Archive | August 2021

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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