41 replies to this topic

[Flex]

Consider that altough Your genes can be sequenced, Your epigenetic status like methylation, acetylation & etc ( which gene is actually activated/deactivated !) cant be sequenced with e.g. 23andMe, because this is too expensive to this date and its only done in studies.

Edited by Flex, 09 January 2015 - 07:16 PM.

[mag1]

I am always on the lookout for new genetic analysis technologies.

 

 

 

Anyone know where a methylation analysis could be done?

 

Or, a protein chip?

 

Copy number?

 

Exome chip?

[CaptainFuture]

I wish I could help more and I would be interested in all parts you mentioned as well but I only know that you can run a small methylation analysis on the 23andMe raw data.

 

https://geneticgenie...ation-analysis/

[mag1]

It is confusing the way in which the methylation analysis is presented on the genetic genie site. The web site seems to imply that a "methylation analysis" will be performed. The actual result of their "methylation analysis" is the genotyping of a few

SNPs involved in methylation. There is a subtle difference between these two interpretations of "methylation analysis".

 

The smart money is really with the exome chips. The research community cannot get enough of them. These chips

are very inexpensive and can call with high quality many of the SNPs that truly matter. I have not been able to find

anyone who will sell to me an exome chip analysis on a direct to consumer basis.

 

Anyone have any suggestions? 

[mmejoanna]

Yes, they don't guarantee it for liability reasons and because funding can be unreliable, but George Church is the most famous geneticist in the world and has no trouble getting funding. Researchers I spoke to at the blood draw told me that there is a queue but that realistically, I can expect my genome within several months.

 

Curious if you got your genome, and if so - did the Personal Genome Project analyze it for you at all? 

[TANKtr0n]

http://www.personalg...harvard/sign-up

Harvard has a project open to volunteers at no/minimal cost or whatever costs you may like to incur to provide more biological material for further study. It's open if you're willing to accept the publicly available privacy caveats.

[Flex]

wow incredible. Thanks for sharing.

For me personally the publication of the personal data bothers me a bit.

On the other hand if they dont send it everywhere, I would agree.

Have to ask them about the concrete consequences eventually,

because if even Your future employer would be able to know that You had e.g. depressions, 

he could assume that You will be it again and would then rather choose someone other.

 

[mmejoanna]

Someone here (Maximum411) participated but did not have their results when they posted in this thread... I'm curious how it went, and if the Personal Genome Project actually helped Maximum411 interpret their data or not. Perhaps they just said "Here's your raw data, thanks!" 

 

 

[mag1]

Something that I have recently discovered is that the exome scan, recently conducted on a family member, actually includes the mitochondrial sequence.
I found this out after running an app and mitochondrial SNPs were reported. I contacted the sequencer about this and they told me that
mitochondrial DNA is "off target" sequence. I'll take "off target" sequence any day. In fact, I have come across an article that notes that 50% of the
sequence generated by an exome scan is "off-target". I have been supplied with this "off target" sequencing.

I asked around about the mitochondrial DNA and was told that in a full genome scan mitochondrial DNA can have coverage up to 10s of thousands of times.
I still do not completely understand the mitochondrial results, though. Even though the mitochondria is covered on average at 40 times, several of the
base pairs do not concord with the results from 23andme. An offspring of the family member whose exome was sequenced also has discordant mitochondrial
results from 23andme.

One problem that appears unsolvable is that some of the mitochondrial reads are exactly the same as those from other parts of the genome. Apparently
mitochondrial genes have migrated to the nuclear genome. How can it be known that a read that perfectly matches 2 different genomic locations ( i.e. autosome and mitochondria) should be assigned to the mitochondria?

[niner]

Something that I have recently discovered is that the exome scan, recently conducted on a family member, actually includes the mitochondrial sequence.
I found this out after running an app and mitochondrial SNPs were reported. I contacted the sequencer about this and they told me that
mitochondrial DNA is "off target" sequence. I'll take "off target" sequence any day. In fact, I have come across an article that notes that 50% of the
sequence generated by an exome scan is "off-target". I have been supplied with this "off target" sequencing.

I asked around about the mitochondrial DNA and was told that in a full genome scan mitochondrial DNA can have coverage up to 10s of thousands of times.
I still do not completely understand the mitochondrial results, though. Even though the mitochondria is covered on average at 40 times, several of the
base pairs do not concord with the results from 23andme. An offspring of the family member whose exome was sequenced also has discordant mitochondrial
results from 23andme.

One problem that appears unsolvable is that some of the mitochondrial reads are exactly the same as those from other parts of the genome. Apparently
mitochondrial genes have migrated to the nuclear genome. How can it be known that a read that perfectly matches 2 different genomic locations ( i.e. autosome and mitochondria) should be assigned to the mitochondria?

 

The majority of the mitochondrial proteome is in fact coded by nuclear DNA, then those proteins are transported into the mitochondria.  The small loop of DNA inside the mitochondrion, known as "mitochondrial DNA"  only codes for a handful of proteins.  I don't know how they prep the dna for the exome scan, so maybe some mitochondrial dna goes along for the ride, but it also might be the case that they are talking about the nuclear-coded mitochondrial genes,

[albedo]

Any comment or recommended on the privacy and security possible issues when using Promethease or Genetic Genie or similar sites dowloading 23andme file?  Just curios about your thoughts about this matter. Thank you.

[mag1]

I have attached the capture from the app. Near the top left, it is indicated that this sequence is from the
mitochondrial chromosome. I have included the blat read out on the bottom left.

What I found interesting was that some of the reads had identical scores from the mitochondria and the autosomal
chromosomes. It is not clear to me why the aligner assigned the read to the mitochondria.

I was very pleased to discover that I had this sequence, though I am still not sure how to reconcile the discordance
between the sequence and the 23andme results.

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