How might one get their genome sequenced, if they can't diy it?

[Fred Kittelmann]

I have neither facilities nor sufficient laboratory know-how at present.  I had been under the impression that 23 and me, when they were in business, did this, but they only examine 200 loci.  Are there any outfits that will do an entire genome?  If not, anyone here willing to work as a hired gun?

Have modern methods rendered this relatively easy, or is it still a monumental undertaking, i.e. no way 23 and me could do it for the $99 they charge?  I actually don't need the entire genome.  I'm only interested in a handful of loci, just not the ones 23 and me examined.

Fred

[Katherine Gordon]

I would be interested in assisting you to find someone who could do your handful of gene sequences.....I know a guy who owns/ runs a somatic gene sequencing lab in California, called the Wiessman Institute, he is a big deal, I lived next to his mom in Great Falls, Montana. I have been interested in all of this for some time now myself, I can not do the work myself but Jerry Wiessman certainly could.

Please contact me on facebook Katherine Gordon from Great Falls, Montana.

or at my regular email here which is kthrn...@gmail.com

Kate;)

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[Patrik D'haeseleer]

23andMe covers a whopping *million* loci, not just 200. Are you certain the loci you're interested in aren't covered?

http://blog.23andme.com/23andme-and-you/upgrading-to-the-new-chip-what-to-expect/

Patrik

[Fred Kittelmann]

Thanks guys.  My situation is that I don't know which loci I'm interested in.  This is for my mom who has HER2 breast cancer.  I thought some knowledge of her genome could prove useful.  I'd be curious about the HER2 gene itself and any genes for transcription factors that regulate it.  Maybe also genes for proteins that regulate the regulators.  I don't know how to find out what genes those are however.  Maybe no one knows.  I've tried searching through Pubmed for articles, but haven't found anything.  Does anyone know where I could turn to learn such?

Once I did, then the question would become: Are all those loci covered by 23andMe's ~million?  If so and they resume operations I'd be interested.  But I imagine I'm looking for something idiosyncratic.  She doesn't fit the usual HER2 demographic.  So even if 23andMe knows of a locus, or several, that predispose one to such a cancer, it might easily have nothing to do with her case.  I'd be interested in a more personal approach.  Kate, if you could provide contact info or what have you so I can inquire as to Jerry's services that'd be terrific.

I'm a little bemused by 23andMe's approach.  It seems both too broad and too narrow.  I imagine they chose the loci they did because something was known about the variability at each and what it meant as far as predispositions to what qualities.  That was believable when I thought they did a mere 200 sites, but a million!?  Can there really be that many about which we have such knowledge?  Also, with such extensive analysis, would it be so much more difficult to sequence an entire genome for someone and thereby cover the possibility of idiosyncrasy which I, and presumably most anyone, would want?  Is there even such a thing as a consensus human genome for comparison?  By that of course I mean the whole genome, not just consensus sequences for particular genes.

Comments anyone?  Thank you so much!!!

Fred

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[Mega [Andreas Stuermer]]

I remember there is a project called something like 1000 genomes, which sequences you genome for free, but you therefore give the rights to them.

[Cory Tobin]

> I'm a little bemused by 23andMe's approach. It seems both too broad and too
> narrow. I imagine they chose the loci they did because something was known
> about the variability at each and what it meant as far as predispositions to
> what qualities. That was believable when I thought they did a mere 200
> sites, but a million!? Can there really be that many about which we have
> such knowledge?

You're right. We don't know much about a lot of those loci. We _do_
know that these loci are variable across the entire human population
(see the HapMap Project) but we don't know what most of them do. My
guess* is 23andMe came up with a way to rank all the SNPs on how
likely they are to actually be useful predictors of phenotype/disease
in the future even if we don't know anything about them now, probably
based on their position relative to coding sequences, transcription
factor binding sites, etc. The technology exists to sample that many
loci (see Illumina BeadChip technology) and it doesn't cost any less
to only use a portion of the chip's capacity, so it's better just to
collect the data now and update your database when information about
those loci becomes available.

* Pure speculation on my part. It's what I would do in their shoes.

> Also, with such extensive analysis, would it be so much
> more difficult to sequence an entire genome for someone and thereby cover
> the possibility of idiosyncrasy which I, and presumably most anyone, would
> want?

The technology exists if you have the money. I think it's under 10k
USD these days.

> Is there even such a thing as a consensus human genome for
> comparison? By that of course I mean the whole genome, not just consensus
> sequences for particular genes.

I suppose GRCh37 (NCBI) is the closest thing to a consensus human
genome currently. Or if you prefer to get your data from UCSC it's
called hg19. Although, GRCh37 is slightly more up to date since they
release patches periodically, currently on patch 13.

-cory

[Katie Kearns]

On Wed, Dec 18, 2013 at 6:23 PM, Fred Kittelmann <pigeonholin...@yahoo.com> wrote:

 Also, with such extensive analysis, would it be so much more difficult to sequence an entire genome for someone and thereby cover the possibility of idiosyncrasy which I, and presumably most anyone, would want?  Is there even such a thing as a consensus human genome for comparison?  By that of course I mean the whole genome, not just consensus sequences for particular genes.

Well, they're not sequencing it, just seeing if it matches a pattern. You can fit a good half million (or is it more now?) of tests on one tiny chip. It takes a lot more work to get the actual base-by-base sequence without errors.

According to wikipedia, they're identified 50 million SNPs...! http://en.wikipedia.org/wiki/SNP_array

-Katie

[jlund256]

Fred,

23andMe doesn't give you the info needed to make decisions about cancer treatment.  23andMe genotypes known SNPs, while with cancer most of the mutations are de novo.

What is typically done is either the Foundation Medicine test or exome sequencing.  Foundation Medicine's FoundationOne test sequences 182 genes commonly mutated in cancer.  The test costs ~$6k, and they offer a fast turnaround of 2-3 weeks.

The other option is exome sequencing, where all the protein-encoding regions of the genome are enriched and sequenced.  This is best done for two samples, one tumor and the other normal.  The pair of samples is sequenced so the de novo mutations in all an individual's cells can be told apart from tumor mutations.  The process involves enrichment of exon sequences, next generation sequencing, and then variant analysis.  The market for exome sequencing is complicated right now.  As a research service, the cost is <$1k - $2k per sample.  Providers offering clinical sequencing are new, the cost is higher.  Most clinical exome sequencing currently occurs at research medical centers.  If the doctor is willing to work with you, I would look into nearby medical centers or the providers online.

Cheers,

Jim Lund

[Dakota Hamill]

I just ordered a 23andMe kit yesterday for $100, and it looks like they just updated their site with the FDA issue.  I'll be interested to see how useful the raw data is, or how much 23 and me is allowed to show me on their website.  Aren't there other websites you can put the data into and get feedback from?  I might have a deficiency of a particular aromatase enzyme and it'd be pretty cool to be able to see if it's true or not.

Is there a place to search all the genes/potential disease related SNP's 23 and m3 screen for?

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[Kermit Henson]

Hi,

An easy way to analyse your 23andme data is with this Promethease (http://snpedia.com/index.php/Promethease), you can see a demo in their website. Another way to analyse your genome is though a company that sells similar products under the Research Use Only (RUO) tag, microarrays 700k SNP $200 or exome sequencing (ngs, 80x) for ~1000$. Another way is though Sanger sequencing (800 bp/~10$). Which technology is best depends on the answer you would like to answer.

Also, you have to now about coverage, which is like "how many times you read the analysed sequence", where higher is better but expensive. Used only in ngs techniques,
Depending on the kind of tecnology (microarrays like 23andme) or exome/genome sequencing (next generation sequencing) you'll need to analyse the generated raw data in diferenet ways. Microarrays are easier, but raw data is a list of AGTC none sense sequences, so you need to convert that list into a human redeable SNP list. Once you get that list, you need to compare with a diseases database like OMIM, CinVar, SNPedia...to know what is the cinsequence of that SNP. Also you could use specific diseases databases, like COSMIC. Like with thge technology choice, the correct database depends on what would you like to answer.
If you choose to use ngs techology, you'll enough cpu power or rent amazon sercices.

One way to know about a SNP function is analysing human diseases with basic sequencing technologies. Another way is using GWAS studies, where large populations are sequenced and genotype-phenotype correlated to know which is the probability that a single SNP causes a disease. Here, developed polygenic models give more accuracy.

In my opinion, medical advice should be welcomed if someone has clinical interest.
All mentioned above is a small resume of what can do anyone at home

[Jonathan Cline]

On Tuesday, December 3, 2013 9:42:59 AM UTC-8, Fred Kittelmann wrote:

  Are there any outfits that will do an entire genome? 

 

Hello
You could join the Personal Genome Project (aka PGP).  But the waiting list to be sequenced is quite long (couple years?) at the moment I think.  With the dropping cost of sequencing in general, maybe their queue will start going faster.  A donation is requested.  Attendance at a yearly Harvard genomics conference is encouraged.  Plus, the third-party experiments such as sequence-your-gut and sequence-your-home are interesting too. 

A link to my own genome thru the PGP is here   http://88proof.com/about
(the genome link itself is really super long and that's the simpler one to mention)

By the way according to my genome sequence, I have a motif similar to one causing a potential yet very statistically unlikely disease which at any time might result in "palpitations,  fainting, and sudden death."    So watch out for black cats crossing your path, etc.  If you believe in that sort of thing.


Happy holidays, ho ho--*thunk*

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