Wednesday, January 26, 2011

23andMe Relative Finder Update

The latest sale at 23andMe appears to have breathed new life into Relative Finder. This morning I have 30 new predicted relatives in my Relative Finder, my sister has 35 and my niece has 42!  In the seven accounts that I handle each has at least 15 new relatives and most of them have close to 30. Many of the new matches are shared between us, but there are at least 100 unique new individuals. My mother even has three new predicted 3rd cousins! Let's hope these new recruits are interested in genealogy!
(It looks promising so far since I have already received a number of acceptances from my sharing invitations.)

Tuesday, January 25, 2011

A comparison of my 23andMe mtDNA v3 and v2 results

There are 13 false positive SNPs that are being found in practically everyone's v3 mtDNA results. No doubt, 23andMe will soon remove them as they are aware of the problem. This post will ignore those since they are clearly in error.

As I mentioned yesterday, my reported mtDNA subclade did not changed in my v3 results and is correct - U5b1b2. According to an analysis done by Dr. Ann Turner of my mtDNA data, there are 795 new SNPs in my v3 results, of which 99 are no-calls for me. I had 28 no-calls out of 2133 SNPs in v2 of the chip. 21 of those had calls in v3. The higher rate of no calls on the v3 versus the v2 is because many of the news SNPs are experimental. If it becomes evident that people are getting no-calls for the same SNPs, the list may be pruned by 23andMe to eliminate them.

All SNPs where calls were made in both chips gave identical results.

I have one miscall 16192C, where I have a mutation 16192T. This also occurred in v2 of the chip (and also in my cousin).  According to Dr. Turner, "It is probably due to the fact that it is very close to the poly-C region surrounding 16189. The probes just don't work well in repetitive regions like that. (Side note: 16189C is a very common mutation, so Mother Nature has a bit of a problem there, too!)."

Here is a list of my CRS values:

16184 C
16185 C
16186 C
16187 C
16188 C
16189 T
16190 C
16191 C
16192 C
16193 C

Thank you to Dr. Turner for her generous time and efforts to help all of us to better understand our mtDNA and 23andMe results.

To read more about my mtDNA tests, you can see my post about my Full Mitochondrial Sequence (FMS) test from FTDNA here.

Update on 23andMe's v3 results: Relative Finder comparison and ~30,000 v2 locations missing from v3

This will not be a scientific analysis, but, rather a preliminary summary of what I have found so far in my new 23andMe v3 results. My v3 Relative Finder matches loaded this morning and I have done a quick comparison to my v2 Relative Finder. There are some minor changes, but nothing that appears to be too significant.

(all are predicted)                         v3        vs       v2
3rd Cousins                                          4                     4
4th Cousins                                        38                   40
5th Cousins                                       262                 258
Distant                                                 33                   32
Public Match - 4th Cousins               3                     3
Public Match- 5th Cousins               10                   13

% DNA shared 
mother                                           50.00              50.42
sister                                               53.10              53.69
paternal uncle                               21.10              21.14
maternal aunt                                22.61              22.77
niece                                                24.31              24.49
1st cousin                                        11.45              11.36
1st cousin                                        11.95              11.94
1st cousin                                         8.38                8.37
1st cousin once removed               3.12                3.12
1st cousin twice removed              1.42                1.42
2nd cousin                                        1.15                1.15

Upon a brief initial review, predicted cousins lower than this appear to overwhelmingly share the same percentage as before.

Jim McMillan, who runs the independent "Cousins" matching project, compared my raw v2 data file to my raw v3 data file and this was his conclusion,

"There are at least 30,346 locations that are in v2 that are not included in v3.  So when a v2 is compared to a v3 there are going to be some longer half-identical segments that might not be there when comparing a v2 to a v2."

He also posted on his project thread on the 23andMe Forum:

"I have received v3 results from a contributor who also contributed v2 results. About 30,000 locations that appeared in v2 are missing from v3. Thus, when a v2 data set is compared with a v3 data set, it would be expected that the half-identical segments would be a little longer, and more segments meeting a 5cM and 700 SNP threshold found. All my software tolerates different numbers of SNPs. Where no SNP is found, it is deemed the SNPs would be at least half identical. On first blush, the missing SNPs do not appear to be evenly distributed among chromosomes 1-X.

In Chromosomes 1-x there are 30337 locations missing, and in Y 250, and in MT 172.

I have uploaded to the locations in v2 that are missing in v3. See the details in the zipped spreadsheet at"

I just received a Twitter message from 23andMe that the v2 SNPs were not removed intentionally. It explained (with some humor), "...some faction always falls out during chip manufacturing process. Biology is messy."

As I mentioned on my blog last night, my Ancestry Painting is still 100% European. However, from a review of the forums, the Ancestry Painting algorithm seems to be much improved for many.

Some customers are seeing improved updates to their haplogroup assignments, however there seems to be a problem with errors in the mtDNA mutations being reported from the new v.3 raw data.  They differ from the FMS results that some of us have received from FTDNA. I will post more information on this as it becomes available.

I am still working on getting details on the new SNPs. Hopefully 23andMe or one of the independent project admins will soon comment on the hundreds of thousands of new SNPs, since that is the most significant change and on what we should be focusing. I hear there is a Spittoon Blog Post on the way. More to come...

Monday, January 24, 2011

Update: 23andMe's New v3 Chip Results Are In

Today there is a lot of excitement in the personal genomics community because 23andMe's eagerly awaited v3 results are finally coming in. The customers receiving their results today are ones who bought their kits near the beginning of the last holiday sale. Making it even more exciting is that, according to 23andMe, they are loading thousands of data sets today in this first round. Apparently, they had a very good response to the last sale. This is very good news for customers who are interested in the ancestry aspects of their genetic scans. Judging from this, over the next month, the number of potential "cousins" should jump substantially from the approximately 60,000 records already in their database.

So far, my health results, Ancestry Painting and U5b1b2 mtDNA haplogroup assignment look identical to my v2 results. I am still waiting for my Relative Finder and Ancestry Finder to load. However, I am hearing that some customers have revised and, apparently, improved Ancestry Paintings as well as updated haplogroup assignments.

Giving a little insight into what changes we can expect, Michelle K from 23andMe posted this in the 23andMe Forums on January 19th:

"The first batch of v3 results will become available by the end of this week. Please note that v2 data will not be overwritten by v3 data, rather the two will be merged into one data file. Here are some changes you can expect to see:

RelFinder and Family Inheritance: The Relative Finder algorithm has been updated. Customers who upgrade to v3 may notice small changes to their percentages DNA shared or segment locations in Family Inheritance. Existing, not-yet-upgraded customers may also see small changes to their results as their relatives upgrade.

Ancestry Painting: The Ancestry Painting algorithm has been updated. Upgrading customers may notice small changes to their percentages. Existing, not-yet-upgraded customers will not be affected.

Haplogroups: Upgraded v3 customers may see a slight change in their haplogroup due to updated haplogroup trees and v3 compatibility. The change, if any, should be very minor -- only affecting resolution and not affecting major group assignments. All other existing customers will have their haplogroups recomputed on the new trees later this year. This means, for example, if a child is analyzed on v3 and their parent is on v2, they may have different haplogroup assignments.
Raw data: Upgraded v3 customers may have data for v2 SNPs they previously had no-calls for, if the SNP is on v3 and it yielded data. A complete list of v3 SNPs is expected to be available in the Mendel example profiles by mid-February."

I will be posting all week with updates about the new v3 results, so stay tuned...