PseudoGeneQuest – Service for identification of different pseudogene types in the human genome

<p>Abstract</p> <p>Background</p> <p>Pseudogenes, nonfunctional copies of genes, evolve fast due the lack of evolutionary pressures and thus appear in several different forms. PseudoGeneQuest is an online tool to search the human genome for a given query sequence and to identify different types of pseudogenes as well as novel genes and gene fragments.</p> <p>Description</p> <p>The service can detect pseudogenes, that have arisen either by retrotransposition or segmental genome duplication, many of which are not listed in the public pseudogene databases. The service has a user-friendly web interface and uses a powerful computer cluster in order to perform parallel searches and provide relatively fast runtimes despite exhaustive database searches and analyses.</p> <p>Conclusion</p> <p>PseudoGeneQuest is a versatile tool for detecting novel pseudogene candidates from the human genome. The service searches human genome sequences for five types of pseudogenes and provides an output that allows easy further analysis of observations. In addition to the result file the system provides visualization of the results linked to Ensembl Genome Browser. PseudoGeneQuest service is freely available.</p

Contribution of Pseudogenes to Sequence Diversity

Pseudogenes are very common in the genomes of a wide range of organisms and, although they were originally considered as genetic junk, now several functions have been attributed to them. One important function of pseudogenes, as discussed in this chapter, is to provide material for genetic diversity. This is most prominent in the case of immunological recognition molecules such as immunoglobulins and B- and T-cell receptors, as well as in the case of antigenic variation in intracellular pathogens. Other examples discussed are olfactory receptors, ribosomal proteins, cytochrome P450s, and pseudokinases

The risk of re-identification versus the need to identify individuals in rare disease research.

There is a growing concern in the ethics literature and among policy makers that de-identification or coding of personal data and biospecimens is not sufficient for protecting research subjects from privacy invasions and possible breaches of confidentiality due to the possibility of unauthorized re-identification. At the same time, there is a need in medical science to be able to identify individual patients. In particular for rare disease research there is a special and well-documented need for research collaboration so that data and biosamples from multiple independent studies can be shared across borders. In this article, we identify the needs and arguments related to de-identification and re-identification of patients and research subjects and suggest how the different needs may be balanced within a framework of using unique encrypted identifiers