"Cracking the Code" -- father unravels medical mystery

[Allyson]

any one see the ABC aus story last night on gene sequencing to discover a new unknown genetic disease

a father and google worked out the diagnosis - good story - catch up on view

ABC 1 Australian story 8 pm 21/10 /13

A

 

[Sushi]

Note--Here is the link: http://www.abc.net.au/austory/

Choose: Cracking the Code to watch the program.

Sushi

 

[SickOfSickness]

Thanks, that is a good story.

Transcript: http://www.abc.net.au/austory/content/2012/s3873533.htm

 

[Valentijn]

Fascinating stuff ... I hope we can do something with our 23andMe data! I've only got about 5 sets of data from ME patients here so far though.

 

[Aileen]

I hope we can use our 23andMe data too. Right now I am concentrating my limited energy and concentration on learning about genetics and related areas so that I can better understand what it means. Right now I'm learning about linkage maps.

 

[Seven7]

Why haven't we done this again??? with complete genoma

 

[Allyson]

the link for the genetic sequencing in Mission Massimo show is here - thanks SickOfSickness and Shell

Transcript: http://www.abc.net.au/austory/content/2012/s3873533.htm

Yes we could do this - was it 10 grand per person for the sequencing or for all three?


cheers

Ally

 

[Allyson]

Fascinating stuff ... I hope we can do something with our 23andMe data! I've only got about 5 sets of data from ME patients here so far though.

that may be enough Val - he did It with just 3 people's DNA - a matter of finding out how he did the algorithm computation - no doubt it will become more common now they have established it can be done

but you need the full gene sequence

Ally

 

[SickOfSickness]

that may be enough Val - he did It with just 3 people's DNA - a matter of finding out how he did the algorithm computation - no doubt it will become more common now they have established it can be done

but you need the full gene sequence

His case was perfect, because of having the parents healthy DNA.

I know little about genetics but I think we need someone close without the defects.

We have the problem where our close relatives may be healthy now, but could still have the ME/CFS genetic defects (that we have ourselves)?

 

[SickOfSickness]

Yes we could do this - was it 10 grand per person for the sequencing or for all three?

The article made it sound like $10,000 just for the kid, and the price would have been higher in the past. (Now $7K or less.)

"In November 2012, Gene by Gene, Ltd started offering whole genome sequencing at an introductory price of $5,495 (with a minimum requirement of 3 samples per order). Currently the price is $6,995 and the minimum requirement has been removed." From wikipedia.

I liked this. "As of June 2012, there are 69 nearly complete human genomes publicly available."

 

[Valentijn]

His case was perfect, because of having the parents healthy DNA.

I know little about genetics but I think we need someone close without the defects.

We have the problem where our close relatives may be healthy now, but could still have the ME/CFS genetic defects (that we have ourselves)?

Yes, our best bet is probably looking at other patients with the same symptoms. But multiple factors can cause similar symptoms, so it's to have a bigger sample to look at.

Plus the boy in the story had a known disease, and there known suspect genes. It sounds like the key was in finding the new SNP on a gene known to cause that disease.

 

[Waverunner]

23andMe is great and I used it as well but in my eyes it is far from being enough.

23andMe looks at SNPs which make up about 1/3000 of a full genome.

Full exome sequencing (only the protein coding parts of our genome; costs around 500 to 800 dollars) covers about 1% of our genome.

So the ultimate goal should be to use full genome sequencing, which covers 100% of our genome.

I know for a fact, that we just reached the 1000 dollar genome. The new sequencing machines of Illumina are able to do the job for this price. Some more months are needed, till this price will be available to the public. Prices should drop to a few hundred dollars within the next 2-3 years. One problem can be the professional interpretation of a full genome, which can become very costly (around $ 10,000) but this problem will hopefully be solved through automation soon.

This could be a major game changer for the whole CFS community.

 

[SickOfSickness]

Plus the boy in the story had a known disease, and there known suspect genes. It sounds like the key was in finding the new SNP on a gene known to cause that disease.

I could be wrong but how I read it: He had an unknown disease. Then they named the disease after doing the genetic work. They referred to it as <name of kid> disease in the article, but they didn't use it as the real name. After the genetic work they found others with the same condition but I think they named it / discovered it.

 

[Valentijn]

I could be wrong but how I read it: He had an unknown disease. Then they named the disease after doing the genetic work. They referred to it as <name of kid> disease in the article, but they didn't use it as the real name. After the genetic work they found others with the same condition but I think they named it / discovered it.

They immediately knew that it was a leukodystrophy due to the MRI results. The protein causing his problems has been known to be associated with some leukodystrophies for at least 24 years, and the gene has been known to be associated with the protein for at least 10 years.

Hence even though the disease-causing mutations found on the gene were novel, as well as was tying in the gene to the disease directly, it would have been on a relatively short list of genes which could cause his problems.

Compare that to ME/CFS, where there's not even an obvious abnormality with a name, much less a list of genes associated with it. ME/CFS is a much bigger puzzle to figure out, with no clues being provided.

 

[Sea]

Fascinating stuff ... I hope we can do something with our 23andMe data! I've only got about 5 sets of data from ME patients here so far though.

I'm happy to contribute my data...but so far I haven't been able to use for your program and I've just let it slide for now

 

[Sea]

...So the ultimate goal should be to use full genome sequencing, which covers 100% of our genome...

This could be a major game changer for the whole CFS community.

I agree and I am really hoping to do this when it becomes available at a price I can afford

 

[Sea]

I know for a fact, that we just reached the 1000 dollar genome.

Where did you get that info from Waverunner? I remember reading that there was a prize on offer ($7 million iirc) for being the first to deliver a fully sequenced genome for $1000.

 

[Waverunner]

Where did you get that info from Waverunner? I remember reading that there was a prize on offer ($7 million iirc) for being the first to deliver a fully sequenced genome for $1000.

George Church said it in one of his lastest talks and I read a new article about the 1,000 dollar genome and how it already is in place (I can't find it however). I would have to refer you to this article from CNN. The 1,000 dollar genome and its realization are mentioned several times but it's from June.

http://money.cnn.com/2013/06/25/technology/enterprise/low-cost-genome-sequencing/

 

[SickOfSickness]

Where did you get that info from Waverunner? I remember reading that there was a prize on offer ($7 million iirc) for being the first to deliver a fully sequenced genome for $1000.

They withdrew the prize, and Wikipedia says they said (I am paraphrasing) motivating them to develop the $1000 genome would not be advancing technology. I interpret that to mean it was going to happen soon anyway.

They do have the technology, but I think it would be a while to go below $500 or $700 and be available to us.

Even at those prices, some of the PR members could get it done.

 

[Allyson]

g

The article made it sound like $10,000 just for the kid, and the price would have been higher in the past. (Now $7K or less.)

"In November 2012, Gene by Gene, Ltd started offering whole genome sequencing at an introductory price of $5,495 (with a minimum requirement of 3 samples per order). Currently the price is $6,995 and the minimum requirement has been removed." From wikipedia.

I liked this. "As of June 2012, there are 69 nearly complete human genomes publicly available."

gene sequencing is already possible for many forms of EDS

my geneticist - at Melbourne Unversity - said it would be possible for EDS 3 but you would need to test for 300-400 genes an that was too expensive/impractical ATM - I guess they would need to analyse it too.

Ally