Tag Archives: 23andme - Page 2

June Update

I have a total of 123 participants in the project right now who have sent me their raw data. Six of those have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.Укладка дикого камня

The following groups are represented:

Most are 23andme data while 4 are from FTDNA.

We are getting close to 100 South Asian participants.

April Update

I have a total of 97 participants in the project right now who have sent me their raw data. Six of those have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.http://mountainsphoto.ru

The following groups are represented:

Let's try to get to hundred soon.

And yes, I am accepting FTDNA Family Finder (new Illumina chip) now.

23andme Sale

23andme is having the DNA Day sale early.

Monday April 11, 2011, they are selling the kits for FREE with a $9/month 1 year commitment. So basically a total of $108. This is compared to $199 + $9/month (=$307) regular price. It's even less than the Christmas sale (assuming you cancel subscription after a year).почему одинаковые на внешний вид дома имеют разную цену?

The sale is on midnight Pacific time tonight (3am Eastern time or 7am GMT) and will end April 11 11:59pm Pacific time (2:59am Eastern time or 6:59am GMT April 12).

Spread the word and get people to participate in our Harappa Project too.

End of March Update

I have a total of 67 participants in the project right now who have sent me their raw data. This is not counting those who have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.http://polvam.ru

The following groups are represented:

I need to post analyses of Tamils, Bengalis and Punjabis soon.

My Genetic Journey II

While my computer's busy running K=12 admixture on batch 7, K=17 admixture on batch 1, some MClust experiments and converting 1000genomes data from vcf to ped and I am reeling from the pollen count (3,939 yesterday), here are some links to my personal genetics blogging.

For the record, my daughter complains about all the "Trantor windows" open on the computer all the time. She calls the terminal windows "Trantor" because of the shell prompt. My desktop is named Trantor. Now who can guess what my laptop, my other desktop and my wireless network are named?

Another Update

I have a total of 51 participants in the project right now who have sent me their raw data. This is not counting three people who have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.

The following groups are represented:

  • Punjab: 7
  • Iran: 7
  • Tamil: 6
  • Bengal: 5
  • Andhra Pradesh: 2
  • Bihar: 2
  • Karnataka: 2
  • Caribbean Indian: 2
  • Kashmir: 2
  • Uttar Pradesh: 2
  • Sri Lankan: 2
  • Kerala: 2
  • Iraqi Arab: 2
  • Anglo-Indian: 1
  • Roma: 1
  • Goa: 1
  • Rajasthan: 1
  • Baloch: 1
  • Unknown: 1
  • Egyptian/Iraqi Jew: 1
  • Maharashtra: 1

I haven't received data from any new participants for more than a week which is the longest lull since I started Harappa Ancestry Project. So go out there and get people to send me their 23andme raw data.

Also, does anyone know if there are a significant number of South Asians who have done FamilyTreeDNA's Family Finder test? Is there a good overlap of SNPs between their test and 23andme's?

We have enough Punjabis, Iranians, Tamil and Bengalis that they deserve separate analysis posts.

Your Genes, Regulated?

The FDA had a meeting the last two days:

FDA is convening this two-day meeting to seek the Panel’s expert opinion and input on scientific issues concerning Direct to Consumer (DTC) genetic tests that make medical claims.

This meeting is focused specifically on issues regarding clinical genetic tests that are marketed directly to consumers (DTC clinical genetic tests), where a consumer can order tests and receive test results without the involvement of a clinician.

The American Medical Association of course wants to limit genetic testing so that you would need a doctor to supervise everything.

We urge the Panel to offer clear findings and recommendations that genetic testing, except under the most limited circumstances, should be carried out under the personal supervision of a qualified health care professional, and provide individuals interested in obtaining genetic testing access to qualified health care professionals for further information.

23andme had two presentations at the meeting which they have posted on their blog.

In our presentations, we take the position that all genetic testing services, whether ordered by a physician or offered through direct access, should adhere to the same standards. We simultaneously request that the FDA consider redefining and establishing regulatory standards, including some fundamental definitions, to accommodate large-scale genetic testing and support innovation of its technologies and applications. We also request that regulation be based upon evidence and not fear of potential harm to individuals which, to date, has not been demonstrated. In fact, growing numbers of participating individuals and independent studies focused on this issue provide preliminary evidence that the vast majority of people understand the information presented and experience no significant negative effects.

Genomics Law Report had an overview of the issues beforehand as well as a Twitter roundup of the meeting. Here are his thoughts after the first day:

First and foremost, I fully expect the MCGP (Molecular and Clinical Genetics Panel) to note, likely more than once, that given the complexity of the questions put to it by the FDA it should be afforded far more time to deliberate and research prior to making any recommendations.

If taking time out for further debate isn’t an option, what is the MCGP likely to recommend? Based on today’s deliberations, I think it’s a safe bet that the MCGP will advise the FDA to (1) demand clear proof of analytical and clinical validity for all genetic tests and (2) require that most, or perhaps even all, genetic tests with demonstrated or potential clinical significance be (to use the FDA’s terminology) “routed through a clinician.”

In other words, I think the odds strongly favor an MCGP recommendation to the FDA that clinical (as defined by the FDA, which is itself a separate issue) direct-to-consumer genetic testing, when offered without a requirement that a clinician participate in the ordering, receipt and interpretation of the test, be removed from the marketplace. At least for the time being.

If you read my blog, you probably know my politics. I do however think that any regulations have to be shown to have actual tangible benefit and prevention of harm. Simple misinterpretation of genetic results by a regular joe causing hypothetical harm is not enough justification.

So what can you do? Razib Khan is already on the task.

1) I am going to release my own 23andMe sequence into the public domain soon. I encourage everyone to download it. I would rather have someone off the street know my own genetic information than be made invisible by the government. That is my right. For now that right is not barred by law. I will exercise it.

2) Spread word of this video via social networking websites and twitter. The media needs to get the word out, but they only will if they know you care. Do you care? I hope you do. This is a power grab, this is not about safety or ethics. If it was, I assume that the “interpretative services” would be provided for free. I doubt they will be.

3) Contact your local representative in congress. I’ve never done this myself, but am going to draft a quick note. They need to be aware that people care, that this isn’t just a minor regulatory issue.

4) The online community needs to get organized. We’re not as powerful as a million doctors and a Leviathan government, but we have right on our side. They’re trying to take from us what is ours.

5) Plan B’s. We need to prepare for the worst. Which nations have the least onerous regulatory regimes? Is genomic tourism going to be necessary? How about DIYgenomics? The cost of the technology to genotype and sequence is going to crash. I know that the Los Angeles DIYbio group has a cheap cast-off sequencer. For those who can’t afford to go abroad soon we’ll be able to get access to our information in our homes. Let’s prepare for that day.

Here are the links to contact your House Representative and your Senators.

Project Update

I have a total of 42 participants in the project right now who have sent me their raw data. This is not counting two people who have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.

The following groups are represented:

  • Punjab: 7
  • Iran: 6
  • Tamil: 5
  • Andhra Pradesh: 2
  • Bengal: 2
  • Bihar: 2
  • Karnataka: 2
  • Caribbean Indian: 2
  • Kashmir: 2
  • Anglo-Indian: 1
  • Roma: 1
  • Goa: 1
  • Uttar Pradesh: 1
  • Sri Lankan: 1
  • Rajasthan: 1
  • Kerala: 1
  • Baloch: 1
  • Unknown: 1

The unknown is Manu Sporny who has put his genetic data in the public domain and I have drafted him into our project.

In addition, out of curiosity, I have accepted data from the following:

  • Iraqi Arab: 2
  • Egyptian/Iraqi Jew: 1

I know a bunch of you have done a lot to make this project known and gotten people to submit their data. But we really do need more participants of every ethnicity and geographic region in and around South Asia. So keep on!

I am working on K=12 admixture runs for the batches we have already done. In addition, the reference I dataset will be used for even higher values of K admixture components to see where the limit is.

Also, I am looking into doing chromosome by chromosome admixture (and other analysis). I have done some experimental runs and once I have pored over that data, I'll have something to report.

As we have seen, even with the removal of the San and Pygmy, the Africans take up 3 ancestral components and most South Asians (excepting me of course) do not have any African admixture. So I am working on a reference dataset without any Africans. I have my own take on how to do that which I'll share in the next few days.

In short, my home computer is running admixture, plink, eigensoft, etc. 24x7.

My Genetic Journey

It all started DNA Day 2010 when Razib tweeted about a $99 sale for the DNA test at 23andme. I ordered one immediately. Over the next few months, a lot of my free time was spent poring over and analyzing my genomic results.

While the health and physical traits information was interesting, I found the ancestry information that can be deduced from your genome to be fascinating. That might be because I was working on collecting together and digitizing our family tree at the time.

So to beat Razib's record of of writing about his personal genome, I have started blogging about mine:

There's much more to come, including: What's wrong with my chromosome 9 and who did I get it from?; my results from Doug McDonald, Dodecad and Eurogenes; why do I have low similarity scores with everyone?; where exactly was my great-grandmother from?; and more.

PS. Since it's Valentine's Day, I should probably mention that my top match among the people (excluding my sibling of course) I am sharing genomes with on 23andme is my dear wife, Amber.

Latest on Participants

I have a total of 31 participants in the project right now who have sent me their raw data. The following groups are represented:

  • Punjab: 7
  • Tamil: 4
  • Iran: 4
  • Andhra Pradesh: 2
  • Bengal: 2
  • Bihar: 2
  • Karnataka: 2
  • Caribbean Indian: 2
  • Anglo-Indian: 1
  • Roma: 1
  • Kashmir: 1
  • Goa: 1
  • Uttar Pradesh: 1
  • Sri Lankan: 1

Keep them coming!

I am going to get some admixture analysis on the second batch (HRP0011 to HRP0020) done this week.