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.

Thursday, 10 March 2011

Lower Limbs - Teaching myself about muscles

OK, Basics. Despite many years of eating various parts of chickens and other animals, I didnt realise that, the 'Leg' is only the bit between the knee and the ankle. It would appear that the bit between the hip and the knee is called the thigh. Of the leg, the bit at the back is the calf and the bit at the front is the shin. (I did know this last part, particuarly in reference to shin-pads).

My first internet port of call happens to be Wikipedia. There's a very in depth discussion of the leg here:, and I have to admit that on first thoughts its much more complicated than I thought. I quite like this click and look view

On second thoughts, its quite clear that for some of the excercises I do at pilates, there's a lot going on, and even when I take a moment to think how clever we can adjust our muscles to be able stand on one leg, then I shouldnt be suprised at the complexity. Therefore, its time to read the detail of the wikipedia page...

Part 1: Basic movements. There are a number of movement terms used in this, and on many other pages:
  • Lateral rotation - rotation away from the centre of the body.
  • Medial rotation - rotation toward the centre of the body.
  • Extension - making the angle of the joint bigger.
  • Flexion - making the angle of the joint smaller.
  • Abduction - movement away from the central plane of the body (i.e. spreading your legs)
  • Adduction - movement toward the central plane of the body (i.e. bringing your legs together in the middle)
There are some 'nice' pictures here which may help picture some of these movements:

Because muscles are only able to do useful 'work' when they contract, they are always grouped in pairs. So, when 'work' is done moving a part of the body one of the paired muscles contracts (with the other muscle relaxed). To reverse the motion the contracting and relaxed muscle swap over. Fortunatley, the various muscles are grouped together and given more accessible names. Apologies if anyone thinks I've over simplified this lot...

  • At the top, the 'Glutes' are your bottom/bum/buttocks/arse... muscles to extend the hip.
  • On the front, the 'Iliopsoas' are the Glutes opposite acting muscles to flex the hip.
  • The muscles at the front of the thigh are called the 'Quadriceps' (or quads) to extend the knee.
  • The opposite muscles at the back are called the 'Hamstrings' to flex the knee.
  • The shin doesnt seem to get much joy in an accessible name. the muscle to flex the foot is the 'Tibialis anterior'
  • The opposite muscles at the back are called the calf muscles to extend the foot. Note here soleus and a second set of triceps...

There are many more muscles which I have not mentioned which have different functions. The conclusion of my part 1 is to look for various leg streches that I can do to try and offset some of the overactivity in my muscles. There are many different web pages with leg stretches on. Here's one page, you may want to find others.

More in part 2 when I look at nerves.