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Using NGS and DNA from saliva to find needles in haystacks

Posted by Shauna White on Tue, Jan 14, 2014 @ 10:01 AM

DNA saliva OrageneWe always enjoy hearing about how our customers are using our products for innovative projects. Recently, we learned about a new project in Germany called GeneTalk, which uses Oragene to collect DNA from saliva. GeneTalk is what many physicians and scientists working on human next generation sequencing (NGS) data sets have been waiting for. We know that NGS is an effective method for identifying rare disease causing variants associated with genetic disorders and as a valuable tool for diagnosing and treating many other diseases. The challenge in analyzing the sequence variants of a patient is to discriminate between all the variants without medical relevance and the mutations that actually have an impact on the disease. Many believe that a large database of exomes from healthy controls may help to create this benchmark and thus speed up the identification of the mutations causing genetic disorders. This is where GeneTalk comes in.

GeneTalk is building a database of genetic sequence variants, which will be freely accessible for the scientific community. Healthy participants are encouraged to join in this study, called the Personal Exomes Project (PEP), by contacting GeneTalk. These healthy controls will help to establish a database of genetic sequence variants that is similar to the other large population studies such as the 1000 genomes project or the 6500 exomes project. The scientists at GeneTalk will decipher how often a certain genotype is observed in all participants and will release an updated collapsed genotype frequency vector whenever there are ten new participants in the project. This genotype frequency vector of healthy individuals will be published for the scientific community to access and leverage in their own research. In addition, PEP participants can analyze their own exome data on the platform and provide their expertise, experience and questions on potentially harmful variants to the community at GeneTalk.

For this study, the scientists at GeneTalk chose to use Oragene for the collection of human genetic material (DNA). For non-invasive DNA collection, Oragene offered the ideal saliva collection kit that is easy for all participants to use, whether they are young or old. The ability to store the collected sample at room temperature and the high quality of the collected DNA convinced the team at GeneTalk to use Oragene for the PEP project as well as for other ongoing exome sequencing projects. GeneTalk’s sequencing service providers were able to successfully extract sufficient amounts of DNA for NGS, even after the samples were exposed to long shipping times and different storage conditions. By the end of 2014, GeneTalk hopes to have sequenced 120 participants for the PEP. They know that increasing the number of participants in the PEP will result in a higher quality publicly available knowledge base.

Encrypted (pseudonymized) personal genetic data (results of sequencing) collected within this study and the published genotype vector are digitally stored separately from each other, thus making it impossible to decipher ones genetic information based on the genotype vector. An individual’s data collected within the study will not be disclosed to third parties and is only accessible by the principal investigator and the participant of the study. The DNA will be stored for the duration of the study. The results of the study will be used in anonymized form for publications in scientific journals.

Participation in the study is free of charge. Those interested should contact alexej.knaus@gene-talk.de or visit the GeneTalk web site at http://www.gene-talk.de/pep

This is an exciting project which we think will benefit many in the scientific community as they strive to understand the wealth of data coming from NGS. We look forward to watching this project succeed and grow for the benefit of all.

Would you use a database of data like that offered by GeneTalk? Leave a comment and let us know.

Tags: Oragene, DNA saliva, sequencing, next generation sequencing, NGS

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This blog is intended to provide information to educate readers about molecular testing and genetic sample collection and DNA Genotek products.  Some of the information on this blog represents emerging scientific research or data developed for research purposes only. More information here.

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Welcome to The Genetic Link, a blog providing new insights into DNA and RNA sample collection by DNA Genotek. DNA Genotek is a subsidiary of OraSure Technologies, Inc.

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