Tag: 23andMe

23andMe v3 chip & me

By Razib Khan | January 26, 2011 2:44 am

Yesterday the first batch of results from 23andMe’s v3 chip came online. Instead of 550,000 SNPs you get ~1 million. The difference is pretty clear when you look at the raw SNPs. Under Account → Browse Raw Data, I can enter LCT, and this is what I see:

I’m line #2. A sibling is line #1. Looking at this sort of stuff makes it really likely I’ll upgrade. My main rationale for not upgrading is that there’s diminishing marginal returns for ancestry related stuff. Speaking of ancestry, let’s compare my sibling’s ancestry painting to my own.

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CATEGORIZED UNDER: Genetics, Genomics, Uncategorized
MORE ABOUT: 23andMe, Genetics, Genomics

Reminder, 23andMe sale through Christmas

By Razib Khan | December 23, 2010 9:50 am

A reminder that 23andMe’s sale is valid until Christmas. Including the mandatory yearly subscription to their “Personal Genome Service”, that’s $160 (though you only get charged $99 + shipping initially, the subscription is $5/month). I didn’t quite go up to the 10 kits per person, but I did come close. There will likely be new amateur and/or open source genome projects in 2011, so if you’re from an underrepresented community this might be useful as a public good. It is true that the probability of finding actionable medical information is low, but you can do whatever you want with your ~1 million SNPs indefinitely. Channeling Sally Struthers, can’t you afford the purchase of ~1 million SNPs for the cost of 10% of a cup of expensive Starbucks coffee drinks per day for a year? That’s 1/60th of a penny per SNP!

(and for the record, I am not getting a cut)

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: 23andMe

My Dodecad results

By Razib Khan | October 29, 2010 11:51 am

A few days ago Dienekes opened up the Dodecad project to a wider range of Eurasians. I decided to send my 23andMe sample to Dienekes ASAP, and the results came back today. I’m DOD075. Dienekes also just put up an explanation of the 10 ancestral components he’s generating from ADMIXTURE (along with tree-like representations of their distances). Below I’ve placed myself in the more local context of populations to which I’m close to:

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CATEGORIZED UNDER: Anthroplogy, Genetics

The Dodecad ancestry project

By Razib Khan | October 25, 2010 3:47 pm

Dienekes Pontikos, Introducing the Dodecad ancestry project:

1) Project goals

The Dodecad ancestry project has two goals:

– To provide detailed ancestry analysis to individuals who have tested with 23andMe; other testing companies may be included in the future.

– To build samples of individuals for regions of the world (e.g. Greeks, Finns, Albanians, Southern Italians, etc.) currently under-represented in publicly available datasets.

I neither endorse nor am I affiliated with any genetic testing company. I have chosen to base the project on 23andMe results, because (i) I perceive that quite a few people have used the service, (ii) the Illumina genotyping platform it uses has substantial overlap with the publicly available datasets on which my analysis depends.

Basically some of you need to send him your 23andMe raw data files. The potential sample space of this group is going to be in the tens of thousands from what 23andMe representatives have stated about how many of the Complete Edition kits they’ve sold. Naturally due to labor and computational constraints he only wants people from particular populations. I think that’s fine. I’m a little taken aback by how demanding and critical Dienekes’ readers have been about the choice of populations he analyzes. You can install ADMIXTURE yourself, get data sets, and manipulate them in PLINK, etc. I hope many people will participate in this project. I would have given my sample, but I’m not of an appropriate population, and even if he wanted South Asians I’m pretty sure I’m not very representative of South Asians (I have very few runs-of-homozygosity and seem to have recent admixture from other world population groups).

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: 23andMe, Dodecad

The confusions of genetic relatedness

By Razib Khan | September 12, 2010 12:12 pm

Last spring I posted ‘Beyond visualization of data in genetics’ in the hopes that people wouldn’t take PCA too far in assuming that the method was a reflection of reality in a definite fashion. Remember, PCA visualizations are showing you two, and at most three, dimensions in genetic variation within the data set at any given time. The fine print is important; e.g., “PC 1 15%”, “PC 2 4.5%”, etc., which points to the magnitude of the dimensions within the data. You see the largest, and likely historically most significant on a population wide scale, genetic variances, but there’s still a large remainder left over. But when I look at referrals from message boards people obviously aren’t careful with what PCA is telling them.

As an illustration, in the 23andMe user interface you can “compare genes” genes across people who you “share genes” with. This comparison operates over ~550,000 single nucelotide polymorphisms out of 3 billion base pairs (you can constrain it to traits, but I’m going to talk about the comparison to the whole data set below). For example, a man of European descent shares 83.2% with his daughter, who is Eurasian (the mother is Burmese, with some recent Indian admixture). Another man of European descent shares 84% with his daughter, whose mother is also European (in fact, both parents are western European). The “gene sharing” with other people of European descent of these two men is in the 75-74% range (for reference, a Chinese person is 71%, and Nigerian 68.5%). On the PCA plot the European and his Eurasian daughter are very far apart, while the European man and his European daughter cluster together. What you’re seeing on the PCA chart is population level information, not the genetic uniqueness within families and across parents and offspring.

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CATEGORIZED UNDER: Genetics, Genomics

Personal genomics & the state

By Razib Khan | July 23, 2010 11:13 am

Dr. Daniel MacAthur & Dan Vorhaus offer their takes on the recent hearings in Congress on the direct-to-consumer genomics industry, A sad day for personal genomics & “From Gulf Oil to Snake Oil”: Congress Takes Aim at DTC Genetic Testing. I guess I lean toward light regulation. I don’t think that DTC personal genomics will result in systemic decrease in human happiness, and tight regulation will increase the costs of innovation and constrain access and reduce affordability. Though I guess that for some that’s a feature, not a bug.

My main point, which I think I got across on the Genomes Unzipped comments is that fraud, error and misrepresentation are rife across many health-related sectors in American society. The nutrition and diet industry are prime examples. Bad journalism on the health beat causes way more suffering than DTC genomics kits ever will, as people who are not intelligent make precipitous decisions based on the latest result which managed to slip through the p-value gauntlet and are sexy enough to be written up in USA Today. And, there are widespread distortions within our health care sector which really need to be addressed (I’m thinking in particular of frank talk about end of life palliative care). With that as the basis for judgement I don’t think that the fraud and misrepresentation one can find in DTC personal genomics is exceptionally worrisome or notable to warrant such attention or focus. This is an inefficient allocation of concern and regulatory resources, driven more by the industry’s puffed up claims and the apocalyptic projections of the skeptics.

CATEGORIZED UNDER: Genomics, Health
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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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