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Tracking down a BRCA2 mutation

Aug30

I suddenly realized that I could find the people who match my late husband Steven M Cooper on his mutated section of the BRCA2 gene at the various DNA testing sites that show chromosome information. His particular BRCA2 mutation, implicated in breast cancer and melanoma, likely contributed to the fatal outcome of his prostate cancer. A problem with doing this is that none of his tested family members match that gene, so there would be no way to know if his matches had his bad maternal BRCA2 or his good paternal one.

image of Amalie LILIEN Tieger

Amalie LILIEN Tieger

So should I contact those many people and warn them? I had previously alerted his known LILIEN side cousins to this issue and already a second cousin once removed on his LILIEN line discovered her breast cancer early due to my warning. However I may be sending a false alarm to many. I decided it was something I should do. My family history investigations left me confident that Steve’s mutation came from one of the the parents of his grandmother Amalie LILIEN Tieger (jewish) born in Kalusz, Ukraine. Of course, it may well have originated further back.

First I had to locate the mutation in a numbering system that would translate to what we get from our DNA testing companies. From various google searches I learned that BRCA2 is located on chromosone 13. Looking at the report from Color Genomics, the test his oncologist ordered, I could see the location was a deletion at base pairs 32,913,602_32,913,605. More googling found that this is not the common Jewish BRCA2 mutation. That explains why his initial 23andme test years ago did not find it. Next I found the actual National Health Institute fact sheet for his mutation (click here) which had a click point to the diagram below. Click here for the cancer.gov discussion of BRCA2

Image and details of the problem mutation from the NIH web site

Image and details of the problem mutation from the NIH web site

Now to find the people who match him on that segment. I downloaded the full list of his matches with segment information from each site. The easiest site to use was GEDmatch because I could use the segment search function to get just the matches to his BRCA2 section of chromsome 13. At the other sites I had to get the full list of all matching segments and then sort by chromosome and start point to find the matching people.

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How to find your haplogroup and why do that?

Aug18

Haplogroups fascinate me because they reveal our deepest ancestry. A haplogroup is a way of assigning a portion of your DNA to a category based on areas of very slowly changing markers. There are two types of DNA that can be assigned haplogroups, because they do not recombine therefore change only slowly via mutations. These are the Y chromosome and the DNA of your mitochondria (mtDNA), which are separate organisms in every cell that provide us with energy and are passed along via a mother’s egg. The groupings for their haplogroups look like family trees when charted, for example the one shown below from Eupedia. That is because each mutation creates a new branch. There are haplogroups assigned for both the all female line (mtDNA) and the all male line (Y). Click here for Eupedia’s wonderful descriptions of all the haplogroups found in Europe.

The female H haplogroup from Eupedia.com on haplogroups

Men have a Y chromosome, which makes them male, which has been passed from father to son, to his son, to his son, and so forth from from time immemorial. We all have mitochondrial DNA (mtDNA ) which is passed from a mother to all her children unchanged. Thus your mtDNA is from your mother’s mother ‘s mother and so on. Both of those parts of DNA inheritance can be traced back to the dawn of humanity. That is unlike the other chromosomes which mix the inheritance from each parent such that after several generations there may be little or no trace of our deeper ancestors. Most of us have no verifiable autosomal DNA from before our 5th grandparents.

Those of you who have family legends about descent from an Indian princess might be able to prove the connection using mtDNA if there is a direct female line to that ancestor, since there are specific haplogroups for Native Americans (click here for the wikipedia article on that).

My Ancestral Haplogroups displayed in Paul Hawthorne’s colorful genealogy chart

One thing that I like to do is figure out the haplogroups of my recent ancestors by testing cousins in the needed line of descent. I made a chart of the ones I know using Paul Hawthorne’s colorful genealogy chart (click here for more about that) with the haplogroups added. As you can see, I have many more lines to chase down. Sadly my Thannhauser Bavarian Jewish line daughtered out, so I am trying to find a male descendant of the one who moved to Albany NY in the mid 1800s.

So how do you find your haplogroup from your DNA test? Well if you tested at 23andme or Living DNA then you will be provided with your high level haplogroup. However if you want to drill down the branches, then test your Y and/or your mtDNA at Family Tree DNA (summer sale until end of August). Ancestry tests enough SNPs to get a high level haplogroup by using other tools on your raw data. My Why Y blog post explains how to use the Morley tool but there is also a tool to find Y haplogroups from Borland Genetics. I have been trying to convince Kevin Borland to write one for mtDNA since the James Lick mthap tool will not currently take ancestry data.

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A Sperm Donor is Found with DNA

Jul15

The DNA results are in and they confirm that we have found the sperm donor, my late husband’s second cousin once removed. This cousin now has 8 children instead of none. Back then, donors were promised anonymity, but DNA testing has changed that; if their close family or cousins have done DNA testing, then it is likely that they can be identified. Continue reading →

Interesting New DNA Features at Ancestry

Jul6

Do you know that Christa Cowan, Ancestry’s Barefoot Genealogist, posts Youtube videos every month describing new features? The changes that a number of readers have asked about were described in her June video. First of all there are some new DNA communities so go have a look at your ethnicity breakdown. These are based on some of the other 20 million DNA testers and their trees on the Ancestry site.

The other new item of interest is a change to the match list page. You are now asked if you know who your matches are. Some long-time users find this annoying, but it gives you a nice way to separate paternal and maternal matches when your parents are not both tested. It also lets you specify a specific relationship which is then listed for that person. Christa describes that feature about ten minutes into her June “What’s New at Ancestry” video below.

Those of us with German ancestry are excited by the new breakdown of those communities. Click here for Ancestry’s blog post about German DNA. My maternal grandmother was born in Munich to Bavarian Catholic parents. Apparently my brother got more of her DNA than I did, since I have much more from our Jewish maternal grandad: 34% as compared to Shipley’s 27% plus I get a Jewish community and he does not. By the way his Ashkenazi used to be only 22% and that is close to what both 23andme and MyHeritage find. To further investigate this, we convinced a Catholic half second cousin in Germany to do a DNA test. This was additional confirmation of our uneven maternal DNA inheritance, click here for that post.

This is the image of my brother’s latest ethnicity results which now include “Central and Southwest Germany” so perhaps Bavaria – red arrows are my addition. By the way, clicking on a community will not only tell you more about that history but will show you those matches who share it.

New ethnicities for my brother

Our father was 100% Norwegian in descent so my brother’s extra 10% Norwegian must be German. My Norwegian has now risen to 49% which pleases me. That plus the 1% Finnish are presumably from my dad.

Many users are starting to see the question “Do you recognize them? “ next to matches on their DNA relatives list with a Yes button and a Learn More button underneath.
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A Nice New Feature at DNApainter.com

Jun28

One tool I use all the time at the DNApainter site is the online shared cM calculator. This shows you the possible relationships that you have to a DNA match based on either the shared centimorgans (cM) or the percentage of DNA shared. It uses both the calculated odds from the DNA geek and the observed odds from Blaine Bettinger’s shared cM project. I find that these are far more useful than the predictions at the various testing companies.

Results of the online calculator for cousin “C’ sharing 1158 cM, red arrow points to new feature

When you input a number in the box at the top under the word Filter, you get a display like the one above which shows the likelihood of various relationships. Additionally those possibilities have their boxes light up in the chart underneath (click the image for the larger version which shows that). I used the 1158 cM that my first cousin “C” shares with me, on the high end for that relationship, to see what would show.

Do you see my red arrow pointing to the new feature? When you click on the words View these relationships in a tree you get a diagram like the one below, showing possible places for you in the tree of your match. Quick tip, right click those words to get a little menu from your browser letting you open it in a new tab or window. This diagram is created by the WATO (What Are The Odds) tool.

WATO image for C

WATO for cousin “C” showing the menu for editing her in the tree (click for larger version)

One thing that takes getting used to for many of us genealogists, is that WATO uses a backwards pedigree format, a sideways descendant tree. The presumed common ancestor is on the left and the descendants fan out on the right. Every person in this diagram can be edited by the way. You can add names, birth years, whether they are half relationships, and so on.

Most people like visual displays of relationships so it is great to see the possibilities laid out in a family tree. Click the Continue Reading below for my experiments with some of my known cousins. However you may prefer to read about the details of this new tool by its author, Jonny Perl, on his blog (click here) – he does a great job of explaining it.

Also to learn more about WATO, click here for the Family History Fanatics youtube video or click here for Leah Larkin’s many more advanced articles on WATO.

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