(Continued from Part 6)
In Part 1 I mentioned that Bridget* hoped to find an older maternal brother who had also been given up for adoption.
In AUGUST 2018 Bridget* matched him after his children bought him a 23andMe kit for his 68th birthday, and they are now happily reunited.
*This is a true story. I have permission to blog about the people who asked me for help but have not used their real names for the sake of their privacy. I have tried to limit my writing here to information pertinent to their DNA searches, but have shared other fascinating details I found with them in tree format.
Monday, November 1, 2021
Wednesday, July 31, 2019
Interpreting GEDmatch AYPR results
If a child inherits the same allele from both parents at the exact same location, on both the paternal chromosome and the maternal chromosome, they are said to be homozygous at that location. When parents are biologically related they can share strings of alleles inherited from common ancestors, and they can both pass on the shared string or part thereof to a child. These homozygous segments are known as runs of homozygosity (ROH) and GEDmatch has a handy tool to calculate the extent of such segments in our DNA. This can be helpful when you don’t know who one or both of your biological parents are, as a) having related parents makes sorting DNA matches into genetic networks and predicting relationships to DNA matches harder so it is best to be forewarned, and b) it gives you useful information if you already know who one parent is.
The meaning of total shared segments reported by the GEDmatch Are Your Parents Related? (AYPR) tool is not obvious. Some genetic genealogists have pointed out that multiplying the total by a factor of four approximates the amount of DNA shared by the child’s parents, from which we can infer some possible relationships between unknown parents (see Homozygosity on the ISOGG Wiki for blog links). I wanted to try explain why, to myself and others.
The first column of figures in the table below will be familiar to genetic genealogists used to working with autosomal DNA statistics associated with the theoretical coefficient of relationship for different relationships (A). The last column of figures containing theoretical total homozygous autosomal segments of the child (H) is based on the theoretical coefficient of inbreeding for different relationships (half the relationship coefficient). I have tried to keep this explanation as simple as possible, assuming an otherwise outbred ancestry. I have listed my scientific sources at the end for those who want to know more about the underlying theory based on Mendelian genetics.
In the table, L is shorthand for the total length of the 22 autosomes in centiMorgans (cM). Because we have two of each chromosome, shared DNA percentages apply to double that length i.e. 2L. The theoretical proportion of a child’s autosomal genome length (L) that will be homozygous is the child’s inbreeding coefficient. We can convert these percentages to cM using the appropriate factor, 2L or L. The GEDmatch AYPR result corresponds to the figures in the last column (H).
Half-siblings M and F share 50% x L (25% x 2L)
ROH segments of their child = 50% x 25% x L = 12.5% x L
In the parent/child or full siblings scenarios, the parents share 100% x L (50% x 2L)
ROH segments of their child = 100% x 25% x L = 25% x L
The autosomal DNA shared by the child’s parents can be approximated as 4 x the child’s total homozygous segments reported by GEDmatch.
Note that these figures are theoretical averages for random processes, not the ranges we observe in practice. Also note that a child's parents may still be related within a genealogical time frame if the GEDmatch AYPR result is zero, as they may not both pass on the same segments above the threshold used by GEDmatch to eliminate false positives.
If you need support dealing with an unexpected positive AYPR result please read the High ROH Infosheet prepared by genetic counselor Brianne Kirkpatrick.
Sources:
Franklin, I.R. “The distribution of the proportion of the genome which is homozygous by descent in inbred individuals.” Theoretical Population Biology 11, no. 1 (1977): 60–80.
Sund, K.L. and C.W. Rehder. “Detection and reporting of homozygosity associated with consanguinity in the clinical laboratory.” Human Heredity 77, no. 1–4 (2014): 217–24.
Sund, K.L et al. “Regions of homozygosity identified by SNP microarray analysis aid in the diagnosis of autosomal recessive disease and incidentally detect parental blood relationships.” Genetics in Medicine 15, no. 1 (2013): 70–78.
Thompson, E.A. "Descent-Based Gene Mapping in Pedigrees and Populations." In Handbook of Statistical Genomics, 4th edition. David J. Balding, Ida Moltke and John Marioni, editors. Hoboken, New Jersey: John Wiley & Sons, 2019. Chapter 20.
Weir, B.S. “Inbreeding.” In Encyclopedia of Biostatistics, 2nd edition. Peter Armitage and Theodore Colton, editors. Hoboken, New Jersey: John Wiley & Sons, 2005.
Wright, Sewall. "Coefficients of Inbreeding and Relationship." The American Naturalist 56, no. 645 (1922): 330–38.
The meaning of total shared segments reported by the GEDmatch Are Your Parents Related? (AYPR) tool is not obvious. Some genetic genealogists have pointed out that multiplying the total by a factor of four approximates the amount of DNA shared by the child’s parents, from which we can infer some possible relationships between unknown parents (see Homozygosity on the ISOGG Wiki for blog links). I wanted to try explain why, to myself and others.
The first column of figures in the table below will be familiar to genetic genealogists used to working with autosomal DNA statistics associated with the theoretical coefficient of relationship for different relationships (A). The last column of figures containing theoretical total homozygous autosomal segments of the child (H) is based on the theoretical coefficient of inbreeding for different relationships (half the relationship coefficient). I have tried to keep this explanation as simple as possible, assuming an otherwise outbred ancestry. I have listed my scientific sources at the end for those who want to know more about the underlying theory based on Mendelian genetics.
In the table, L is shorthand for the total length of the 22 autosomes in centiMorgans (cM). Because we have two of each chromosome, shared DNA percentages apply to double that length i.e. 2L. The theoretical proportion of a child’s autosomal genome length (L) that will be homozygous is the child’s inbreeding coefficient. We can convert these percentages to cM using the appropriate factor, 2L or L. The GEDmatch AYPR result corresponds to the figures in the last column (H).
Degree
of parental relationship with examples
|
Theoretical
total shared autosomal DNA of parents
(A) |
Theoretical
total homozygous autosomal segments of child
(H) |
|
First (parent/child, full siblings)
|
50% x 2L
|
100% x L
|
25% x L
|
Second (half-siblings, uncle/niece,
grandparent/grandchild, double first cousins)
|
25% x 2L
|
50% x L
|
12.5% x
L
|
Third (first cousins)
|
12.5% x 2L
|
25% x L
|
6.25% x
L
|
Fourth (first cousins once removed)
|
6.25% x 2L
|
12.5% x
L
|
3.125% x
L
|
Fifth (second cousins)
|
3.125% x
2L
|
6.25% x
L
|
1.5625%
x L
|
Consider the example of half-siblings M and F below, where
their shared parent P has a section of DNA at a specific
chromosomal location that I will call pq, the p half inherited from one of their parents and the q half from the other. Two out of four (50%) possible ways M and F can inherit
DNA from P at this location result in them being identical by descent (IBD) at
that location. I will call the IBD half i and the
half each child inherits from their other parent j and k. One out of four (25%)
possible ways a child C of M and F can inherit DNA from both parents at this location results in
them being homozygous at that location.
Parent P
(pq)
|
IBD
probability
|
Half-sibling
parents
M (ij) and F (ik) |
ROH
probability
|
||
Child M
|
Child F
|
Child C
|
|||
p
|
p
|
25%
|
i
|
i
|
25%
|
q
|
q
|
25%
|
i
|
k
|
–
|
p
|
q
|
–
|
j
|
i
|
–
|
q
|
p
|
–
|
j
|
k
|
–
|
Total 50%
|
Total 25%
|
||||
ROH segments of their child = 50% x 25% x L = 12.5% x L
In the parent/child or full siblings scenarios, the parents share 100% x L (50% x 2L)
ROH segments of their child = 100% x 25% x L = 25% x L
The autosomal DNA shared by the child’s parents can be approximated as 4 x the child’s total homozygous segments reported by GEDmatch.
Note that these figures are theoretical averages for random processes, not the ranges we observe in practice. Also note that a child's parents may still be related within a genealogical time frame if the GEDmatch AYPR result is zero, as they may not both pass on the same segments above the threshold used by GEDmatch to eliminate false positives.
If you need support dealing with an unexpected positive AYPR result please read the High ROH Infosheet prepared by genetic counselor Brianne Kirkpatrick.
Sources:
Franklin, I.R. “The distribution of the proportion of the genome which is homozygous by descent in inbred individuals.” Theoretical Population Biology 11, no. 1 (1977): 60–80.
Sund, K.L. and C.W. Rehder. “Detection and reporting of homozygosity associated with consanguinity in the clinical laboratory.” Human Heredity 77, no. 1–4 (2014): 217–24.
Sund, K.L et al. “Regions of homozygosity identified by SNP microarray analysis aid in the diagnosis of autosomal recessive disease and incidentally detect parental blood relationships.” Genetics in Medicine 15, no. 1 (2013): 70–78.
Thompson, E.A. "Descent-Based Gene Mapping in Pedigrees and Populations." In Handbook of Statistical Genomics, 4th edition. David J. Balding, Ida Moltke and John Marioni, editors. Hoboken, New Jersey: John Wiley & Sons, 2019. Chapter 20.
Weir, B.S. “Inbreeding.” In Encyclopedia of Biostatistics, 2nd edition. Peter Armitage and Theodore Colton, editors. Hoboken, New Jersey: John Wiley & Sons, 2005.
Wright, Sewall. "Coefficients of Inbreeding and Relationship." The American Naturalist 56, no. 645 (1922): 330–38.
Monday, January 15, 2018
Desperately seeking Susan: Part 6
(Continued from Part 5)
Within a year of starting her DNA search for her biological family, Bonnie* matched two maternal aunts Bridget* (Part 3) and Grace* (Part 4), and her birth father (Part 5), and identified her birth mother Gail* (Part 5). She has now reunited with both birth parents in person.
In JANUARY 2018 Gail received her AncestryDNA results, confirming their parent/child relationship.
Gail also matched Grace as expected, and asked for my help understanding what their match means.
In Part 4 Bonnie's search inadvertently revealed that her birth mother was a subject of misattributed paternity, also referred to as a non-paternity event (NPE). My working hypothesis was that Bonnie was the daughter of Grace’s paternal half-sister, who was unknown to Grace. (Incidentally, there was also a recent NPE on Bonnie's paternal side. Even if we could have identified the ancestors of her highest paternal match at 23andMe, a second cousin, it would not have led us to her birth father.)
Possible relationships for matches in AncestryDNA's CLOSE FAMILY – 1st COUSIN category include half-sibling, full aunt/uncle, full niece/nephew, grandparent/grandchild, and double first cousins sharing all four grandparents.
People with any of these relationships share on average 25% of their DNA, and it is not obvious from shared autosomal DNA amounts alone which relationship is the correct one, so we also need to make use of any other information available, such as:
– We can exclude relationships that are not possible based on circumstantial evidence (ages and other tree data).
– We can analyze shared X-DNA at GEDmatch to check whether possible paternal half-sisters satisfy the requirement that they share their father's full X chromosome.
– We can analyze shared autosomal DNA at GEDmatch to check whether matches share fully identical segments, which double first cousins sharing paternal and maternal grandparents are expected to share.
Grace and Gail were born in the same area only four years apart and neither has any full siblings to my knowledge, so we can exclude the grandparent/grandchild and full aunt/niece possibilities. They have unrelated known mothers and don't share fully identical segments (established by a one to one autosomal comparison with graphics at GEDmatch), so we can also exclude the double first cousin possibility.
A one to one X-DNA comparison at GEDmatch confirmed they share a full X chromosome, consistent with my working hypothesis and the only remaining possible relationship for their DNA match, paternal half-sisters. Furthermore, their shared matches belong to the tree of Grace's known father Carlo* Jr, indicating that they are both his biological daughters.
Gail's biological father was not the person she thought it was, and none of her parents are alive to ask about it. It is a hard pill to swallow. I can explain what the DNA is saying, but any new information revealed must ultimately be processed emotionally by those affected in their own time.
*This is a true story. I have permission to blog about the people who asked me for help but have not used their real names for the sake of their privacy. I have tried to limit my writing here to information pertinent to their DNA searches, but have shared other details I found with them in tree format.
{Related resources can be accessed via ISOGG's Wiki page on DNA testing for adoptees.}
(Continued in Postscript)
Within a year of starting her DNA search for her biological family, Bonnie* matched two maternal aunts Bridget* (Part 3) and Grace* (Part 4), and her birth father (Part 5), and identified her birth mother Gail* (Part 5). She has now reunited with both birth parents in person.
In JANUARY 2018 Gail received her AncestryDNA results, confirming their parent/child relationship.
 |
| Gail in Bonnie's match list – DNA confirmation |
Gail also matched Grace as expected, and asked for my help understanding what their match means.
 |
| Gail in Grace's match list – note her Italian ethnicity |
In Part 4 Bonnie's search inadvertently revealed that her birth mother was a subject of misattributed paternity, also referred to as a non-paternity event (NPE). My working hypothesis was that Bonnie was the daughter of Grace’s paternal half-sister, who was unknown to Grace. (Incidentally, there was also a recent NPE on Bonnie's paternal side. Even if we could have identified the ancestors of her highest paternal match at 23andMe, a second cousin, it would not have led us to her birth father.)
Possible relationships for matches in AncestryDNA's CLOSE FAMILY – 1st COUSIN category include half-sibling, full aunt/uncle, full niece/nephew, grandparent/grandchild, and double first cousins sharing all four grandparents.
 |
| AncestryDNA does not list the half-sibling possibility under actual DNA results |
People with any of these relationships share on average 25% of their DNA, and it is not obvious from shared autosomal DNA amounts alone which relationship is the correct one, so we also need to make use of any other information available, such as:
– We can exclude relationships that are not possible based on circumstantial evidence (ages and other tree data).
– We can analyze shared X-DNA at GEDmatch to check whether possible paternal half-sisters satisfy the requirement that they share their father's full X chromosome.
– We can analyze shared autosomal DNA at GEDmatch to check whether matches share fully identical segments, which double first cousins sharing paternal and maternal grandparents are expected to share.
Grace and Gail were born in the same area only four years apart and neither has any full siblings to my knowledge, so we can exclude the grandparent/grandchild and full aunt/niece possibilities. They have unrelated known mothers and don't share fully identical segments (established by a one to one autosomal comparison with graphics at GEDmatch), so we can also exclude the double first cousin possibility.
 |
| Gail and Grace share their father's X chromosome |
A one to one X-DNA comparison at GEDmatch confirmed they share a full X chromosome, consistent with my working hypothesis and the only remaining possible relationship for their DNA match, paternal half-sisters. Furthermore, their shared matches belong to the tree of Grace's known father Carlo* Jr, indicating that they are both his biological daughters.
Gail's biological father was not the person she thought it was, and none of her parents are alive to ask about it. It is a hard pill to swallow. I can explain what the DNA is saying, but any new information revealed must ultimately be processed emotionally by those affected in their own time.
*This is a true story. I have permission to blog about the people who asked me for help but have not used their real names for the sake of their privacy. I have tried to limit my writing here to information pertinent to their DNA searches, but have shared other details I found with them in tree format.
{Related resources can be accessed via ISOGG's Wiki page on DNA testing for adoptees.}
(Continued in Postscript)
Subscribe to:
Posts (Atom)