Friday, 25 March 2011

Interpreting the genetic test results

There appear to be two levels of information on the different variants of HSP. There's a listing where the genetic loci (i.e. the place on the gene where the HSP occurs) are labelled SPG1 for the first one discovered, SPG2 for the second one discovered, and so on. It is easy to find out that SPG4 accounts for 40%-45% of HSP cases. These different types appear to be well documented, including the effects of each. See, for example It may be worth noting that the name "SPG" refers to SPastic Gait and not to Vyvyans hamster from the young ones.

On the other hand, the results of my genetic test were in a very different form, as noted in my Intron 12 post, and it would appear to be tricky to find a cross reference between the two. There are links that follow links that follow links all over the place, so I am still unsure. So, the first step is to try to understand what the coding of my test result means.

This would appear to be no easy task either! The human genome variation society was a good find.

The first part of the test result (c.) indicates that a coding DNA reference sequence was used. Other letters are used for genomic, RNA etc. sequences.

The next part of the result (1493+2) indicates where on the gene we are talking about. In this case I am looking at the 2nd nucleotide of an intron located between nucelotides 1493 and 1494. (nucleotide = DNA building block, intron = sequence of DNA building blocks). If there is no '+' or '-' part, then it just means the building block on the 'main road' of the gene rather than one of the intron 'side streets'.

The last part of the result (T>A) is what has happened. In my case a T has been changed to an A. (The four building blocks are A,C,G and T). Instead of '>' there could be 'del' for deletion of a block, 'dup' for duplication of a block, or 'ins' for insertion of a block.

For my test result, this was expressed as [=]+[1493+2T>A]. The square brackets are used to denote that the test has been done on both of my chromosones, and the [=] part shows that the sequence is normal in one chromosone.

Please read more here: and here

The final part of my investigation was to look at the SPAST gene itself. It would appear that the SPAST gene used to be called SPG4, and that would have answered the question much quicker, but not quite so interestingly. Details of this are here: This tells me that the SPAST gene is on chromosone 2 between positions 24 and 21. You can find out where some of the other SPG genetic locations are.

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