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Archiver > AUTOSOMAL-DNA > 2011-06 > 1307493819


From: "Tim Janzen" <>
Subject: [AUTOSOMAL-DNA] Chromosome mapping
Date: Tue, 7 Jun 2011 17:43:39 -0700


Dear All,
I recently wrote a long e-mail that I posted on the ISOGG list about
how to link specific segments of your autosomal DNA to specific ancestors in
your pedigree chart. Because I think that this is a very important topic, I
thought it would be wise to reproduce that message on this list as below.
It can be very helpful to have mapped your chromosomes when you are trying
to sort out multiple potential genealogical connections such as in the
situation that CeCe Moore blogged about recently at
http://www.yourgeneticgenealogist.com/2011/05/confirmed-another-23andme-cous
in-today.html.
The following are specific instructions on how to map your
chromosomes. If you haven't already reviewed my genome map file at
http://dl.dropbox.com/u/21841126/chromosome%20map%20Betty%20Janzen.zip, I
would suggest that you do so before trying to understand the details. It is
important that you note that in that file column G is the chromosome that I
received from my mom and that column H is the chromosome that my mom has
that she didn't pass on to me. You can delete the data in those columns and
then use this file as the file for which you do your analysis of your own
data.
To start with you need a parent's 23andMe results or Family Finder
results and you need one of their children's results. You then need to
compile a list of all of the known relatives of the parent who have been
tested who are either first cousins to the parent or more distantly related
to that parent. If you are using 23andMe data for comparison you then go to
the "Family Inheritance: Advanced" section in "Ancestry Labs". You then set
the parent as the person whose genome is open in 23andMe by clicking on that
name in the drop down menu up at the top of the screen next to "Account".
Then set the child as the 2nd optional family member in the "Family
Inheritance: Advanced" section. Then select the person to be placed in the
"Select a person in question" box. This person needs to be a first cousin
or someone else known to be a distant relative of the parent. Then click on
"Compare". Then click on "View in a table". This will generate a list of
matching segments for both the parent and for the child. If you are
comparing data in Family Finder the technique is somewhat different. What I
do there is to first log into the parent's account and go to the "Chromosome
Browser" section of Family Finder. I then find the relative in the list of
matches. I then click on the box next to the relative's name and then click
on "Download to Excel". I save the Excel file on my hard drive. I then log
into the child's account and go to the "Chromosome Browser" section of
Family Finder. I then find the relative in the list of matches. I then
click on the box next to the relative's name, click on "Download to Excel",
and save the Excel file on my hard drive. I then open both Excel files and
copy the data from one Excel file so that it is included right below the
data in the other Excel file. I then sort that file by the chromosome and
then by start location so that I can see all of the matching segments for
both the parent and the child adjacent to each other in the file. I then
delete all segments that are under 5 cMs for which the parent and the child
do not both share a corresponding matching segment with the relative. It
may be reasonable to map some segments in the 3-5 cM range if both the
parent and the child share that same segment with the relative but caution
is warranted when mapping segments that don't contain at least 700 or more
SNPs because some matching segments could be IBS (identical by state) and
not IBD (identical by descent).
In the Excel file I mentioned above in the first paragraph first fill in
the start point in column G with the name of the ancestor that the parent
must have received the segment from for all of the segments in which the
child also matches the other relative. For example, if a first cousin of
the parent is being used for comparison then you would enter into the cell
the name of the grandparent of the child who was related to the first cousin
in the appropriate cell in the file, the grandparent's year of birth and the
name of the relative used for comparison. For instance, if the child's
start point was at position 80,000,000 on chromosome 5 then you would fill
cell G177752 with the name of the grandparent, their YOB and the name of the
relative. Then copy the contents of cell G177752 and drag the contents down
to fill in all cells in column G down to the endpoint of that segment. If
the end point was at position 104,500,000 then you would fill in the column
all the way down to cell G181568. Simultaneously fill in the contents of
cells H177752 to H181568 with the name of the spouse of the grandparent and
their YOB. I like to add "inf" after the name and the YOB to designate that
I have inferred this information from the fact that I have already filled in
the corresponding cells in column G. Repeat this same procedure for every
segment that the child shares with the relative used for comparison.
Once you have done the above then review the segments that the parent
shares with the other relative but the child does not. For instance, let's
say that the parent's matching segment on chromosome 5 starts at 65,000,000
and continues to 110,000,000. You would then go to cell H174981 and enter
the name of the grandparent of the child who was related to the first
cousin, their YOB, and the name of the relative used for comparison. I also
like to add "inf" after this information to indicate that I inferred the
information from the fact that the child doesn't share that matching
segment. You would then fill the contents of cell H174981 down to cell
H177751 with the same information as is in cell H174981. You would next
fill in cells H181569 to H182595 with the same information. This would
cover the segment between position 104,500,000 and 110,000,000. I would
simultaneously fill in the contents of cells G174981 to H177751 and G181569
to G182595 with the name of the spouse of the grandparent, their YOB, and
"inf" after that. In similar fashion continue filling in all the
appropriate cells in column H for the segments that the parent shares with
the other relative but the child does not and adding the corresponding
information for those segments in column G.
Once you have recorded the information as recommended for the first
relative selected for comparison in the paragraph above then continue in
similar fashion for all known relatives who are related no more closely than
at the first cousin level of relationship to the parent. If there are
segments that multiple relatives share in common with the parent, then I
like to modify the contents of the corresponding cells to include the name
or the initials of each relative who shares that same segment. This
information can be helpful in situations where there is some ambiguity about
the start or stop locations for a particular segment. For instance, if you
look at my file you will see that in cell G182987 the entry JY1823 Darryl
Youngman, FM, and MY. This information continues down to cell G185532.
This means that my relatives Darryl Youngman, Frederick Mock, and Mason
Youngman all share this segment with both my mom and I. Thus it appears in
column G. The ancestor that all 5 of us share in common is Jacob Youngman
(b. ca 1823). The segment of DNA just above this segment in the file was
shared by Darryl Youngman, Mason Youngman, my mom and me, but not by
Frederick Mock.
Once you have gone through the comparisons for all of the relatives in
your list save it and keep it on hand for reference. When you have a new
match in 23andMe compare them in "Family Inheritance: Advanced" section in
"Ancestry Labs" to the parent and the child or compare them in Family Finder
as I described above. If both the parent, the child, and your new match all
share a segment that you have previously mapped in the file you created as
described above then you know that the ancestor listed in column G for that
particular segment of DNA must have shared ancestry with your new match. If
the parent shares a segment in common with your new match, but the child
doesn't share that segment with the match then you know that the ancestor
listed in column H for that particular segment must have shared ancestry
your new match.
It is important to bear in mind that small matching segments can be
problematic for the purposes of mapping, particularly for data in 23andMe.
Let's say for instance that a parent shares a matching segment that is 8 cMs
in length with a known second cousin but the child doesn't share that
segment. You would thus have mapped that entire segment to column H in your
file. However, if by chance there had been a crossover during meiosis in
the middle of that segment before a portion of it was passed on to the child
then about 4 cMs of the 8 cM segment would be inappropriately mapped to
column H when it actually should have been placed in column G. For this
reason, I initially started by mapping matching segments that were 10 cMs or
longer if a relative shared a segment with the parent but not with the
child. If there was a crossover in a segment 10 cMs or longer then the
child should have received a segment that was at least 5 cMs in length and
would thus show up as a matching segment for the child. One advantage of
Family Finder is that FF has a 1 cM threshold for matching segments. If a
parent and a child both have a matching segment that is in the 2 to 5 cM
range and if the number of matching SNPs is 500 or more then there is a
reasonably high likelihood that the matching segment is IBD (identical by
descent) and not IBS (identical by state). Another advantage of Family
Finder is that Family Finder doesn't round to the nearest millionth base
pair like 23andMe does, so there is greater clarity as to the precise
boundaries of each matching segment. I have been able to get around the
first issue partially and the second issue entirely for 23andMe data by
including my family and their relatives in the Mennonite project at
http://kquilting.homeserver.com/23andme/index.html where we use a 4 cM
threshold for matches and where the matching segments are not rounded to the
nearest millionth base pair.
Endogamous populations represent another challenging group for mapping
purposes since there is a higher likelihood in such populations that
matching segments will be IBS (identical by state) and not IBD (identical by
descent). In such populations it might be wise to initially start by
mapping segments that are at least 10-15 cMs and/or contain greater than
1000 or so SNPs. Phasing data from endogamous populations before doing
comparisons is a very good approach and reduces the probability that any
particular matching segment will be IDS.

Sincerely,
Tim Janzen



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