Tuesday, May 27, 2014

Genome Mate: ICW, Triangulation and Overlapping Segments

The purpose of the blog is to describe ICW, Triangulation and Overlapping Segments from the profile perspective in Genome Mate as that is how the data is presented in the application.

One of the most frequently asked questions is what is the difference between In Common With (ICW), triangulation and overlapping segments.  Let's start with a definition of each in relation to the Genome Mate profile person before moving on to more details.

  • In Common With (ICW) - ICW simply means that two Relatives have some DNA in common and are thereby related to each other but not necessarily on the same segment as the profile person.
  • TriangulationTriangulation means that the profile person plus two or more people are related to each other on the same DNA segment and thereby share a common ancestor. 
  • Overlapping Segments - Overlapping segments are DNA segments from two or more Relatives whose start and end points overlap each other.

Loading data in Genome Mate is complicated due to the need to accommodate different data sources and formats.


Getting Started Guides

Here are the links to some of the Getting Started guides.  The focus of this blog will be limited to just ICW, Triangulation and Overlapping Segments.

In Common With (ICW) in Genome Mate


In Genome Mate, there is an ICW indicator next to the Relative's name and if you hover your mouse over it, it will highlight the other relatives on that segment who are related to that person.  However, it says nothing about if they are all related on that particular segment.

When a segment crosses a centromere, there is a greater chance the segment is a mismatch or IBS (identical by sequence) rather than IBD (identical by descent).  When this occurs, the ICW group on the graph will be an orange color to alert to the possibility.

The ICW group can be set to any value by clicking on a DNA segment and setting the value in the Match details page.  However, note that, if known, it should start with M for maternal or P for paternal for surname matching and chromosome mapping to work correctly.

Keyboard shortcut:  If you left click on the ICW indicator, you can mark every person highlighted with a value you enter except for those who have an * in their ICW.  If you right click on the ICW icon, it will copy the ICW group value contained in that Relative record to all highlighted relatives except for those who have an * in their ICW value.  Use this with caution since ICW relatives are not always related to each other on the highlighted segment.

There are several ways to load ICW data depending on the data source but note that Relative data must have been loaded first or the ICW data will be rejected.

  • 23andMe - The recommended method of loading ICW for 23andMe is to use the 529andYou CSV file but there are other, more time consuming and less comprehensive ways to get the data.  In order of preference:
  • On 23andMe > My Results > Ancestry Tools > Countries of Ancestry > Select Relative name > Click Download {Relative's Name}'s Countries of Ancestry Matches (CSV)
  • In Genome Mate > Select one of the Relative's DNA Segments > Add ICW >  Import Data from CSV File >Select file named ancestry_finder_{name}{date}.csv 

  • FTDNA - The only way to import ICW data for FTDNA is to use DNAGedcom.
  • On DNAGedcom > Family Tree DNA >  Download Family Tree DNA Data > Enter Kit # > Enter Password > Get Data > Wait for processing to finish > Find zipped file in your download folder and extract files 
  • In Genome Mate > Import Data > Select Data Source > Load ICW CSV file from DNAGedcom > Import Data from CSV File > Select file named {kit}_ICW.csv

  • GedMatch -  ICW is loaded when loading the segments from Segment Triangulation (see blog) but it is limited to the top 200 matches.  
More ICW data can be loaded one relative at a time by:
  • On GedMatch > 'One-to-many' matches > Enter kit number > Display Matches > Select data (Ctrl or Cmd a) > Copy data (Ctrl or Cmd c)
  • In Genome Mate > Select one of the Relative's DNA Segments > Add ICW >  Copy Data (Ctrl or Cmd v) > Format
ICW data provides clues that the researcher can use to dig further into family trees to see if there is a connection between Relatives on the DNA segment in question.  Not having an ICW between two relatives is a good way to avoid researching people not related.


Triangulation

Triangulation means that the profile person plus two or more people are related to each other on the same DNA segment and thereby share a common ancestor.  This is determined by a three way match between the profile person and two relatives (P = A, P = B, A = B).

Automation of triangulation is only available for 23andMe data imported from the 529andYou CSV file and the Segment Triangulation data from GedMatch (limited to first 200 top Relatives).  

If triangulation data has been loaded into Genome Mate then clicking on a Relative's DNA segment will show the triangulated data in the upper middle box of the match details page. 

Triangulated relatives establish an ancestral line on which they all share a common ancestor even if that ancestor is not currently known.

Overlapping Segments

Overlapping segments are DNA segments from two or more Relatives whose start and end points overlap each other.  Each overlapping segment contains DNA from both the paternal and the maternal sides of the family so segments that overlap are not necessarily related to each other.  

Use DNA matches to known family members to set the segment's ICW group to either P (paternal) or M (maternal).  Otherwise, any ICW value is okay to indicate a group of triangulated matches.

Segments that have been identified as maternal or paternal but whose overlap is small may not be related.  To to filter those out, a default overlap value can be set and compared to the segment's start and end points to determine if it should be displayed.  To set the default value:

  • In Genome Mate > Options > Set Minimum Segment Overlap

There are tools in Genome Mate to work with overlapping segments:  

  • On Genome Mate graph:  Left click on the circle icon next to the profile name and all of the segment overlaps for that particular segment will be displayed.  If the segment has been identified as maternal or paternal, it will display the corresponding maternal or paternal segments plus those that have not been identified.  This display ignores the default overlap value and shows all overlaps. Use ESC to return to a full display.
  • On Genome Mate graph:  Right click on the circle icon next to the profile name and an Overlapping Segment Page will be opened showing all of the DNA segments for all sources (23andMe, FTDNA, etc.) that overlap the selected segment by the default overlap value.  It shows the common surnames shared among those listed on the page. Clicking on a Relative in this list will open their Match details page.
  • On Match Detail page:  In the lower right corner is a list of segments overlapping the selected DNA segment by the default value along with shared surnames.
Overlapping Segment Page

The Overlapping Segment Page is my primary work space when trying to identify common ancestors as it gives a global view of the segment in question.




Backups & Restores

Creating backup files cannot be overemphasized.   Experimentation is encouraged, but make sure you have a safe harbor.

Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

3 comments:

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  3. I have been trying to find out why the "Mark ICW Segments" symbol to the left of the name is sometimes orange. Nobody on the Facebook page seems to know why. Can anyone explain this? It has nothing to do with the orange ICW group which indicates a segment that crosses the centromere or a false positive region.

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