Tag Archives: 23andme

Gene Envy. I haz it.

Last night I had a fun conversation with some non-scientists on personal genomics. A lot of my conversations on this topic are “inside baseball” with people who know the field (and the minefields) really well. So it’s fun for me to explore the larger social and ethical issues with people who are just beginning to think about them. And they coined a phrase to describe my feelings on something I had seen: gene envy. They were right :)

We talked at some length about what you can and can’t learn from the “reader’s digest” version of your genome that you get from a SNP scan like 23andMe provides. How SNPs can be informative, but are not the only types of variations that might be important in your genome, and they certainly don’t represent all the SNPs possible. We talked about the kinds of things you can learn from the SNPs right now–silly trait sorts of things like whether you have wet or dry earwax (as if you didn’t know already), as well as some information about potential disease incidence and response to certain medications–but even that data is sometimes preliminary and subject to change still.

That’s all the stuff I expected. One thing I wondered about was if I was going to be affected by knowing about other people’s genes…and how I might react to that. Well, now I know. I haz gene envy. [for my color-blind siblings, I wrote that in green, btw]

I hate to admit it. I want to be better than that. But maybe I lack a gene for that or something…. I should state right off that I’m not mad at anyone personally–nobody has control over what’s in their genes. It’s not about them per se, it’s about my reactions.

I’m not a hugely introspective person, but I have been trying to pay special attention to my responses to the new landscape of personal genomics. We have a front-row seat to this, and a decent copy of the program. So I feel a responsibility to be aware and honest about what my reactions are. And this is one I don’t like in myself. But it’s there.

I’ve downloaded some other people’s genome scans that they made publicly available. I use them to test out some of the software that I run. And if I want to make screen shots of stuff I refuse to reveal my SNPs right now as I don’t feel safe doing so.

One day I was looking around at obesity variations for some project I was working on. I had forgotten that I had my SNPTips tool on. When you have SNPTips on and search the medical literature at PubMed, the abstracts can be a bit of a roller-coaster. You can read about this research, and roll over the SNP IDs and be shown your own variations (or in my case other people’s). It looks like this as you are reading:

Note: that is NOT the paper I was reading nor the SNP and gene I’m referring to; this was just an example image.

So I am reading along the text, and check the genotype of this individual’s SNP. In that case, a result of AA meant that you had the “skinny” version of the gene in that study. It bugged me. I rolled my eyes, and thought of course it’s easy for this person to be thin….sigh. I was jealous.

In another case I was relieved that someone’s genes didn’t carry a variation I have. I saw the results for someone and thought: oh, good, they probably won’t have peanut allergy like I do. I’m glad for them.

One time when reading in the 23andMe discussion boards I found myself looking at the results for people who are probably resistant to HIV. I thought: nice for them. But the ones who didn’t have that–I was sort of shocked to see them telling everyone. I wonder if that’s wise when we know that data scraping is going on at some medical social networking sites. I easily could have written down their results and their names if I had been an insurance investigator. (If you want to check your own data there, search for CCR5 at 23andMe.)

Another “variation” on my response came when the Alzheimer’s alleles were recently released by 23andMe. I saw several people celebrate their alleles. WOOT!! Even before I looked at mine I resented this. Yeah, I think, you lucky dogs: goody for you. Now shut up and stop rubbing it in. Some people are not going to have a good outcome of this.

And I think to myself: it’s easy to be cavalier about the results you get from personal genome scans if you are healthy and have good genes–and stuff that won’t affect your insurability. Or if you live in a place where your health insurance is guaranteed or you are otherwise secure in your insurance. That’s not the case for all of us.

What I’m feeling is a mixture of things. I’m jealous and irritated by other’s “good” genes. I’m relieved in some cases. I’m anxious for my own outcomes in others. Even though I know that what we know today is only part of the story in most cases, and even with “bad” genes there are probably other modifiers or interactions that may mean you can get off scot-free with your alleles. But will insurers want to take a chance on me? I am skeptical that they’ll lean to the liberal side of the interpretations.

I still think we’re likely to see what I called Genorexia Nervosa–where some fraction of people get so wound up about their genes–or their kids’ genes–that they go overboard with how they think they should eat, or exercise, or allow themselves to be exposed to. (There’s probably an OCD sort of gene that influences that….). But I didn’t see the personal envy coming. That’s what happens when you have a front-row seat on a roller-coaster. And that’s exactly why I ended up doing the 23andMe scan–to join the ride, for good and for bad.

I’ll get over it. Although I do think I have a variant of the hold-a-grudge gene. I may mutter things about your skinny genes if I see you in skinny jeans….

Your genome scan for Free*

*while supplies last, plus 9 dollars a month for one year.

23andme is having a sale (again, I did our family’s scan when it went down to 100 late last year). This time the up front cost is $0. Of course you have to pay for shipping and the 9/month fee for updates (for one year). Still, that’s nearly a 2/3rds price reduction from just yesterday when it was $200 plus the 9/month fee.

They are doing this in advance of DNA Day, a national day to raise awareness among students and the public about genetics and genomics. The sale is today only (or while supplies last :).

So, if you had been considering a dna test, maybe now is the time to do it. And then come back to Genomes Are Us and we’ll help you decipher it :D.

This got me to thinking why 23andme is cutting their prices so drastically so often. I’m sure part of it is a market share and marketing ploy. I’m wondering also if there isn’t some thought that the more average citizens invested in the technology, the more likely they’ll fight draconian (in their eyes) regulation. But I’ll bet it’s the former more than the later, but it couldn’t hurt to have more people invested and interested.

Well, I did my duty and ordered my maximum of 5 tests :D.

 

 

(crossposted @ Genomes Are US)

 

Tip of the Week: SNPTips and viewing personal genome data

Today’s tip of the week is on SNPTips. We had a guest post on this earlier. We usually do tips on databases and analysis tools, but after getting our 23andme data, we’ve been using SNPTips often and thought it might be of use to some of our readers. SNPTips was created by 5am Solutions for 23andme* customers to easily view their genomic data while browsing the web. The tip will quickly show you how to install the browser extension and what it does. At the end of the tip, I  briefly show a custom annotation track I created of my 23andme data using UCSC Genome Browsers** Personal Genome SNP format.  The format is not perfect for 23andme data (doesn’t allow for rsID field, has fields of little use with 23andme data, etc), but it does help tremendously if you want to browse your data with the genome browser. You basically take the 23andme data that looks like this:

and rearrange the columns, add a few to make it look like this:

You can do this in a spreadsheet program like I did, it’s a bit labor intensive. If I decide to do it for my daughter’s and husband’s genome data (which is a distinct possibility), I’d created a perl script to change the format (or maybe there is something already out there?).

It basically entails:
*eliminating the  rsID column
*rearranging the columns to the correct order
*adding “chr” to the chromosome number
*adding four columns, 1 with the number of alleles, 2 with 0′s (frequency data the 23andme data doesn’t have)
*changing the genotypes from xx to x and xy to x/y.

Remember also that the 23andme position data is from build 36 (2006, hg18) and the genotypes displayed in 23andme data are oriented with respect to the positive strand on the reference assembly.

It’s not the most elegant solution, but it works and nicely with SNPTips. It has been quite addictive for me :). I’m sure there are more elegant ones that can be done.

*OpenHelix and it’s employees have no commercial connection or financial interest with 5amsolutions or 23andme.
**UCSC sponsors tutorials and outreach with OpenHelix through as a subgrantee.

Of Mormons and Mozambique: a cursory look @ 23andMe ancestry data

So, as a lot of people, I received my family’s 23andme results yesterday. Well, 3 of 4. Our youngest daughter’s spit apparently has little DNA, she had to spit again. Her results are to come later. As I mentioned in earlier posts, I wasn’t planning to be surprised of my own or my husband’s results. And even if I was on the ancestry front, I didn’t expect it to have too much meaning. Of course, since our daughter is an adopted African-American, I expected to find interesting information there, information we have little knowledge of. So, today I will look at our ancestry, later I’ll take a look at health.

I’ve only had a chance to look at 23andme’s analysis reports for ancestry. To go deeper later,  I’ve downloaded the raw data, installed SNPTips and am starting to preparing for some other analysis. But for now, here is what we found, surprises and confirmations.

The Haplogroups find… nothing surprising for me.

My paternal lineage is haplogroup I1*. A haplogroup predominantly found inScandinavian populations. No surprises there, and possibly a confirmation of anecdotal evidence. The Lathe/Leathe/Leeth name (all variations of my last name through 500 years of history) is English, but our research suggested that it originated from the Norse invaders/settlers of Danelaw. Well, that seems to confirm that.

My maternal lineage is haplogroup I1a1, a European, possibly Celtic, group. Makes sense, my maternal lineage is Irish/Scottish. No surprises.

Who really is Indian?

I found something interesting with Ancestry painting (where the determine the geographic location of chromosomal inheritance). I was 99% European, 1% African. See that little box on chromosome 8, it’s African. What does this mean? Where is the Asian?

My great-grandmother is of Native American descent. Her ancestry is Mattaponi. That much is documented. Why does it not show up here? 23andme says that ancestry painting won’t pick up Native American ancestry (it uses Asian populations in the HapMap data for it’s analysis) if there isn’t a “full-blooded” native American in the last 5 generations. My great-grandmother is 4 generations back. In her photos she looks at least partially native, her birthplace was a Mattaponi town and family documents and stores are pretty conclusive. But that’s why I said “descent.” Though we assume from oral history and documents her mother was full-blooded, we don’t know that for sure and we don’t know her father’s heritage completely. More importantly, the Virginia native groups such as the Mattaponi (and Chickahominy, Pumunkey and others) have lived among and intermingled with Americans descended from Europeans and Africans for nearly 400 years. So, as I suspected, my great-grandmother wasn’t full-blooded, but rather mixed-race individual of Indian culture. But as I said in my previous post, what was most important to her life and who she was, her genetic heritage with possibly African and European admixture, or her cultural heritage with it’s large native American foundation? The latter I suspect, though the former was obviously an influence.

Of course, this all goes to the argument of ‘who is an Indian’ which I won’t delve into too deeply. Early in the 20th century, obsessed with racial purity, some Virginia officials tried to prove Virginia’s native population wasn’t native because of the admixture. Today the discussion continues among the tribes themselves. I would fall on the side of culture and heritage over genetics, but it’s not a simple thing.

The African descent I see? Perhaps it’s carried over from her, or from my maternal lineage with it’s origin in plantation and slave-holding families. I believe it’s from my Mattaponi great-grandmother because of a story my grandmother once told me.

To get more data about the Native American lineage, I’d probably have to get my father’s maternal lineage and haplogroup and his ancestry painting. It might tell us more. For example, my husband’s ancestry painting showed 100% European, but his father had 3% Asian (from a Mediterranean lineage). Ancestry markers disappear eventually.

If there is anything that DTC genomic testing does, I hope it does change our view of who we are. I hope that it reinforces my belief that our culture is less ‘genetic’ than we seem to think today and that our culture is a vibrant mix of influences. That only time and a million tests will tell. I am quite sure it will have some impact.

Mormons and Africans:
An interesting side note to this is that our family story, as related to me by my grandmother, suggested we indeed had an African American ancestor from our Native American lineage. When I was 17, I joined the Mormon church. The church at the time did not allow people of African descent to hold the priesthood (all lay males held the priesthood in this lay church). They insisted it wasn’t the color of one’s skin, but rather their ancestry. When I mentioned the possibility of our ancestry (and some documentation that suggested it), I was barred from the priesthood. I finally was ordained almost a year later, right before the ‘revelation’ (long story).

So, 30 years later, it’s confirmed with data. I have a drop of African ancestry. I think it would be highly interesting to do genomic scans on white Mormons today who held the priesthood before 1978. Did they have African ancestry and hold the priesthood? I dare say a good number did. Perhaps another reason the policy was changed.

Speaking of Africa, Mozambique:

Our oldest daughter’s scan was also completed. Out of privacy concerns (which I’ll talk about in another post) I will only post some basic ancestry and no healthinformation.

Her maternal haplogroup is L3e1e, a lineage that most likely starts in Mozambique. Some preliminary data suggested that much of our daughter’s African ancestry was Nigerian region and possibly from what is now Angola, and it probably still is, but this was a surprise.

But for the maternal lineage, interestingly, very few slaves came from Mozambique directly to the United States. Mozambique was a Portuguese colony and they sold and transported slaves mainly to South America and the coasts of the Indian ocean. Where and when did this maternal lineage arrive to the Southern parts of the United States?

Tantalizingly, I found one voyage of the slave trade that goes carries Africans sold into slavery in Mozambique and transports them to the Caribbean from the Voyages database. What do I find that tantalizing? Because we do know that one of our daughters genetic grandmothers was ‘creole’ as reported by her birth mother. We weren’t sure what that meant in this context, but perhaps it’s Caribbean? Perhaps these are frayed ends of a lineage we could connect someday.

Looking at her ‘ancestry painting’, she is typical for African Americans, a strong admixture of African (76%), European (21%) and Asian (3%, possibly Native American) background. I haven’t figured out completely how to interpret this, but I suspect one parent was more “European” than the other.

What have I learned from the ancestry part of the 23andme test? It has confirmed, as I suspected most of my ancestry as I know it from my genealogy. It has clarified and added a slight question to my Native/African ancestry I would like to delve into more (and the genealogy since that is the least-researched line frankly).

For our adopted daughter we learned a bit more and possibly able to transport her genetic heritage back several centuries.

Has it affected how I see who I am or my daughter is? No, not really. It confirms our genetic heritage and strengthens our understanding of our cultural heritage.

But I’m intellectually fascinated by it…so now comes more analysis, Admixture, Haploview, UCSC Genome Browser, SNPTips, here I come.

PS. Also have a bit of Neandertal in my genetic heritage, but I have a bit more research to do to confirm that  :D.

The meaning(lessness) of genetic genealogy

Many years ago, and in another lifetime it seems, I was fascinated by my genealogy. I was a Mormon which made genealogy part of a religious duty, but I also found my early-American
settler, German and Native American heritage fascinating. Due to Ph.D. studies, a marriage and two children, I stopped delving into my genealogy over twenty years ago. Yet, in the last month I’ve
been diving back into genealogy in preparation for and to compare with our soon-to-come 23andme data.

I don’t expect to find out much more from my 23andme data than I already know from my genealogy. I expect our adopted daughters will find out more, but I am beginning to come to the conclusion that it’s not all that particularly meaningful. Forgive this personal, and long, rumination on the meaning of genetic (or any for that matter) genealogy.

I have jumped back into genealogy in a world much changed from 20 years ago, personally and technologically. Adopting two girls has altered my entire definition of “family history” and technologically the ability to research one’s genealogy has increased beyond what I could have imagined 20 years ago. With huge amounts of data online and millions of people researching their genealogy, it has become magnitudes simpler to go back hundreds of years. Huge amounts of data and millions of genealogists online; I’ve always had a pretty good understanding of my family genealogy, but because of those two, I’ve been able to push back my documented genealogical history several hundred years in most lineages.

I’ve found of my 16 great-grand-parents, 12 are fully from Anglo-Scottish-Irish lineages that stretch back to the early 1600′s in Virginia, Massachusetts and South Carolina. 2 are from German immigration in the mid 1800′s and 2 are Native American. I’ve found (or re-found)some interesting stories, like the XGGrandfather who was accused of witchcraft in the Salem witch trials (imprisoned and later freed), or the signer of the Declaration of Independence. On a few lines I’ve been able to push back the history hundreds of more years. In one case, it reaches back over 1,000 years. I learned that some of my ancestors were French (le Strange… no, not ofHarry Potter fame) who came over during or soon after the Norman invasion  of England. Some where Welsh with names like Madog ap Madog who married into the aristocratic English families that were taking over their lands. Some possibly French and German aristocracy, and of course we all go back to Charlemagne one way or the other don’t we?

So, I’ve jumped deep into my genealogical pool. I don’t expect the 23andme data will tell me much more than I already know. Of course, that will be different for our adopted daughters, but is there really anything of significant meaning for any of us?

The further back I traveled my family history, the more meaningless it has become. Go back 10 generations and you have over 1,000 direct ancestors. Go back 20 and you have a possible million direct ancestors. And in the case of the one lineage I was able to trace back 32 generations? A possible 8 billion direct ancestors.[LINK] Well, of course that isn’t true, there weren’t 8 billion people on earth in 1,000 AD, in fact there were only anestimated 250 million people on Earth. So I’m possibly descended from over 30 times the number of people on earth at the time. There was a lot of lineage collapse I’m sure (cousins, 1st, 2nd, 3rd and further, and removed, marrying each other). There’s two points to this paragraph. The first is, if I have thousands, hundreds of thousands, even millions of ancestors, what relevance do any one of those have to who I am? And the second? The further back I go in my history, I must be related to a larger and larger percentage of the population in the world at that time. I haven’t done the statistics, wouldn’t know where to begin (there’s a project I’m sure that must have been done), but I suspect the percentage of the population of the world in 1,000bc that I am a direct descendent of is much greater than the percentage in 1,000ad.. and so on. Eventually, my story is the world’s story. But I don’t need to go back 30 generations to find that the meaning of an individual ancestor, or entire lineages become well, minimal at best. Sure, I can go back 3 or 4 generations and find meaning. I am pretty sure the reason we were served scrapple, weisswurst and liverwurst at home is because of my grandfather grew up in a half-German household. I now know that many of the stories and aphorisms my grandmother told me had roots in native lore, and so forth. I can see my grandfather in my face and mine in my nephews’. But, there is much I don’t share even with my close ancestors. Much of their culture was not passed down to me even though there is an unbroken line. I don’t speak German, nor Algonquin. I’m sure there are holiday traditions that have been lost. To look at my native American-descended great grandmother is to see someone who I don’t see myself in.

Go back even further and the things that are passed on genetically and culturally become even more minimal. What is the chance that one of my 10x great grandparents pass on specific alleles. It’s there, but go back another 10. Of course something gets passed on, otherwise the 23andme ancestry component would be completely useless. But culturally? I don’t speak French, German, Welsh, Italian, Algonquin or any of the languages of my ancestors. The more I learn about my genetic ancestors, the more I learn that I have inherited only a small part of their culture, and even then it’s an unbalanced inheritance. Some recent ancestors contributed more to my family culture than others. Some contributed very little.

And from studying my genetic ancestry, I’ve found that a large portion of the culture I was raised in has nothing at all to do with my genetic heritage. The music we listened to, the food I eat, the holidays we celebrate, the history that shaped my locality and my nation, all the myriad things that make up my culture that I grew up in, these were as much shaped by genetic strangers as they were by my genetic ancestors, perhaps more. Yes, my signer of the declaration of independence ancestor affected my culture tremendously, but he would have if he were my ancestor or not. And, I am quite certain the slave who sang his songs, or the abolitionist who fought the battles, and the writings of William Faulkner and Mark Twain have affected my culture, who I am and how I think, as much more more than my South Carolinian plantation owner ancestors. I know that the Mormon pioneers who crossed the plains affected who I am today much more than many of my direct ancestors, even though I am not related to them. The same goes for the Spanish settlers of California. Who I am culturally is only tangentially related to who I am genetically.

This has become more clear to me as my husband I have adopted two children. We each inherit two histories when we are born, our genetic history and our cultural history. For many of us, the two are deeply intertwined, but as I’m finding out, not necessarily at all the same. For an adopted child, they are separate. Contrary to what a well-meaning family member, and what some adoptive parents, believe, we do not inherit our cultures genetically. One’s taste in food, language, literature preferences and all the things that make up that complicated beast called ‘culture’ is something we learn and react to. If you took me as a new born and dropped me into a Siberian household, I’d be Siberian. Drop me into a Chinese household, I’d be Chinese. Sure, who I am in that hypothetical Chinese family would be shaped tremendously by my genetics, people’s reactions to a blond-haired, blue-eyed boy would affect my personality, but I wouldn’t be any more culturally “American” or “European” than any other child in that town. People have asked us if we are teaching our daughter “her” culture. But she came to us as a newborn infant. “Her” culture is whatever she is learning from us and the world around it. It’s not somehow genetically tied to her skin color or race. She didn’t bring with her a set of cultural values she biologically inherited from her genetic forebears. In fact, none of us have.

This is not to say we should not teach her about the African-American history and culture. She didn’t genetically inherit it, but in the culture she is apart of, and the reactions people have to her skin color, requires her to understand that cultural heritage. But the more I thought about it, the more I realized it requires _me_ to understand that cultural heritage. In fact, a couple years ago Andrew Sullivan and a thread about how African American culture actually is. From the music we listen to (Rock, Jazz,  Blues) and the instruments we play on (Banjo), to the food we eat (mac and cheese anyone?), the prose of Mark Twain, down to our fundamental understanding of the phrase “All men are created equal,” Africa and African Americans have not only impacted American culture they are fundamental to it.

To understand who I am, how I think and where I came from I must understand African heritage as much as my genetic heritage. Perhaps more.

So it comes down to this, studying my genetic genealogy can and has heightened my understanding of who I am. I’ve learned about the founding of this nation, about the movement of peoples across seas and continents, stories of ancestors that profoundly affect my culture and how I think.

You see, Lane Wallace is wrong in her flippant remark about about novelist Erdrich.

The element of the last PBS episode I found most intriguing was Gates’ interview with novelist Louise Erdrich, who declined to have her DNA tested because her identity as a descendant of the Chippewa Native American tribe is so important to her. She said that she felt her tribe and family were what made her who she was. And, as she explained to Gates, she “didn’t want to add any confusion to it.” Erdrich, in other words, didn’t want cold, scientific facts to confuse her cherished notion of who she was, based on her assumed heritage.

The cold hard  facts are that her assumed heritage is indeed her heritage, not the genetic finds.

Genetics it is neither necessary, and definitely not sufficient, to understand my culture and who I am. If I was focused on my genetic family history, I’d be missing out on the major part of who I am. I’d be missing out on all the other stories of the non-genetic ancestors who have had as great , and sometimes greater, an impact on my culture and who I am. The Mormon pioneers, the African American, Irish and Italian immigrants and so many others.

Focusing on my genetic genealogy will give me part of the picture of who I am and I find interest in it. It does inform some of my study, but I can get a broader, deeper and more meaningful understanding of who I am by studying history.

So, I will be interested in our 23andme ancestry data, we’ll use mine, my husband’s and our daughter’s to guide us in the creation of our family history and our family map*, but with the understanding that alone, it tells us only one part of the story about who we are.

*instead of a family tree, our family has a family map. Places our ancestors and major cultural influences come from are pinpointed on a world map (Germany, England, Spain, Eastern N. American, West Africa, Mexico, Korea, Scandinavia) with lines drawn across the map showing migrations, all eventually pointing to and ending up at our home in San Francisco. It better represents who we are.

Guest Post: SNPTips, Andrew Evans

Andrew Evans – Sr. Information Architect and blogger at 5AM Solutions, Inc. This blog post is also published at http://blog.5amsolutions.com/

When I became a customer of the 23andMe personal genomics service back in 2008, I remember the sense of awe I had when I opened up the raw data file for the first time and looked at the actual A’s, G’s C’s and T’s of my genetic makeup. In reality it’s only a tiny portion of it since 23andMe assays 600,000-odd “single nucleotide polymorphisms,” or SNPs (now close to a million with their v3 chip). SNPs are locations in the genome where individuals differ from one another. SNPs (pronounced “snips”) are interesting because they might help explain in part why my personal traits and health have developed the way they have – how I might respond to certain drug treatments, why my eyes are brown, or whether I am a carrier of known Mendelian disorders, for instance. More and more new research arrives every day, attempting to link SNPs to every conceivable health condition and trait.

23andMe does a good job of providing interesting and carefully-researched reports for their customers, available on their website, and tailored to your personal genotype. They sift through the flood of research data and determine what is really worth your time to consider. They also maintain an informative blog that tracks breaking developments that might eventually make it into their official reports.

Those of us who are more adventurous, however, and perhaps better-schooled in the science behind personal genomics, can outgrow 23andMe’s filter. We wander to the scientific literature and other technical online resources where there is a lot more data, much of it preliminary, to explore. Such information can tempt one to jump to erroneous conclusions. But I understand this environment and I’d rather decide for myself.

This is the situation I found myself in not long after becoming a 23andMe customer. I discovered Mike Cariaso’s SNPedia.com, for instance, and ran my data through his Promethease tool – and I realized there was a lot more information on SNPs in the literature than 23andMe was showing us. Also, I became a more technical reader of the 23andMe reports, and now routinely follow up their references and go back to the original journal articles to understand why they draw the conclusions they do.

But there is one problem with all this Web wanderlust – once you leave 23andMe’s website, you must look up your genotype at each SNP on your own if you want to see what impact a particular finding might have on you. This can get quite tedious – especially for journal articles that mention batches of SNPs at a time. To the eye (and my memory), it’s not clear which SNPs are on the 23andMe chip at all, since they assay a subset of the known frequently-occurring SNPs.

This led me to a rather straightforward idea – why not build personal genomics smarts right into the web browser? That way, the browser could enhance web pages that mention SNPs and show you relevant information without you actually having to break your reading flow and go look up genotype information. A browser extension can do this, and so SNPTips was born.

SNPTips is a Firefox browser extension that links to your 23andMe raw data and pre-processes web pages as they are loaded, adding color-coding and tooltips to SNP IDs that are mentioned in web content. If you simply hover your mouse cursor over the SNP RS number, your personal genotype at that SNP is displayed. SNPTips also adds a little icon next to the ID – clicking this icon brings up a balloon with smart links to other web resources, including SNPedia, Google Scholar, and NHGRI’s dbSNP – so you can delve deeper with a single click.

Web page content without SNPTips

Same page, SNPTips-enhanced

(green SNPs are on your chip, gray ones are not)

Looking up each of these SNPs one at a time is a major pain, and a true impediment to getting value out of 23andMe raw data – switching windows, logging in, searching, etc. With SNPTips, a simple mouse gesture is all that’s required, without even losing your place as you read!

SNPTips is currently in public beta. To get SNPTips, simply visit snptips.com with your Firefox 3.6+ browser, and click the Install Now button, and follow the directions on the website to configure. After you’ve tried it out, we’d love to hear from you and hear your questions or suggestions for improvements. Just send e-mail to snptips@5amsolutions.com

I’m excited about our future plans for the tool as well (additional browsers, other personal genomics services, for instance) – stay tuned here (and follow @SNPTips on Twitter) for updates.

Genomic Poetry

23andme came out with their poetry winners today. Robert Frost is one of my favorite poets, so of course I do love this winner:

The Haplogroup Not Taken
by Robin Goldstein (with deepest apologies to Robert Frost)

Two SNPs diverged in a Chromosome
and wonder I the meaning thus
A lifelong need for brush and comb
or sullen gaze at polished dome;
The benefit, a lack of morning fuss.

And so I spit into a tube
and learned of things like Phenotype
and Gregor’s bees, though I a rube
more like to solve a Rubik’s cube
Or chat with Stanford doctors using Skype.

Now “The waiting is the hardest part”
Tom Petty sang (left-handedly)
And “Cogito Ergo Sum”, said Decartes
Though philosophy cannot impart
That smell of asparagus to my pee.

I shall be blogging this with a sigh
To cousins 2 and 4, first, fifth and 3
Two SNPs diverged in my genes and I
Intent to learn the reasons why
Now wait results from 23andMe

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Edit: check out what one of the top searches over the last week has been:

non-Traditional family structures and genomics

As I and my family await our 23andme kit to scan our genomes, family history has come back to the forefront of my thoughts. I used to be very fascinated by my own genealogy, and with adopted children, the concepts of descent, biology and culture have taken adjusted meanings for me. It’s why we have a ‘family map’ instead of a ‘family tree’. The difference between our cultural genealogy and our genetic genealogy has been become quite clear to me. Obtaining our family ancestry through these tests will bring a lot of these issues back to focus.

But there is a specific issue that is directly related to genomics, genomics tools and my family: same-gender headed household representation in pedigree and genealogy software. It’s non-existent or takes a difficult workaround to make it happen.

With the rising use of personal genomics data, there is a corresponding rise in the use of pedigree software for medical purposes and genealogy software for family history purposes. Neither of these handle non-traditional family structures well. I use ‘non-traditional’ lightly here though because even though same-gender headed households might be relatively new as a recognized family structure, the concept of family can be quite fluid across time and cultures. What is traditional and considered the ‘norm’ today in US culture (nuclear families of  two genders with children born to them) for ‘family’, is obviously not the case in the past, nor in contemporary cultures in other parts of the world.

A paper published last year entitled When Family Means More (or less) than Genetics by Burns and Edwards focuses on this inability of current tools to model family histories that aren’t within this norm. As they state:

One challenge in using family history as a health technology is that the geneticist or clinician defines family based on biology, whereas individuals often include those linked socially.

Genetic heritage and history is indeed important in determining disease susceptibilities, but ignoring or misunderstanding socially-defined kinship can lead to misdiagnosis, the lack of understanding of environmental influences and worse. Tools for modeling pedigrees must be able to flexibly model these family structures in order to be useful.

The researchers look at two groups and conclude that current tools are inadequate to model their family structures. Samoans were one group (Japanese-Americans the other):

When Samoan American participants were asked, “tell me about your family,” persons fulfilling social roles were described by that relationship. For example, an individual raised as a brother was identified as a brother whether or not there was a biological basis to the relationship. Similarly, individuals adopted in to or out of a family were described as the children of the family in which they were raised, not as offspring of the biological family. When further questioned, the participants could identify the biological link. But even when the biological relationship was known, the Samoan Americans reported family relationships based on social rather than biological ties.

They go in to good detail into why this is a problem. They also, early in the paper, suggest modern American society is changing. Americans already are one of the most ‘adopting’ nations in the world. And, as the authors note, our family structures are becoming more fluid (perhaps converging with Samoan concepts in some ways?):

For example, the Western postmodern family has looser kinship ties than in the past, with relationships that are diverse and fluid (Stacey, 1998). Blended, adoptive, and gay families, as well as those resulting from a variety of assisted reproductive technologies, place an emphasis on choice rather than genetics. For many, family is about social relationships and not solely concerned with the transfer of genes from one generation to the next (Finkler, 2001;Lévi-Strauss, 1969Peletz, 1995). Nonbiological social factors, such as role behavior, determine family membership, so that a mother’s sister’s son who has been raised with you is your brother (Finkler, 2001). Both formal and informal adoptions are traditional practices and very common in certain societies: Polynesia often being presented as the exemplar (Brady, 1976Carroll, 1970Levy, 1973).

So, let me side step adoption or other non-genetic descent issues for a moment, and hone in on gay families and representation in current pedigree tools available. Though the Recommendations for Standardized Human Pedigree Nomenclature (pdf)  mentions it in passing (“For example, information that is commonly recorded on a pedigree (e.g., same-sex relationships…)”) there is no standard suggested. In my and my colleague’s research so far we have yet to find a software or online medical pedigree tool that easily accepts same-gender parental groups, or represents them well.

I took at one excellent online tool, Madeline 2.0. If one enters a parent, entering a second parent automatically forces an opposite gender. Though there is the ability to model adoptive relationships, there is yet no way to model same-gender couples. I wrote the developers of the tool and received a thoughtful reply. No, there was ability to do this, but considering adopt-in and adopt-out relationships are model, it would make sense to include same-gender couples. They suggested they indeed will consider implementing this. Of course, as with all software and online tools, funding, timing and priorities I know will be an issue. I’ll definitely will keep an eye on developments. So as to not single Madeline out, no other tools that we know of (see here, here and here) allow for same-gender couples or headed families.

When going to family history modeling software for genealogy, the omission is as stark. Every individual has two family trees: a cultural/historical one and a genetic one. For most individuals, those histories overlap. The culture you received from your parents and they from theirs is pretty close to the genetic descent. Even then, its not a perfect overlap. What is important to who you are from a cultural or historical perspective might not at all be related to who are you from a genetic one, and who you are is as much cultural as it is genetic. I am as interested in where I got my cultural ancestry as where I got my genetic one, this has become quite clear to me as we’ve adopted children.

And in the future, descendants will look at their family genealogies and it will be very important to them that one of their ancestors was raised by two men, or two women whether adopted or biological from one parent. As these genealogies are built, those relationships which are very important to their family culture and histories should be represented. I know I personally will hope that this will be the case for our family history in the years to follow.

Yet, for software available it is impossible, a complicated workaround or awkward to allow for same-gender parents in the representation (not to mention paper family trees!). GEDCOM is the defacto standard for exchanging genealogical information. There is no simple standard in GEDCOM for including same-sex parents. That it was developed by the Mormon Church probably has something to do with that ‘oversight’, but frankly given the oversight across the board in pedigree and genealogy standards and software, I doubt that was a deliberate one.

So far I have found software that requires complicated workarounds, like Legacy, or it’s not easy to figure out (though once you do, it’s simple :). Of the many I’ve tried, none even allow it.

In a world where the number of same-sex couples is increasing annually (not to mention adoption, blended families and many other types of structures) and increased interest in family history through both genomics and culture and history, I look forward to seeing the software catch up to the ability to model my family for future researchers and historians.

Burns McGrath, B., & Edwards, K. (2009). When Family Means More (or Less) Than Genetics: The Intersection of Culture, Family, and Genomics Journal of Transcultural Nursing, 20 (3), 270-277 DOI: 10.1177/1043659609334931

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…