SNPedia

Promethease 0.1.126 UI2

2012-01-21T03:33:00.000-08:00

Promethease version 0.1.126 is downloadable. The most recent improvements have been to UI2, which is only available in the $2 paid runs. The improvements make it easier to sort, filter and explore your genome. You can try them out by clicking on this Lilly Mendel UI2 report or just watch them in the video below.

Notable features

Sort by Magnitude, Frequency or # of References

Green/red highlighting of good/bad news

Turn on/off good, bad, not set, SNPs or genosets

Filter out genos based on the Magnitude, # of References or both using AND/OR logic

Type a question mark ? to bring up a help menu

Ball & Spring graph is now in its own window, and can be zoomed with the mouse wheel

A chooser for Medicines, Medical conditions and Topics, with progressive text search

Each geno has a footer showing what categogies it belongs to, and allowing to to select all genos belonging to that category

At the bottom of the page press '2x more' or just type the number of records you want

Editor mode to link directly to the edit pages

That last feature is intended to encourage more edits to SNPedia. We welcome your edits big or small.

The reports may be too large to view on iPads, and there are still some problems with the graph under IE, but more improvements will certainly follow. Your bug reports and feature requests to info@promethease.com can help it to grow in the right direction.

Give it a try! Lilly Mendel UI2

The SNPedia Paper

2011-12-09T09:37:00.000-08:00

SNPedia: a wiki supporting personal genome annotation, interpretation and analysis
Michael Cariaso; Greg Lennon
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr798

Abstract

Full Text

Using Promethease

2011-11-18T23:41:00.000-08:00

Last year 23andMe introduced a pricing model with a one year minimum subscription. I think it's a great service and will continue to pay my monthly fee to continue participating in the online discussions and get their updated analysis, but I'm sure a few people will decide updated genetic information is not in their budget this year. This post will show you how to keep getting new information about your genome for many years to come, with zero further expense.

To do this, you will need to download your raw data while your account is still in good standing. To begin, visit https://www.23andme.com/you/download/

After logging in, you will be presented with security questions such as these

.

After a few moments your download will begin and you will receive a file named similar to genome_John_Smith_Full_201112034567.zip. Remember where you save it, once your subscription runs out you won't be able to get it again!

Now visit http://www.snpedia.com/index.php/Promethease and download the latest version from the bottom of the page.

Run Promethease.

Here you can see the Windows and Mac versions side by side.

Click Next to move to the Genotype Files page.

Click on the Load button and then find your genome_John_Smith_Full_201112034567.zip file from the beginning of this walk-through.

Then click Open to select your file. The filename will appear in the box.

Press Next to validate your file and move to the next screen. Along the way it will show how many genotypes are in your file. The number is probably just a bit below 1 million.

The next screen asks you to choose your Ethnicity. For many of us there is no perfect match, and that's fine. It has only a minor effect on the report that will be produced. This just shows some reference values for comparison to highlight how rare or common your genotypes are. Pick whatever seems closest and don't worry if it is rather distant from your true origins.

There are several more screens to go. You can just click Next on all of them until you get to the last one.

Output Folder -- On this screen you choose where to store your completed analysis. You are specifying both the directory for all of the supporting files as well as the name for the top level report. The default values are based on your usual 'My Documents' folder and the name of your genotype file from the earlier step.

Optional -- This screen allows registered commercial users of Promethease to identify themselves after their initial email to info@promethease.com . But if you're just running Promethease for youself or familiy members and not charging you should just leave it blank and click Next.

Payment -- Click this button to pay $2 and unlock extra features such as running much faster or predicting the genetics of your children based on your partner's genotype file. That also introduces extra screens which are fairly self explanatory, but not further discussed in this blog post.

Promethease Wizard -- The last screen before the system begins your analysis. Just click Next to begin.

Status -- Promethease has begun your analysis and will contact the central server to figure out what SNPedia knows about your genotypes. This will need approximately 4 hours to run.

After approximately 4 hours you will see text similar to the above. It should have launched your web browser and showed you the report which looks similar to this one. In the report click on '...show more...' to drill deep into everything SNPedia knows about your data. Click on hyperlinks to be taken into SNPedia to see the full text, and find links to primary sources. As you learn more about your genome we hope you'll make edits to SNPedia and help teach all of us more. It's a big genome and we can't understand it without your help. We hope what we've learned so far is helpful to you. Rerun your report every few months to watch our growth and improved understanding.

0.1.116 - It's a Family Affair

2011-07-17T12:59:00.000-07:00

Russell: I just ran the newly released Promethease 0.1.116, it's getting better and better. It has me nailed pretty well.

me: I notice your report isn't clear on your ancestry and we now do a better job of that for some reports so in time I'd like to see what I can do to polish up that side of your data. SNPedia has you and your mother publicly, but since you have so many family members privately, take a look at these images from another family which shows where the chromosomes agree between family members. promethease_corpas_family_comparison_newfamily.html

me: Looking at you and your mother genome_Russell_Letkeman_20081023161035_newfamily.html I notice a region of similarity on chromosome 2 with a run of
similarity, and a little red spot on chromosome 11 where you and your mother are quite distinct.

Russell: I'm an identical twin, are they sensitive enough to distinguish us?

me: yes, I think you'll find this article about twins very interesting.

Russell: Wow, if they can distinguish identical twins, that's deep medicine. What about the epigenome? Is any of it sampled?

me: a new sequencer from PacBio exists, it fundamentally sees the epigenome as well as the usual ATCGs

Russell: I read somewhere if the coverage was deep enough you could estimate CNV. Does v3 detect any CNVs?

me: Generally, no. 23andMe does not provide CNV information. we have one CNV which is currently replicable with a SNP gs217 but it's just a test case. We don't yet have any interesting literature except for some horribly obvious birth defects which you don't have. Standard naming is still new.

me: if you want CNVs Complete Genomics will a full genome do for $5k. They have released 57 full genomes and about 7 of those are one large multi-generation family tree. If you can find anything interesting in there then you're ready for $5k per family member for your own.

Russell: You've cover 6k+ snps on my v2 sample. What human mind could learn something that big? And it's just a start. It's going to get weird from here on, my twin became a licensed GP in 2005 and genetics was hardly covered and personal not at all. So the data is coming in faster than the medical profession can keep up with.

me: http://stanford.edu/class/gene210/web/html/projects.html is the first class anywhere to expose pre-meds to their own genomes. I think it defines the '1st wave of doctors' with genuine exposure to the topic. More will follow every year, but every doctor practicing today, will someday describe themself as 'PRE-' in some way. And if your 6k seems like a lot, consider David Ewing Duncan is now over 20k annotated snps thanks to mixing his 23andMe v2 with Complete Genomics.

ESHG2011

2011-05-26T16:44:00.000-07:00

Today was the end of the Galaxy 2011 conference and on Saturday, May 28 the European Society of Human Genetics (ESHG) will begin in Amsterdam. Ramunas of http://cancergenetics.wordpress.com and I would like to invite other netizens for a meetup. Bloggers, wiki editors, and lurkers are invited to

join us

Party like it's 0.1.99

2010-08-08T14:24:00.000-07:00

Promethease 0.1.99 is out and there is a new video tour of it's features. The most important is an interactive x-y scatter plot which you will see at the end.

If you have more questions see Promethease/Features

SNPedia's Top 10 SNPs of the Year

2010-01-04T05:41:00.000-08:00

SNPedia now contains nearly 10,000 SNPs and to welcome 2010 we'd like to highlight at least 10. These SNPs have been selected based on an elusive and ultimately subjective combination of medical importance, statistical believability, and overall general interest. This isn't objective science though, so feel free to comment about why your favorite SNPs should have made the list.

1. rs4244285: The antiplatelet drug clopidogrel (Plavix) is the #2 selling drug in the world. This SNP in the CYP2C19 gene can tell you if it's unlikely to be doing you much good; carriers of 1 or especially 2 A alleles don't benefit much in terms of lowered heart attack incidence based on several studies published over the last year. And actually, this fairly common SNP affects how you metabolize plenty of other drugs as well, including anti-depressants and anti-ulcer drugs.

2. rs4149056: Speaking of bestselling (>100 million prescriptions/year) drugs, one of the adverse effects associated with statin use is the possibility of myopathy (muscle problems including weakness, cramping or pain). Carriers of 1 or 2 C alleles for this SNP in the SLCO1B1 gene taking statins are at ~5 or 17 fold higher risk, respectively, for statin-triggered myopathy. Ouch.

3. rs1799853, rs1057910 & rs8050894: How about one more - actually three more - affecting a widely prescribed drug? When assessed together, these SNPs in the CYP2C9 & VKORC1 genes help predict something that's otherwise both tricky and overly empirical to determine: the optimal dose of the anticoagulant drug warfarin (Coumadin ), used primarily to help prevent thrombosis and embolism in patients with high blood pressure. The FDA now recommends - but doesn't require - testing warfarin patients for these SNPs. Here's a long-standing wish, good for 2010 and most likely beyond: Medicare announces it will reimburse for testing these SNPs, given that over 1 million Medicare beneficiaries take warfarin each year.

4. rs10757278: The region of chromosome 9p21 with this SNP (and it's neighbor, rs1333049) has been shown in 2009 by several large studies to indicate at least somewhat increased (~1.3 or 1.7x) risk for coronary artery disease and it's consequences (like heart attacks). But has it added anything to what a cardiologist would already have known based on traditional risk factors like hypertension and family history? Actually, yes - you can classify a patient's risk better when you add the status of this SNP to all the other factors you've already assessed.

5. rs1537415: Sure, lots of SNPs are of interest to MDs, but here's one for DDS's. Over half of us carry at least one allele of this SNP and are therefore at increased risk for periodontitis - so keep flossing!

6. rs3892097: This SNP encodes the CYP2D6*4 allele, the most common nonfunctional variant for this gene. While it can therefore affect the metabolism of about 25% of all known drugs, it's on our list this year due to increasing evidence for poorer outcome among breast cancer patients treated with tamoxifen, the gold standard drug for roughly the last 30 years. Women are typically treated with tamoxifen for 5 or more years, but evidence is mounting that less functional CYP2D6 alleles lead to less endoxifen, which is the active form formed via CYP2D6 metabolism of tamoxifen. Less of the active form means a poorer outcome, so now the question is becoming, can higher doses of tamoxifen overcome this, or should alternative drugs replace it as the gold standard?

7. rs1447295: And now here's one for the guys: this SNP has turned up in studies totaling tens of thousands of patients across multiple ethnic groups as connected to an increased risk for prostate cancer, the second deadliest cancer among men. Although on it's own the increased risk isn't that high (perhaps a doubling of risk even for those carrying two copies), there are now over 20 more SNPs that can be used together to help classify risk. We can hope that more aggressive screening of those deemed to be at higher genetic risk will help decrease prostate cancer deaths.

8. gs138, gs139, gs140: These three genosets (hence the 'gs' prefix) represent the rapid, intermediate, and slow metabolizers amongst you for the detoxifying enzyme NAT2. Debuting in 2009, the algorithms described in SNPedia using seven NAT2 SNPs allow the Promethease software to classify your NAT2 status and thus estimate just how fast you'll clear various toxins (or that hangover?) out of your system. Looking into the 2010 crystal ball: we foresee the use of lots more genosets to predict phenotypes (and ancestry) based on combinations of SNPs.

9. rs17646946 & rs11803731: Two SNPs, both on chromosome 1, yet 27 million bases apart; one is part of the trichohyalin gene, the other abuts a trichohyalin-like gene. One found by a genome-wide association scan by academic researchers, the other by a company harnessing the power of the internet , DNA chips, and customer interest in correlating their DNA with common traits - in this case, hair curliness. We applaud the use of people-power to help prove (and disprove) DNA associations, and in 2009 we began having SNPedia/Promethease users self-report their own associations for a variety of SNPS, regardless of which company they got their genome data from.

10. rs2395029: This SNP just keeps getting more associations every year! As the SNP predicting the presence of an HLA-B*5701 allele, it's been previously associated with a variety of conditions (like psoriasis, or as the FDA agreed last year, abacavir hypersensitivity). This year, it demands attention for the remarkable increase in risk (45 to 80 fold) for liver damage among patients taking the antibiotic flucloxacillin (aka floxacillin). While this SNP is quite rare, it's a good example of a more "deterministic" type of SNP that we can carry.

On that last note, the intersection of less expensive full genomic sequence with greater coverage of rare variations bodes well for all. Think well of all the researchers who make this possible - we thank you for your hard work, we encourage you to choose open access publications, and we look forward to all of your contributions in the coming year!

Interpreting a Promethease report

2009-11-24T13:25:00.000-08:00

This new video helps to explain what is inside a Promethease report.

Self Explorimentation

2009-11-05T06:14:00.000-08:00

SNPedia is pleased to have contributed "Self Explorimentation" to the What ELSI is New series -- especially during the moment when it is generating such interesting blogosphere traffic about access to genomic data. Of course, Genomics Law Report has this well covered, but this is a topic close to my own heart.

As suggested by Anne Wojcicki of 23andMe and Eric Topol M.D. -- SNPedia is here for you. Whether you get your data from a DTC, Kaiser, or the melting curve analyzer in your garage, we can help you to understand your data, and you can help us.

People without their data have little interest in SNPedia. Expanding this access helps SNPedia become a better resource. For these reasons, I might be too inclined to rush towards this (seemingly) inevitable future. I'm grateful that Daniel, Anne and others are raising this issue. But I can understand why Kaiser might feel that releasing information compromises their original study design. Mostly I'm excited by a future where the next study of this sort will need to consider sharing data with patients.

SNPedia poikkeaa Suomeen

2009-09-14T08:38:00.000-07:00

It is the day after the very enjoyable Human Genetic Variation conference in Tallinn, Estonia. Preparing for my talk motivated a new 'tag cloud' section in the Promethease reports as well as the new overview at http://www.snpedia.com/files/promethease/outputs/cloud.html. When reading it, bear in mind that the word "baldness" doesn't mean that Promethease is necessarily predicting baldness, merely that the report will be talking about baldness -- perhaps with decreased risk. This section is only supported in the paid Promethease reports. Unfortunately that feature, and all of Promethease are not (currently) supported on the recently released Mac OSX Snow Leopard. Such is the price of being an early adopter and Apple's fondness for 'shock and awe' marketing.

Tomorrow I'm off to Finnland to continue exploring my new European home and a presentation at the Helsinki Institute for Information Technology.

Conferences

2009-07-15T08:49:00.000-07:00

I'll also present SNPedia at HGV2009, the 11th International Meeting on Human Genome Variation and Complex Genome Analysis 11th - 13th September, 2009 in Tallinn, Estonia.

AM I? I AM . A MIA !

2009-07-13T16:50:00.000-07:00

SNPedia will be presented at the American Medical Informatics Association Symposium 2009 November 14-18 in a favorite old home, San Francisco. I'm looking forward to seeing Mark Porter again. Email me if you're around the city by the bay.

I enjoyed ISMB and expect to be a next year's in Boston. Warm hellos to James Diggans, Aaron Darling, Michael Imelfort, Barend, Brian, Isabelle and a lot of other exciting scientists.

Promethease 0.1.68 video tutorial

2009-06-22T00:04:00.000-07:00

Curious about Promethease? Now you can watch a full run.

Conferences

2009-06-14T09:11:00.001-07:00

SNPedia will be presented at the European conference on Python for scientific July 25th and 26th in Leipzig, Germany.

I'll also be attending ISMB June 27 - July 2, 2009 in Stockholm, Sweden.

If you're near those areas and interested please say hello.

Promethease 0.1.66 is out

2009-05-24T11:50:00.000-07:00

As always there are many improvements since the last blog post, but these standout.

There is a new syntax for genosets. Older clients don't know how to read this, and will not be able to see these genosets. This is a good reason for you to upgrade to the latest version.

Since 0.1.50 it has been possible to pay $2 via Amazon.com and reduce the runtime to about 5 minutes. In doing so you're downloading a single compressed cachefile instead of making thousands of requests for individual pages. At the moment this cache file is updated approximately weekly, however in the future we expect to have this updated in realtime as the wiki is edited. There will be a new blog post when that works. Until then the $2 version is faster, but the free version uses slightly fresher data.

The upper right corner has a new button labeled 'Wizard'. Press this to use a simpler UI which walks you through setting up your run. If you pay the $2, not only will you get the cachefile for a faster run, but you'll also have access to 2 new features with this wizard. The first is the ability to only show pages which have been modified recently. This might be useful if you ran your report 2 months ago, and want to make a new report which only shows what is new since then.

The wizard also enables a highly experimental new kind of report. This report is based on loading multiple genotype files and predicting what is possible in the offspring. You might wish to use this if you have data for you and your spouse, and you'd like to see some possible genotypes in your children. Its really not quite ready for the general public, but it never will be unless it is released for wider testing. Most folks should just click 'Next' and move on to generate a traditional report.

안녕, 서울, 한국에서

2009-04-16T10:35:00.000-07:00

Greetings from Seoul, Korea home of User:Hongiiv and the KNIH/KCDC. In a previous blog post I asked about Singapore, but plans have changed for the better and now I am testing the rs671 status of my excellent hosts, Chang Bum Hong and Dong-Joon Kim.

I think Hongiiv says it best:
꼭 5시가 아니더라도 그 후에 넉넉한 시간에 오시면 되겠습니다.
But for those of you who do not read hangul, I think google's translation is nearly as eloquent:
After that it was not five cigars will come in early.

For the full story see either the Korean invite or English translation to join us for the Open Bioinformatics Korea meetup April 17 17:00.

Promethease 0.1.46 released

2009-02-27T22:09:00.000-08:00

Promethease 0.1.46 is released. It is worth upgrading. The most visible change is in how the status window updates. Many other improvements are here too.

2009-01-06T04:45:00.000-08:00

2008-08-08T20:49:00.000-07:00

snpedia.com is 2 years old today. olympic dreams to all. especially the burmese.

0.1.24 public genomes

2008-07-18T16:56:00.000-07:00

Promethease 0.1.24 has been released.

A growing collection of public genomes allows you to see how magnitudes have improved the system.

Mendelian Inheritance

2008-02-24T12:30:00.000-08:00

Promethease 0.1.8 now available with an important new feature called a genoset. Genosets allow us to talk about specific combinations of SNPs.

As an example: 77% of Europeans who lack the rs4988235(T) and rs182549(A) haplotype will be lactose intolerant.

Previous releases could show you had the high risk form of each, but it couldn't highlight that you actually had both. Genosets resolve this. Each genoset gets a unique gs#, similar to an rs#. It also has a criteria which must be met for you to see the consequence. It works like the connection between a genotype and a phenotype.

Here is the genoset which predicts lactose intolerance and it's criteria
http://www.snpedia.com/index.php?title=gs100
http://www.snpedia.com/index.php?title=gs100/criteria

A criteria is a little computer program which evaluates to True or False for your specific genotypes. If True, your report will show the text from the main genoset page. Relax, only hardcore SNPedians will ever see another criteria.

Here's what the promethease reports look like for 23andMe's demo user Lilly Mendel and Greg Mendel.

Lilly Mendel should have no problems with lactose. Greg Mendel is probably lactose intolerant and may also be at increased risk of ALS. But look just below that and you will see that both Mendels carry a rare rs4253208(G;G).

Here from 23andMe's original file is the raw data

rsid	chromosome	position	genotype
rs4253208	10	50348728	GG

And NCBI/HapMap shows that the the (G;G) genotype is possible but rare. In fact it even suggests the Mendels may be closer to African than European ancestry?!

What's actually happening is strand confusion. SNPedia is oriented to NCBI dbSNP. 23andMe probably oriented to the opposite strand. However, there is nothing in their data file which indicates this. Without it, promethease has to recognize the (G;G) as possible.

deCODEme's file format does pass strand information, but perhaps the time has come to consider what a long-term personal genomics file format should look like. XML is well suited to this. Strand information is clearly important. I'd discourage 23andMe's fondness for pushing both allele's together to avoid confusion when dealing with multinucleotide snps such as rs34815109. Ideally it would also be able to handle sequence information since microarrays can't really see haplotypes.

Lastly, several people have reported seeing the message 'Not a win32 application' when trying to run promethease. It seems all were caused by failed downloads. If you see that message please ensure you have the full 7M file from
http://www.snpedia.com/files/promethease/promethease.exe

Promethease deCodes 23andMe

2008-01-14T19:36:00.000-08:00

Promethease annotates your genome using SNPedia.

It is possible thanks to the Personal Genome Explorer which allows 23andMe customers to export all of their 550,000 genotypes. Promethease reads this export format, and uses it to generate sample reports.

Your genotypes will probably be a bit more boring, since these random files get some pretty weird diseases. The report format isn't yet as intuitive as it should be, but you'll manage.

Your changes to SNPedia will appear in future reports. To generate a report simply drop an export file onto promethease.exe . From the DOS command line you can compare to other hapmap populations, instead of the default CEU. Runtime is about 2 hours. It doesn't eat much of your net or cpu, it just moves slowly to be courteous to others.

PGE does not yet provide information to orient snps relative to dbsnp. As a result many of the genotypes are flipped. This causes Promethease to ignore population frequencies. These SNPs will show with a 'None' along their left side.

http://www.snpedia.com/files/promethease/promethease.exe

GBrowse SNPedia

2007-12-08T10:11:00.000-08:00

It is now easy to overlay SNPedia on the Gbrowse databases. This means you can generate images like

(click for full)

which shows a cluster of snps around TCF7L2. The upper track identifies SNPedia snps. The the lower track identifies all snps present on the Illumina 550 microarray. All are hyperlinked to their SNPedia pages. If you click on the image above, you'll see the full image with the LD plot at the bottom. This allows you to determine how much two neighboring snps can say about each other.

To generate your own visit the hapmap of Chr10:114724078..114764077

At the very bottom of the page add these two 'remote annotation urls'
http://www.snpedia.com/files/gbrowse/snpedia
http://www.snpedia.com/files/gbrowse/microarrays
The snpedia file is a modest 300kbytes, but the single illumina chip is 58Mbytes!

Every snpedia rs# page now has a direct link to the hapmap site. Loading will take a while. Scenic spots along the genome include:

rs7901695
*click on hapmap
*set Scroll/Zoom=40kbp (upper right)

rs9939609
*click on hapmap
*set Scroll/Zoom=100kb (upper right)

I'm aware of a problem with rs3135506, but unable to explain it. Other times, snps listed in the snpedia files files aren't rendering onto the images. Other bugs probably remain. Your bug reports are always helpful.

Annotations will be updated approximately weekly, along with the fasta.

(click for full)

Fasta format available

2007-11-03T13:32:00.000-07:00

The fasta formatted version of all the SNPedia snps is now available at
http://www.snpedia.com/files/snpedia.fasta.gz
The above link will be updated regularly.

SNPedia was mentioned in the current issues of Nature [1] and Science [2]

Venter’s Genome: No Genome Is An Island

2007-09-04T13:07:00.000-07:00

With the release of the research paper describing the personal genome of J. Craig Venter, ostensibly the first individual genome to ever be made public, we’ve got an incredible opportunity to muse about what we know so far about human genomes. And the answer is: not much today, but wait until tomorrow.

I don’t know about you, but finding out that Venter has the ear-wax characteristics of most Caucasians and has European ancestors isn’t that surprising to me. His risk for heart disease and Alzheimer’s was already known and could have been found out a lot quicker and cheaper using microarrays. And although we believe that in these early days of personal genomics, you haven’t really released all your sequence unless you’ve released the primary sequence reads with their quality score files, the release by Venter of his assembled sequences (even without the primary data) does at least allow some geno-dumpster diving. We’ll probably post a few nuggets of information about Venter that aren’t mentioned in the PLoS article in future blogs, but suffice it to say for the moment, Venter is mostly pretty normal for a white guy.

So where’s the beef? Think about any nascent network. Who did the very first people with telephones get to call? The first people establishing a network get – initially – very little benefit, aside from the well-deserved credits. The value to scientific research? Priceless. The value to the individual? Hardly.

Venter reports a lot of novel genetic variants, including copy number variations, deletions, insertions, duplications, you name it … and of course, since they are by definition novel, we don’t know what they mean other than at least they aren’t fatal or associated with obvious overt disease(s), given that Venter is alive and reasonably healthy.

For all the hoopla over the Human Genome Project, the reality is that we still know very little about the complex interplay between millions of genetic variations and environmental factors and lifestyle choices. It will take many, many individual genomes, and even more daunting, detailed comprehensive medical records, before we are able to make many of the correlations that will ultimately matter to us on a daily basis. Venter estimates a minimum of 10,000 individual genomes, and maybe, a million or more.

Let me put it another way. What’s it worth to you to get your own genome sequenced, compared to just using microarrays to determine your genotypes? Here’s my first rule of thumb: it’s worth one penny times the number of already released complete personal genomes that also have medical histories. So with Venter being #1 (OK, he actually hasn’t released any medical info really, but let’s cut him some slack), in just another 9,999 genomes I’d say your personal genome sequence will be worth about $100 more to you than whatever you could learn from genotyping yourself with microarrays (and using SNPedia, naturally).

One corollary to this is that it will be essential to get as many genomes sequenced as possible, and whether it’s from government support or celebrity genome sequencing shouldn’t matter. What matters is that the medical histories of the individuals are also made available. As is the case with genome association studies, both case-control (groups of patients with a disease; why not one of the patientslikeme.com communities?) and ‘genome cohort’ personal genome sequencing studies should be funded by whoever’s got the bucks. Comparative personal genomics, here we come!

I recall a joke that probably plenty of folks have told; I heard it from Francis Collins, the head of NIH’s Genome Project.

A previously-married woman heads to bed for the first time with her new beau, and to his surprise, she admits to being a virgin. When he wonders why, she says, “Well, I was married to a genome biologist, and every night, he just sat in bed and talked about how great our sex life would be someday.”

Someday personal genome sequences will be great for each of us to have, and it’s fantastic to have the first personal genomes coming out this year. As of today, it’s 1 (personal genome) down, at least 9,999 to go …