision Biomarker toll free 888-857-0752 or e-mail sales@precisionbiomarker.com. Be sure to include your name, institution and contact information (phone number and e-mail) so that they can contact you if we need any additional information.
What do you think of DNA partners offering special incentives for Oragene•DNA customers? Would you like to see more offers like this? If so, leave a comment and let us know.
Photo credit: Alexandra Simms
We were recently introduced to an organization at the heart of a movement focused on the fight against HIV/AIDS, tuberculosis and malaria. It’s a movement that is designed to end these diseases faster.
The organization is called the Global Business Coalition (GBC) on HIV/AIDS, tuberculosis and malaria and DNA Genotek has joined the GBC in its fight to end these diseases. DNA Genotek chose to join the GBC because there is a natural fit between their mandate and our technologies. GBC brings together businesses across various sectors to help fight global epidemics. Our products, designed to enable safe, easy and reliable collection of DNA and RNA samples, are the building blocks to genetic research and analysis of these diseases. The Oragene family of products is unique in that they facilitate research in low-resource settings where these diseases are most prevalent.
John Tedstrom, GBC’s president and CEO commented on DNA Genotek’s involvement: “DNA Genotek, with its expertise as a leader in enabling genetic research, will be a powerful asset to the Coalition. It is by connecting the technical expertise of companies like DNA Genotek with our partners in government, civil society and the multilateral community that we’ll be able to defeat these diseases faster.”
Ian Curry, president and CEO of DNA Genotek commented: “Understanding the genetic basis of HIV/AIDS, TB and malaria is critical to discovering new prevention and treatment options. DNA Genotek’s Oragene•DNA family of products has facilitated the genetic study of many diseases. It is our hope that our work with the GBC will enable research that may one day lead to the identification of the genes involved in these diseases or genes which cause resistance to treatment so that effective measures can be taken.”
Our involvement in the GBC allows us to continue to pursue our goal of enabling worldwide health improvements. We are all looking forward to working with the GBC.
What do you think of initiatives like this? Leave a comment and tell us your thoughts.
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.
The Genetic Link welcomes guest blog authors. This guest submission is from Megan P. Hitchins, PhD. Medical Epigenetics Laboratory, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia. We thank Dr. Hitchins for her submission and welcome her as a guest author. I hope you enjoy this article.
A host of familial cancer syndromes have been described in which several members of the same family develop cancer at a young age due to an inherited genetic susceptibility. It has been well established that germline mutations in the DNA sequence of genes that are protective against cancer, including tumour suppressor and DNA repair genes, are the culprit in most familial cases of cancer. Because they are inherited, these germline mutations are present in every cell of the body from conception into adulthood, knocking out one of the two copies of the protective gene. They confer a high risk of cancer development at a young age, although the cancer itself arises when the remaining normally-functioning copy of the gene is knocked out in susceptible tissues due to contributing environmental conditions, taking with it the last remnants of protection it once afforded against cancer. However, for a number of individuals with young-onset cancer, as well as entire families, the inherited defect remains unidentified, which complicates genetic counselling and clinical management of family members. Lynch syndrome is the most common of all family cancer syndromes, in which patients develop a range of cancers, the most frequent of which are colorectal and uterine cancers. Lynch syndrome is usually caused by germline mutations within one of the four genes that encode the mismatch repair system, most commonly MLH1 or MSH2. Loss of protection from the mismatch repair system results in the accumulation of mutations during cell division, and ultimately, cancer ensues. However, in about a third of Lynch syndrome patients, standard genetic screening fails to identify any pathogenic sequence change within the mismatch repair genes that might be responsible for their disease.
The focus of the Medical Epigenetics Laboratory at the Lowy Cancer Research Centre in Sydney, Australia, led by Megan Hitchins PhD, is to determine the role of a new type of defect, termed a "constitutional epimutation" in predisposing to young-onset cancer syndromes. The first case of a "constitutional epimutation" was reported for the MLH1 gene in a patient with Lynch syndrome in 2002.1 This represents a new epigenetic mechanism of cancer susceptibility, in which the gene's promoter (the equivalent of its engine) is clogged with the chemical methylation, causing the affected copy to be switched off, even though its DNA code is entirely normal. Thus, "epimutation" refers to the nature of the defect, which occurs over and above the context of DNA sequence, whilst "constitutional" denotes the intrinsic presence of this epigenetic defect in normal tissues. Cancer similarly develops after the active copy of the gene is lost in the vulnerable tissues, giving rise to the same clinical profile as carriers of conventional sequence mutations of MLH1. However, one of the key differences between a constitutional epimutation and a sequence mutation is that the gene methylation can be unstable and sometimes show a "mosaic" pattern, that is, it may be present in a patchwork of some cell or tissue-types, whilst absent in others. The level of methylation in the body may even vary during the course of the carrier's life-time. This facet of epimutations adds to the challenge of identifying those who carry them, since their identifying factor - the presence of methylation - may not necessarily be detectable in DNA extracted from a single source, typically peripheral blood. A further complicating factor is that unlike germline mutations that demonstrate classic Mendelian patterns of inheritance, transmission of epimutations from one generation to the next is unpredictable. This non-Mendelian inheritance is attributable to the fact that methylation is stripped away during the reproductive life-cycle, and so epimutations tend to be reversed between generations and may, or may not, be re-imposed after fertilization in the developing fetus. Indeed, it is likely that the degree of methylation mosaicism witnessed in carriers reflects the stage of embryogenesis during which the methylation was established in them. Therefore, when it comes to screening for epimutations, for instance in the family members of a cancer patient found to carry one, it is prudent to test the DNA extracted from more than one tissue-type. Otherwise, it begs the question of whether a negative test means those relatives are safe from cancer as non-carriers, or whether it is just didn't show up in the tissue tested due to the mosaic nature of methylation. To minimise the possibility of failing to detect an epimutation, we have adopted the approach of testing DNA extracted from different tissue sources, namely blood, hair bulbs, buccal swabs, and thanks to the Oragene kits, saliva. In fact, since saliva is originally derived from the same embryonic cell lineage as the colon, it may even provide a more accurate representation of the epigenetic changes that have occurred in the colon than blood. In our recent article in the International Journal of Cancer,2 we show for the first time that in one case, Patient YT, who developed colon cancer at the age of just 18 years due to a constitutional MLH1 epimutation, that methylation was present in his saliva, as per other normal cells (Figure 1a). Thus his saliva showed a consistent pattern with other sources of tissue, indicating a severe soma-wide epimutation (Figure b). Furthermore, using the saliva RNA extraction kit, we were also able to show that the methylated copy of the gene was completely switched off (Figure 1c). Interestingly, screening of his parents showed that neither of them had any detectable methylation, despite screening multiple tissues including their saliva, and so we could say with confidence that the epimutation had arisen spontaneously in their cancer-affected son, but that they themselves were not at an elevated risk of developing cancer from the same type of defect.
Figure 1. Constitutional MLH1 epimutation in "Patient YT"
A: Schematic overview comparing a constitutional epimutation of MLH1, as found in Patient YT, with the normal gene of a healthy individual. Rectangles denote the two copies of the gene and its mRNA product. Methylation of the promoter is depicted by black lollipops. Gene activity is denoted by a waved arrow. The common c.655A>G SNP within the protein-code portion of the MLH1 gene is shown, which enables the two copies of the gene to be distinguished from one another, allowing the activity of the two alleles to be traced in the mRNA. B: Allelic patterns of MLH1 methylation showed methylation was widespread in normal somatic tissues, including saliva collected using the Oragene kit. The "beads of string" represent individual strands of DNA from the MLH1 promoter with dots showing positions of methylation present (black) or absent (white) at CG sites within the DNA sequence, at which methylation is capable of binding. C: Quantification by pyrosequencing of the two copies of the MLH1 gene in the genomic DNA and mRNA samples derived from saliva collected using the Oragene kits. The yellow-shaded region shows the peaks representing each allele at the SNP site. Two peaks showing equal levels of the ‘A' and ‘G' alleles in his saliva DNA show the patient is heterozygous for the benign c.655A>G SNP, allowing the two copies of to be differentiated. However, in his saliva mRNA, only the ‘G' allele was detected, indicating that the ‘A' allele has been switched off by the promoter methylation further upstream.
Our laboratory now routinely collects saliva using the Oragene kits from patients with colon cancer who we suspect may have been caused by intrinsic epigenetic changes, since we believe methylation may be elevated and hence more easily detected in this source of DNA than in blood. Furthermore, we are finding that our rate of compliance in providing samples for diagnostic or research purposes has increased. Firstly, those who are elderly, sick or have an aversion to needles are more willing to provide a sample of saliva than blood for DNA or RNA extraction. Secondly, in our research endeavouring to unravel the inheritance pattern of constitutional MLH1 epimutations, we rely on the voluntary contribution of specimens from the asymptomatic relatives of cancer patients who carry this defect. Relatives are happier to provide a specimen of saliva at their own convenience and in the comfort of their own home, than in visiting their clinician or pathology laboratory to provide a blood sample. Following contact by phone with the genetic counsellor or research nurse, they simply place their saliva sample in the stamped addressed envelope we provide and return it to the laboratory by post, along with their signed consent form approving the inclusion of their sample in our research study. To this end, the Oragene saliva kits have greatly facilitated our research from a logistical perspective, whilst also providing a new dimension for testing different tissue-types for epigenetic changes that may vary from one tissue source to another.
References.
- 1. Gazzoli, I., Loda, M., Garber, J., Syngal, S. & Kolodner, R.D. A hereditary nonpolyposis colorectal carcinoma case associated with hypermethylation of the MLH1 gene in normal tissue and loss of heterozygosity of the unmethylated allele in the resulting microsatellite instability-high tumor. Cancer Res 62, 3925-8 (2002).
- 2. Goel A, Nguyen T-P, Hon-Chiu E Leung H-CE, Nagasaka T, Rhees J, Hotchkiss E, Arnold M, Banerji P, Koi M, Kwok C-T, Packham D, Lipton L, Boland CR, Ward RL, Hitchins MP. De novo constitutional MLH1 epimutations confer early-onset colorectal cancer in two new sporadic Lynch syndrome cases, with derivation of the epimutation on the paternal allele in one. International Journal of Cancer 2010, in press.