Solving Genealogy Puzzles with DNA: May 2014

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.
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.
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:

529andYou: See the Getting Started with 23andMe guide Step 2.

DNAGedcom: See the Getting Started with 23andMe guide Step 2.

23andMe CoA: Import for each relative, the data from the 23andMe Countries of Ancestry file.

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.

Saturday, May 17, 2014

Getting Started with Genome Mate using 23andMe Data

Genome Mate is a desktop tool used to organize in one place the data collected while researching DNA comparisons. Besides data storage it has many features to aid in identifying common ancestors. It can be downloaded at http://genomemate.org/

The following guide was originally put together by George Cunningham and published with his permission. It has been edited to reflect changes in the application.

23andMe Getting Started Guide

There are three steps required to load 23andMe data: Setting up a profile, load DNA segments and loading associated Relative data. Under step 2, loading DNA segments, there are multiple options for obtaining that data. Please read each carefully before proceeding.

Step 1: Create a Profile

First create a profile in Genome Mate for each kit that you manage

Profiles > Add new profile

Put in a name, any name will do, but

You are a good choice for the profile person.

If your going to use data from 23andMe for the profile person, the profile name MUST match the 23andMe name.

Load a gedcom file for each profile if you have one. If not just continue.

The gedcom file can be all of your relatives and more

Genome Mate will ask you for the name to associate with the profile person, and will strip out all but the profile person's direct ancestors.

The gedcom file format must be 5.5 in UTF8 format

Step 2: Load 23andMe DNA Segments

Import Data Page

There are several methods for loading the DNA segment data for 23andMe profiles that can be mixed as needed.

529andYou: The recommended method of importing 23andMe segment data is to use Neanderling's Chrome Plugin, 529andYou as it not only provides DNA segment data but triangulation and in common with (ICW) information as well. The Chrome browser is required.

Get Chrome Browser here

Get 529andYou here and be sure to click yes when asked to create a Chrome database.

Read about 529andYou here

On 23andMe > My Results > Ancestry Tools > Family Inheritance: Advanced > Select any Compare profile > Compare > View in a Table > Click on 529 icon in upper right corner to open new tab

On the 529andYou tab > Create 'To Do' Table > Highlight list of names > Copy & Paste into Notepad to use later

Click the button next to each Match name

Close the tabs that were open when they finish processing

On the 23andMe tab > Switch Profiles if there are more than one and repeat this step for each.

Refresh the 529andYou tab or close then reopen through 23andMe

For each person in the Notepad list: On the 529andYou tab > Display mode: Profile and Overlapping Segment Links > Show matches of {name from Notepad list} > Create Match Table [Note: That the very first time it is faster to do this for each of your profile names rather than the Notepad list.]

Click on button next to a Profile person match

If available, Ctrl click on each link saying compare {name1} and {name2} to open FIA tabs for the comparison

Close new FIA tabs when finished processing

On the 529andYou tab > Create Match Table and repeat for next profile person on list

On the 529andYou tab > Show matches of All > Download CSV

In Genome Mate > Import Data > Select Data Source 23andMe > Load FIA Matches and ICW from 529andYou CSV file > Import Data from CSV File > Select file named 529andYou_{date}.csv

DNAGedcom: This is the second preferred method of loading bulk DNA segments from 23andMe into Genome Mate. It is the best method for loading Country of Ancestry DNA segments and also updates ICW data.

On DNAGedcom.com> 23andMe > Download 23andMe > Enter Email address > Enter 23andMe Password > Enter 23andMe Profile Name > Check Run FIA > Check Run AC > Check Run AF > Get Data and wait for it to finish processing

This loads the shared matches: In Genome Mate > Import Data > Select Match Data Source 23andMe > Load FIA Matches from DNAGedcom CSV file > Select file named {email name}_{profile name}_23andMe_FIA.csv

This loads the Country of Ancestry (CoA) data: In Genome Mate > Import Data > Select Data Source 23andMe > Load CoA Matches and ICWs from DNAGedcom > Select file named {email name}_23andMe_AF.csv

23andMe: This is the least preferred method for loading DNA segments as it requires the data to be manually copied and pasted from the Family Inheritance: Advanced page into Genome Mate for up to 5 comparisons at a time.

On 23andMe > My Results > Ancestry Tools > Family Inheritance: Advanced > Select any Compare profile > Select up to 5 With Family Members > Compare > View in a Table > Select all (Ctrl A) > Copy (Ctrl C)

In Genome Mate > Import Data > Select Data Source 23andMe> Copy/Paste Family Inheritance Advanced (FIA) > Follow directions

The following loads the 23andMe CoA file:

For each profile: On 23andMe > My Results > Ancestry Tools > Countries of Ancestry > Show Results for: {profile name} > At bottom of page Download {name} Countries of Ancestries Matches (CSV)

For each profile: In Genome Mate > Import Data > Select Data Source 23andMe > Load CoA Matches from 23andMe CSV file > Select profile name > Import Data from CSV File > Select file named ancestry_finder_{name}_{date}.csv

Step 3: Load 23andMe Relative's Surnames

This step loads the Surnames for existing Relative records into Genome Mate.

For each 23andMe Profile: In Genome Mate > Import Data > Select Data Source 23andMe> Load Relative Finder CSV file from 23andMe > Follow directions

Hints and Tips

There are two small arrows going in a circle to the left of your profile name.

Left click to show overlapping segments. Escape to return to the original screen.

Right click to bring up an overlapping segment dialog

Choose a Relative Name in the list of matches.

Choose a relative who matches you on more than one chromosome.

Right click on it to show all matches

Escape to return to the original screen.

Some Relatives will have a small symbol (Mark ICW segments) to the left of their name. Hover (do not click) your mouse over the symbol.

A series of colored bars will show you the relatives who are in common with the one you are hovering over.

These people are related but not necessarily on the currently selected segment.

Some ICW group symbols are in orange.

The orange color means that the segment crosses a centromere, so the meaningful length is much shorter than the displayed length.

If you hover over the symbol, it will show the length of the centromere.