Patenting of ESTs

Author: Claire Baldock, Partner, Boult Wade Tennant

The letters EST are just one of an enormous number of acronyms used in biotechnology. This one belongs to the rapidly developing and hugely exciting new field of 'functional genomics' and stands for 'expressed sequence tags'. The term EST is used by scientists to describe DNA molecules and parts of DNA molecules, as well as virtual representations of those molecules.

How are ESTs generated?

In any particular eukaryotic cell only a small portion of the total DNA is transcribed into messenger RNA and then translated into protein (termed expression). Not only will different genes be expressed in different cell types from the same organism but within individual genes there are stretches of non-protein-coding sequence called 'introns'. Projects are underway in laboratories all over the world to sequence all the genes in the genomes of various organisms, including humans. The way this has been approached is to purify the total messenger RNA from a given cell type and convert it back to DNA again in vitro. The DNA so produced is termed cDNA and because it is a copy of the messenger RNA, it represents only those sequences in the total genetic material of the cell which are expressed. The cDNA is fractionated and then the individual fragments cloned to form a library of the expressed sequences in any given cell type. The cDNA clones are then partially sequenced by an automated sequencing procedure and the sequences generated are termed expressed sequence tags or ESTs. The sequences are stored electronically in databases. Some of these can be freely accessed, such as GenBank and dBEST. However, some specialist genomics companies have made businesses out of generating ESTs in sequencing projects and constructing EST databases which their customers pay to access.

What is an EST used for

An EST is, as its name suggests, a 'tag'. Each EST represents a unique characteristic of an individual gene and may be unique to the particular tissue of origin. Because of DNA's ability to detectably hybridise to corresponding molecules in a DNA sample, an EST can be used in tissue typing, chromosome identification or for localisation of the sequence on a particular chromosome. This latter application can, for example, identify a disease as having a genetic origin where this has not been observed before. Another application is an anti - sense reagent or triplex probe which can be used to suppress expression of the corresponding protein, even where the protein and its function is known.

However, perhaps the most significant application of ESTs is as a tag to identify the whole gene of which it forms just a part. These days this is done using the new science of 'bioinformatics'. Because of the vast amount of DNA and amino acid sequence information which is available on databases it is possible to search for other ESTs whose sequences overlap and align them to give the nucleotide sequence of the coding region of the entire gene or a substantial part of it. From there one can search other databases to look for genes with a predetermined amount of sequence homology to the candidate gene (termed homologues), for which a function has already been assigned and/or look for sequence homology with nucleotide or amino acid sequence fragments known to be associated with a particular functional domain of a protein. This way a putative function or functions can be assigned to the gene and corresponding protein in question. Once the function of a gene is known it can be a target for the screening of compounds with the aim of finding one which modifies the function of the gene or corresponding protein and hence has therapeutic potential.

Why patent ESTs?

It has been noted above that the specialist genome sequencing companies are generating income from their sequencing efforts by licensing others to use their EST databases, so one might conclude that patents are not necessary. In reality, however, patents are a very attractive proposition because of the possibility of domination for 20 years over others who wish commercially to exploit the full gene, perhaps as a therapeutic agent, for production of recombinant protein or in compound screening. A patent claim such as:

A nucleic acid sequence comprising a sequence of nucleotides as shown in SEQ ID No X

could be granted which would not, on the normal principles of claim construction, exclude the full length gene.

The possibility of such domination has caused some alarm in academia and industry alike. It has been suggested that EST patents will be detrimental to the free transfer of scientific information and put barriers in the way of further useful developments which may or may not have needed access to the patented ESTs.