Wednesday, March 05, 2014

Genetic mixture in the USA

An interesting post at the 23andMe blog:

March 4, 2014
Published by ScottH under 23andMe Research, Ancestry

Scientists have long used DNA to inform our understanding of big epochs of human change and migration. But what about the smaller changes, can DNA tell us something about recent human history? diversity photo

23andMe researcher Katarzyna “Kasia” Bryc, who is also a postdoctoral research fellow in David Reich’s lab at Harvard Medical School, gathered anonymous aggregated data from our customers to look at the mix of African, European and Native American ancestry in the United States. What she discovered was an illuminating genetic portrait of the U.S. that both confirms some of what we know about America’s social history but also other things that are surprising and new.

“Perhaps one of the greatest discoveries stemming from recent advancements in genetic genealogy is that previously held assumptions about race and identity are being brought into question,” Harvard Professor Henry Louis “Skip” Gates Jr. wrote recently. “It was always known throughout American history that there was at least some intermixing of races, but only now, through DNA testing, can we see the extent to which this actually occurred.”

Continued here.

Saturday, March 01, 2014

Looking at Countries of Ancestry (formerly Ancestry Finder) at 23andMe

23andMe has a survey, Where Are You From? that asks people who test where their four grandparents were born. If you take it and agree to let people who match you know the information, the results are placed in the Ancestry Finder database.  The pictures below show the results of looking at my Ancestry Finder matches without and with colonial (USA, Canada, Australia, New Zealand) matches included.

Chromosomes 1 through 22 and the X chromosome are shown. In the application you can select the number of grandparents who must be from the same country and the size of the match in centiMorgans (cM). You can also mouse over a match and see where their grandparents are from, the length of the match, and, if a public match, the name of the person.  Other data can be downloaded in a spreadsheet format for further examination.

The default view is of all 4 grandparents from the same country and a match of at least 7 cM in size and no Colonials.

The first picture below shows the results of looking at my matches with the grandparents matching or non-matching and the size set to the smallest length of 5cM or larger with no colonial matches. You can see that some chromosomes have greater coverage than others. Chromosomes 14, 21, and 22 have no matches. The large gold match on chromosome 1 is with someone with all four grandparents born in Norway.

The second picture has the same parameters but it includes Anglo-American Colonial countries.

Steven C Perkins' Ancestry Finder matches, 1gp, 5cM+, no Colonials
Steven C Perkins' Ancestry Finder matches, 1gp, 5cM+, with Colonials

Debbie Cruwys Kennett on The Big Y results

Posted today by Debbie Cruwys Kennett is an analysis of early results from the Big Y test at Family Tree DNA (FTDNA):

Big Y results starting to come out at FTDNA

At the FTDNA Administrators Conference FTDNA announced the Big Y test. This test sequences the Y Chromosome and returns millions of results. As others have written, it will greatly increase the definition of the Y Tree. Results were expected in December 2013, then a series of delays occured and 28 Feb was announced as the release date. As it happened, only 100 results were released on 28 Feb. Other results will be released over the next month. This has caused a number of people to complain that FTDNA has been cavalier in it's treatment of customers with unrealistic release dates. Today FTDNA sent out the following email:

Dear Valued Customer,

Yesterday, February 27th, we began releasing results for the Big Y orders. We have received some incredibly positive feedback and this is much appreciated.

We are also hearing the frustrations from those who have not yet received their results, and we would like to address the matter publicly in the form of a sincere apology. The entire FTDNA team has been working very hard over the last few months with high determination and many late nights. Launching a new product is always a challenge with many moving parts, some more predictable than others. Unfortunately we ran into some surprises beyond our control when one of our suppliers ran out of certain reagents we needed for running the Big Y product. However we recognize that it is our responsibility and duty to meet our deadlines and keep our customers informed when problems arise.

With the Big Y launch, we failed to properly manage the expectations of our customers. This was an honest oversight, in which we internally had a target to release first results in February, but we didn’t pay close attention to the dates being communicated on the status pages for those orders. Big Y was a new product and the status entries were updated automatically. We should have manually adjusted these dates earlier on as needed. So while we were thrilled to release the first results in February, we failed to realize that everyone expected results this week. I personally take responsibility for this miscommunication and mishap with the website delivery dates and hope you accept my sincere apologies.

I am well aware that as a company we have a bit of a history in missing deadlines. A big contributor to that is that we have typically been very ambitious in taking on difficult projects while still wanting to deliver information quickly to customers. The Big Y product is a great example. It was a cutting-edge project that pushed us deep into next-generation sequencing and advanced data analysis. Our ambitious, risk-taking attitude has won many of you over and delivered incredible thought leadership and leading products over the years. Unfortunately, our poor estimates and turnaround time expectations have frustrated many of you along the way as well. We are committed to continuing to be the company that is willing to push the envelope and take risks to bring you the best in genetic genealogy, but moving forward we will strive to be more careful in setting accurate time expectations.

Again, we are sincerely sorry for any frustration we caused with the delays and miscommunication of turnaround time. We are very proud of our achievements with the Big Y and feel confident about the high quality product we are delivering! We hope you will let the wonderful product we produced make up for delays that were needed to refine it! We have updated expected results dates on customer pages and will work around the clock to beat them.


Nir Leibovich
Chief Business Officer
Gene by Gene Ltd.

Thanks to Tim Jansen, M.D. for the notice.