Jim Sims

Making genetic genealogy more understandable...

The numbering scheme for the tutorial is tied to an article I published in Acorns to Oaks 38(2) 2017, 40-49

S1. Vendor chromosome browsers

A chromosome browser provides a method to visualize on which chromosomes you and your matches share DNA. Distant matches may share only one DNA segment, while close family members will share many segments.

Vendor: 23AndMe
(Updated 12 May 2019)

1. Log-in to your kit at 23AndMe. Navigate to your DNA Relatives page.

2. Click a match to see their match page.

3. Scroll the page slightly to the section labeled Your genetic relationship. In this example, the match is a predicted 2nd cousin. In this particular case, 23AndMe got that right. This is a paternal 2nd cousin related to Jim Sims through his paternal grandmother.

At the bottom of this section of the Match page, there is a diagram of the 22 autosomal chromosomes and the X chromosome. 23AndMe provides two different colors or shared DNA segments: a light purple showing half-identical sharing (sharing on only one chromosome) and a darker purple color for fully identical sharing.

Full siblings will will have a mix of dark purple, light purple regions, and unshared regions on all the chromosomes. The expected ratio of sharing for full siblings is 25% fully identical, 50% half identical and 25% no sharing averaged over chromosomes 1-22. Sharing will vary by chromosome.

A child and a parent will have the light purple color on the full length of chromosomes 1 through 22.

In the case of other family member, like the 2nd cousin in this example, half-identical sharing is expected when sharing occurs.



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3. To see a more detailed view of the shared segments, click the DNA Comparison tool (see red arrow in image above). If the web page does not populate the Compare box with the DNA you were viewing, you must search for that match by name by typing in the text box (see red arrow in image below). There is no need to press the return or enter key to perform the search. Simply typing in the box and pausing will initiate a search

4. In this example, the name of the 2nd cousin will be typed. When their icon and name appears below the text box, the icon should be double-clicked to place this person in the Compare box at left of the screen. Then, if you want to compare this person to yourself, type in your name in the search box, then double-click your icon to place you in the With box.

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4. Press the compare button at bottom left of the tool (see image above). This will show you an expanded graphical view of the shared DNA segments and below the diagram is a detailed table of start and stop locations where the matching segments occur and the size of the segment measured in cM.

The diagram can fail to convey the length of the segment accurately, so be sure to check the cM values in the table below the diagram. For example, looking at the shared segment on chromosome 1, it looks shorter than the segment on chromosome 3. Looking at the table below, we see that the segment on chromosome 1 is actually about 25% larger than the one on chromosome 3 measured in cM!

In the interest of space, not all of the segments are shown in the table below the chromosome diagram.

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Vendor: AncestryDNA

(Updated 12 May 2019)

AncestryDNA does not offer customers a chromosome browser. Customers of AncestryDNA can transfer their raw autosomal data to another vendor and use their chromosome browser .

Vendor: Family Tree DNA
(Updated 12 May 2019)

1. Log-in to your account at Family Tree DNA and navigate to your Family Finder Matches page.

2. Select one or more matches by clicking the check box to the left of the match's name in your match list (not shown). Then click the Chromosome Browser tool (see red arrow in image below).

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In this example, four matches were selected. The matching segments in blue are for a full sibling, red is for a first cousin, green is for a second cousin and orange is for a fourth cousin. Only the image for the first eight chromosome is shown. Full siblings will share many and frequently large DNA segments; first cousins will share fewer DNA segments and on average they are smaller segments compared to siblings. This trend continues with fewer and fewer shared segments and smaller segments shared as the biological distance increase: 2nd cousins, 3rd cousin, 4th cousin, etc. This is due the the biological mechanism of autosomal DNA inheritance. Chromosomes 1 though 22 undergo genetic recombination in every generation. This recombination in every generation makes interpreting autosomal matches tricky.

In the image below, the gray colored area is Jim Sims' DNA. The colored segments are overplayed on top of the gray where a shared segment occurs. It should be noted that each person in a comparison has two copies of each chromosome. One copy inherited from the biological mother, the other inherited from the biological father.

Family Tree DNA's chromosome browser displays matches that are at least half-identical. This browser is not capable of showing fully identical regions.

Detailed Segment Data is also available at Family Tree DNA. See the text tab Detailed Segment data next the the Chromosome View text tab.

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Vendor: MyHeritage

(New 13 May 2019)

A chromosome browser view of shared segments is available at the bottom of a match page at MyHeritage. This example shows shared segments with a first cousin once removed.

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1. You can also use a one-to-many chromosome browser at MyHeritage. Starting at the DNA menu, click on DNA Tools menu to navigate to the tools page. Click the Explore button in Chromosome Browser panel.


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2. On the Chromosome Browser One-to-many page, click additional matches to compare in the browser. In this example, two sisters were clicked on (see red arrows in the image below) who both have a first cousin once removed relationship to Jim Sims.

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3. Next, click the pink Compare button to see the result in the chromosome browser, shown in the image below.

Notice that Jim Sims and these two cousins have triangulated segments (boxed areas; see red arrows) and other segments are not triangulated. In order to see triangulation in the one-to-many browser, there must be at least one triangulated segment shared by everyone in the comparison.

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S2. GEDmatch chromosome browser
(Updated 13 May 2019)

GEDmatch is not a vendor that sells DNA test kits. It is a third party web site with tools you can use to analyze your raw autosomal data. This site has free tools and paid tools. Be sure to read the privacy policy before creating an account. Law enforcement in the USA has used this site to apprehend rapists and murders who left DNA evidence at crime scenes, and to name victims of such crimes long after the fact. In this tutorial, only the free tools are discussed. To learn more about GEDmatch than this tutorial, see Beginning GEDmatch tutorial.

1. This example uses the free One-to-One Autosomal DNA Comparison tool at GEDmatch. Enter kit GEDmatch kit numbers for the two kits to compare. In this example, the kits for Jim Sims and his full sibling were entered in the text boxes for this purpose.

2. To initiate the comparison, click the Submit button (see red arrow near bottom of the image below).
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The graphic below shows only the top part of the results of comparing the two siblings. Only chromosome 1 is shown. See the figure legends at the top of the page for the meaning of the colors. This browser is capable of displaying half identical regions (solid yellow color above the blue bar) and fully identical regions (solid green regions above blue bar). Full siblings are expected to have a mixture of half-identical, fully-identical and regions were there is no shared DNA (red regions). Half siblings will not have significant fully identical regions.

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S3. What's in my raw data?
(As of 23 Feb 2017)

Jim Sims analyzed his raw autosomal data he downloaded from 23AndMe, AncestryDNA and FamilyTree DNA using the R statistical programming environment. A pdf shown the results is available at here. Those who wish to inspect the computer code and do so here at GitHub.




S4. cM values matter: single segment recombination simulations
(As of 27 Feb 2017)

Jim Sims conducted computer simulations of single DNA segments undergoing recombination on different time scales measured in generations. The results are available as a pdf here, and the computer code is available at Jim's GitHut account.




S5. R code for Figures 2 and 3
(As of 20 Mar 2017)

The R programming code to simulate recombination of a 6 cM DNA segment and to produce a histogram of the recombination distribution (Figure 2) and an x-y plot (Figure 3) of segment percent survival as a function of cM value at six different genealogical time scales in posted in a repository at the author's GitHub account.

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