Nov. 8, 2012 DNA sequence data is an indispensable source of research information in biology. But not all data are reliable. Almost 10% of all fungal DNA sequences are, for example, incorrectly identified to species level. A international team of researchers, with it's core at the University of Gothenburg, Sweden, has therefore prepared a guide to assist the scientific community in the quality control process.
A new scientific study sees the researchers putting together a number of guidelines to help other researchers to ensure a high level of quality among their newly generated DNA sequences.
DNA sequences make it possible to study biological samples and environments at a level of detail that traditional tools, such as microscopes, cannot provide. It is, for example, possible to investigate what species are present in seemingly barren substrates such as soil and seawater. Such studies often reveal an astonishing and hitherto unimagined diversity, and biology has made major advances as the use of DNA-based methods has become more widespread.
But as with many other sources of information, DNA sequences vary in quality and reliability. Several studies have found considerable quality problems in existing DNA sequence databases.
To verify ones DNA Sequence dataset for basic quality and authenticity has thus become an important part of biological research.
"Many researchers perceive quality control as difficult," says Henrik Nilsson at the University of Gothenburg. "There are, quite simply, no guidelines that you can hand out to new or established researchers so that everyone is using the same approach. Which is why there are major differences in how, and to what extent, quality control is carried out in the research community."
Henrik Nilsson is the lead author of a new scientific article on DNA sequence quality which has been published in the open-access journal MycoKeys.
One complication is that the software that is available to carry out parts of the quality control is cumbersome and often requires considerable computer capacity. The research group feels that it is not appropriate to require all biologists to have access to and be able to use such complex computer systems.
This is why they have written an article describing how quality control can be carried out manually without any tools beyond an Internet browser.
The article features a number of principles and observations on DNA sequences at different quality stages. Although the guidelines focus on fungi, where DNA sequences have had a particularly significant impact as a research instrument, they are general and can be used for most genes and groups of organisms.
The guidelines relate to traditional DNA sequencing as it is used in systematics, taxonomy and ecology.
The researchers hope that it will help readers to improve their DNA sequences and so halt the trend of increasing noise in the public DNA sequence databases.
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- Henrik Nilsson, Leho Tedersoo, Kessy Abarenkov, Martin Ryberg, Erik Kristiansson, Martin Hartmann, Conrad Schoch, Johan Nylander, Johannes Bergsten, Teresita Porter, Ari Jumpponen, Parag Vaishampayan, Otso Ovaskainen, Nils Hallenberg, Johan Bengtsson, Martin Eriksson, Karl-Henrik Larsson, Ellen Larsson, Urmas Koeljalg. Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys, 2012; 4 (0): 37 DOI: 10.3897/mycokeys.4.3606
Note: If no author is given, the source is cited instead.