Last week, I shared a process for calculating the DNA that I inherited from my grandmother Fern Laurine Stoddard (1929-2020). In that case, I was fortunate in that Fern performed DNA testing before her death, but what about cases where one of your grandparents is already deceased? For me, determining how much DNA I inherited from Grandpa Woodbury took some additional work.
In another post, I shared some of my memories of my Grandpa Frank Alan Woodbury (1923-2001). He died when I was still quite young, even before I had taken an interest in genetic genealogy. While he did perform DNA testing for family history prior to his death as part of the Sorenson Molecular Genealogy Foundation database, he died before the advent of autosomal DNA testing. How can I figure out the amount of DNA I inherited from him? Again, this process may not be useful from a genealogical standpoint, but I do find it interesting to determine how much of my DNA came from specific grandparents.
Fortunately, in cases where one grandparent has tested, it is fairly straightforward to determine the amount of DNA inherited from the other grandparent on the same side. Each of us inherits 50% of our autosomal DNA from our parents: one set of 22 chromosomes from mom and one set of similar chromosomes from dad. Beyond that, the amounts of DNA we inherit from more distant ancestors are more variable. As a result of recombination, we inherit increasingly smaller amounts of DNA on increasingly smaller chunks or segments from our more distant ancestors. At any given site in our DNA, we inherit DNA from just two grandparents: a paternal grandparent who contributed DNA to our paternal chromosome and a maternal grandparent who contributed to a corresponding maternal chromosome. Those same two sites of DNA were inherited from just two great-grandparents: a paternal great grandparent who passed it on to your paternal grandparent who passed the DNA on to you and a maternal great grandparent who passed DNA on to your maternal grandparent who passed it on to you. The same is true for more distant generations of ancestry. At any given site, you inherit DNA from just two individuals in a generational level: one paternal and one maternal. Since we inherit autosomal DNA from just two paternal grandparents and two maternal grandparents, by process of elimination any DNA we do not share with a tested grandparent has to have come from the other untested grandparent.
It is important to note that without testing Frank, we cannot be absolutely certain that I actually biologically descend from Frank without additional DNA analysis. In my case, my Y-DNA test results connect to members of the Woodbury family. My autosomal DNA matches also include my aunts, uncles, great aunts, and more distant matches who are related through Frank’s ancestry and those individuals share appropriate amounts of DNA with me given their proposed relationships. Before assuming that the DNA you do not share with a tested grandparent came from your untested grandparent, make sure that there is genetic evidence supporting your relationship to your untested grandparent to guard against the possibility of misattributed parentage.
It might be tempting to say that since I inherited 27.4% of my DNA from Fern Stoddard, I must have inherited 22.6% of my DNA from Frank Alan Woodbury, Fern’s husband. Afterall, I get 50% from each parent. However, it is not quite that straightforward. The percentage previously calculated for Fern takes into account my entire genome (not just my autosomal DNA). As we found last week, biological males actually have fewer base pairs than women because the Y-chromosome is smaller. As a result, even though I get 50% of my autosomal DNA from my father, my paternally inherited DNA only accounts for about 49% of my entire genome. Also, there are some regions of autosomal DNA that are not tested at the various testing companies. In particular, large sections of chromosomes 13, 14, 15, 21 and 22 are not tested. Since these regions are not tested, we cannot assign them to either grandparent. Finally, there are some segments of DNA that cannot be assigned to a particular grandparent because they are too small to determine if they are a valid segment. Did I really inherit them from Grandpa, or were they not assigned to Grandma because they were too small, because there was a no call or because there was a matching error? In order to determine the percentage of DNA I inherited from Frank, I will have to do a little more work.
First, I have to find out which regions of DNA are actually tested as part of genetic genealogy tests. This can be done by downloading raw data from the test results and looking at the first and last marker tested on each chromosome. Next, I assign the tested regions I do not share with Fern to my grandfather Frank. This assignment assumes that my grandparents are not closely related or from the same endogamous population. In my case, this is true, but this is not necessarily the case for all individuals. After assigning segments, I analyze the results to see if there are any very small segments that are unreliable, and I remove those. Finally, I calculate the total number of basepairs that can be assigned to my grandfather and divide that by the total number of basepairs in my genome.
The following table describes the ranges of tested markers for each chromosome at Family Tree DNA in build 37:
|Chromosome||Start||Stop||Length (bps)||Untested Basepairs|
From this, we see that approximately 93 million basepairs, or about 3% of the genome is not even tested at Family Tree DNA. The testing coverage for other genetic genealogy testing companies is similar. If we assume that the tested DNA I do not share with my grandmother came from my grandfather, then we are a few steps closer to determining how much DNA I inherited from him.
Genetic genealogy tests do not analyze every DNA marker in your genome. Most humans share 99.9% of their DNA with all other humans, so instead of analyzing all the markers that most people share in common, genetic genealogy autosomal DNA tests analyze just those markers where there is known to be significant variation in the population. These markers known as single nucleotide polymorphisms (SNPs) are hotspots for variation. Major genetic genealogy testing companies test anywhere between 500,000 and 700,000 SNPs depending on the company and depending on the test version. When two individuals share identical values on a long stretch of consecutive markers, then it is assumed that they also share the other markers in between which are more typically shared in common between most members of the human species. In order for one of these segments to be considered valid and most likely due to recent common ancestry, individuals must share a large number of consecutive markers. Genetic genealogy testing companies commonly use thresholds of 5 centimorgans and 500 consecutive SNPs to identify shared segments likely due to recent common ancestry.
Sometimes, the values of SNPs that are usually read as part of a DNA test cannot be determined and instead no-calls are issued. Other times (and infrequently), the incorrect value might be assigned to a particular marker. When this happens, this can cause “breaks” in a segment of shared DNA when in reality it is most likely that two individuals in fact share DNA spanning the break. These small blips should not be assigned to an untested grandparent from the same side of the family. In other cases, a segment of DNA shared with the tested grandparent might be so small that it is unclear whether that DNA came from the tested grandparent or from the other untested grandparent. It can be difficult to determine the centimorgan values for segments assigned to an untested grandparent by process of elimination. Instead, I consider any segments smaller than 4 million basepairs in length and any segments containing fewer than 500 tested markers to be suspect. To find the number of tested markers in a particular region I consult my raw data download for the corresponding regions. If any of the segments I assigned to Frank are less than 4 million basepairs in length or are composed of fewer than 500 tested SNPs, I exclude them from my analysis.
After excluding these small segments, we are left with long stretches of DNA that most likely came from Frank. By subtracting the start points from the end points and adding the resulting values together we can determine a number of basepairs of autosomal DNA we are fairly confident came from Frank. Remember that I also got my Y-chromosome from Frank. I add the total length of the Y-chromosome to the number of basepairs assigned to Frank by inference and divide the resulting number by my total shared DNA. The result: I inherited about 27.4% of my DNA from Fern Laurine Stoddard, I inherited 20.1% of my DNA from Frank Alan Woodbury, and about 1.6% of my DNA is paternal DNA that cannot be assigned to either grandparent.
In this case, I was fortunate to have tested my grandmother before her death. However, even if testing a living grandparent is not an option for you, don’t get discouraged quite yet. It may still be possible to estimate how much DNA you inherited from your grandparents through visual phasing. We will explore that approach in a future post.