Tag Archives: chromosome mapping

Down the DNA Rabbit Hole – DNA Painter

My latest DNA obsession is the online program DNAPainter. To be honest, I’ve been hearing a lot of great things about the program for awhile, but hadn’t wanted to venture into these waters. Because I just knew, once I did, I would fall deep into this rabbit hole.

The purpose of DNA Painter is to map chromosomes, using shared segment data from one’s matches. The program accepts data from several sources, including Gedmatch, 23andme, and familytreeDNA. AncestryDNA data is not usable since the company does not provide a chromosome browser. A match would have to transfer their raw data file to Gedmatch or familytreeDNA first.

As a highly visual person, I like to see how all the different segments I share with my relatives line up. This is especially useful when tracking triangulation groups. Entering data into the program can be time consuming—depending on how many matches one has. I chose to import data from only known relatives at first. I wanted to see how much data I had and if I already had some triangulation groups forming. Below is a screen shot of my chromosome 7. As you can see, I already have a lot of data for this chromosome.

Chromosome 7

The purple bars on my paternal chromosome all belong to relatives on my paternal grandfather’s side—the Yegerlehners and Schieles. Based upon the members of the purple group, I can assign this group specifically to the Schiele side. The small purple segment on the far right belongs to a distant Yegerlehner relative. The red bars are matching segments I have with my paternal grandmother’s side—the Fosters and Lawheads. The first red bar on the left can be attributed to my ancestral couple George Rea and Sarah (Jewell) Rea; and, the longer red bars to James B. Foster and his wife Lydia (Dicks) Foster.

Since I have matching segments with a variety of relatives, it is easy to see where my recombination points occur. There are three recombination points on my paternal chromosome—at about 14 cM, 103 cM, and 152 cM. Compared to the visual phasing that I did between my brother’s DNA and my own last year, the two charts align well together.

Two-sibling visually phased chromosome 7

DNA Painter has many great features, such as the ability to see all the members of a shared group, or how a specific individual matches the profile person. Matches can be assigned to either the maternal or paternal side of the family, or even to an “I don’t know” group if the relationship is unknown. Matches who share more than one set of common ancestors can have each individual segment assigned to different ancestors. Groups can be named or color-coded to the user’s preferences. For my preliminary profile, I used color-coding based on my four pairs of great grandparents. If you haven’t tried playing around with DNA Painter yet, I highly recommend it. There are many great features that I continue to discover as I work with the program, and I have barely mentioned a fraction of them in this review. Happy mapping!

©2018 copyright Deborah Sweeney
Post originally found: https://genealogylady.net/2018/01/23/down-the-dna-rabbit-hole-dna-painter/

Down the DNA Rabbit Hole – More Visual Phasing with Two Siblings

[Editor’s note: Several months ago, I wrote a post on visual phasing, or chromosome mapping, with two siblings. That post can be found here.]

Phasing is the task or process of assigning alleles (the As, Cs, Ts and Gs) to the paternal and maternal chromosomes. The term is usually applied to types of DNA that recombine, such as autosomal DNA or the X-chromosome. Phasing can help to determine whether matches are on the paternal side or the maternal side, on both sides or on neither side. Phasing can also help with the process of chromosome mapping – assigning segments to specific ancestors. The use of phased data reduces the number of false positive matches, particularly for smaller segments under 15 centiMorgans (cMs).

—ISOGG wiki

In my quest to map the chromosomes of sibling pairs (vs. sibling trios), I turned towards phasing kits on GEDmatch earlier this summer. In order to use this technique, at least one parent must have been DNA tested. Since both my parents have tested for me, I was able to use their results to create phased kits for my brother and myself. To phase a kit, use the GEDmatch phasing tool.

Image courtesy of GEDmatch

After I created phased kits for my brother and myself, using the one-to-one comparison tool, I compared the maternal kits against one another, and then the paternal kits. As a result, the crossover, or recombination points, for each chromosome are clearly delineated. Because only one chromosome from each pair is being compared, the colors are different from a standard one-to-one comparison. We see purple on the top bar where my brother and I share DNA. Red indicates where no DNA is shared. Likewise, on the bottom bar, dark blue shows where DNA is shared, and grey where it is not.

Maternal phased chromosome 13

Paternal phased chromosome 13

Because the kits are phased, I can see which crossover point belongs to which parent, instead of having to spend the extra time deducing—maternal vs. paternal.  Afterwards, I assign the segments based upon collected data from close relatives.

Unassigned segments for chromosome 13

Every time I obtain new segment data, I record it in my master spreadsheet. I place only the data from known relatives in this spreadsheet. By known, I mean the lineage is documented and I know where the person fits into my tree. None of this data is speculative. Below are my brother’s and my matches for chromosome 13. We have plenty of good matches on chromosome 13 due to several of our father’s first cousins having tested. Additionally, two close relatives from our maternal side—who share segments on chromosome 13—also tested for me. A sprinkling of third and forth cousins assist in the mapping as well.

Segment data for chromosome 13

My brother and I share a segment with my father’s paternal cousin S.Y. I continue with the Yegerlehner segment for much of my paternal chromosome. My brother has a crossover point (31) and can be seen sharing with my father’s maternal cousin J.R. for the bulk of his paternal chromosome. Around the crossover point at 92, I begin to share with some more distant cousins on my paternal grandmother’s line. While at the end of his paternal chromosome my brother crosses over to where he inherited a Yegerlehner/Schiele segment.

On the maternal chromosome, my brother and I share part of the McGraw/Kerschner segments. However, I match some New England cousins from my maternal grandmother’s line.

Chromosome 13 – Mapped between two siblings

I continue to collect data where I can. One thing to remember about mapping (like all genealogy research) is that new data may affect how we interpret all the data. I recently discovered that I had misattributed a segment shared with a 1C1R (and it was throwing off how I had assigned a segment on my map). It was a small segment, and I assumed because he was a known relative it was a real segment. It turned out that once I analysed this segment with my mother’s kit, they did not share this segment at all! So either the small segment I shared with my 1C1R was a false segment (a random alignment of DNA), or we have another common relative on my paternal tree. Happy mapping!

©2017 copyright Deborah Sweeney
Post originally found: https://genealogylady.net/2017/10/03/down-the-dna-rabbit-hole-more-visual-phasing-with-two-siblings/

Down the DNA Rabbit Hole – Visual Phasing with Two Siblings

Visual phasing of two siblings, a method of chromosome mapping, is possible with the assistance of first, second, and more distant cousins. The methodology of this technique is very similar to three-sibling visual phasing. One of the biggest differences is how segments are assigned to the four grandparents (two maternal, two paternal). For more in-depth coverage of the three-sibling technique, Blaine Bettinger’s five part series on Visual Phasing is essential (see links below). This how-to assumes that the reader has basic knowledge of the three-sibling technique. The following is a condensed version of how I visually phase my chromosomes using my brother’s DNA in comparison with my own DNA.

In the beginning, I used Microsoft Word for my mapping. The process was clunky, and I moved on… I mention this step because there are various programs one can use to achieve the same results. Feel free to use the program that works best for you!

Lars Martin published a fabulous how-to YouTube video on using Excel to map chromosomes. There is no volume (so don’t worry!).

Instead of having three bars comparing each of three siblings to each other, my visual phasing only has one (since I am only comparing myself to my brother). Using Lars Martin’s method, my blank frame looks like this. In the example below, I have already filled in the recombination points and drawn the lines and boxes. To find the numeric recombination points on Gedmatch, both the “Graphics & Positions” button and the “Full Resolution” button must be checked when viewing a one-to-one match. (see diagram 1)

Diagram 1

The other key factor in visual phasing with only two siblings is having close family members, generally at the first and second cousin relationship. But any known cousin relationship will work. Parents will not work, nor will immediate relatives beneath the generation being phased. For example, my first cousin’s son will not work because I can not differentiate his DNA between our set of shared ancestors. He descends from both of my grandparents as well. First cousins can also be tricky because they share one set of grandparents with the siblings being phased.

I use an Excel spreadsheet to keep track of my close as well as more distant established cousins. For each chromosome, I keep track of which relatives match my brother or me, recording the start and end points of each segment that is shared. Paternal cousins are on the top of the chart while our maternal matches are at the bottom. The example shows our matches for chromosome 13. (see diagram 2)

Diagram 2 – Excel spreadsheet showing matches on chromosome 13

The Paternal Chromosome

Next, I begin to fill in the segments like a giant logic puzzle. I could start anywhere on the chromosome, but I have started on the far right. Between recombination points 108 and 114, my brother and I share nothing. We inherited different segments from each of our four grandparents. Luckily we have data that shows who inherited which segment from whom. I also created a color key for each of my grandparents.

Jack shares a segment from cousin 1C1R – RG between 108-114 on the paternal chromosome. I did not. 1C1R – RM belongs to the Yegerlehner side of the family so this segment is colored green. Since I did not inherit the Yegerlehner segment, my segment is colored blue for the Foster family. On the maternal chromosome, since Jack inherited a segment from the McGraw side of the family while I must have the Leonard segment. While I share several segments with my second cousin MM, I do not share this segment. So logically, I must have a Leonard one. (see diagram 3)

Diagram 3 – End segments colored

For the next portion, I am moving on to the green blimp between points 28 and 31. The bright green on the top line of of the chromosome comparison indicates that my brother and I share the same segment on both our paternal and maternal chromosomes. We share the same paternal segment with 1C1R – SY, in this case, another Yegerlehner segment. My brother stops at point 31, while I continue to share the segment with 1C1R – SY for a little longer. From approximately point 33 through 104, Jack has a series of matches with cousins on the Foster side of the family. Since he does not have recombination points at either 33 or 104, I have extended this segment from recombination point 31 to recombination point 108. (see diagram 4)

Diagram 4

Since I do not match any of the Foster relatives until recombination point 92, I continue my green bar until point 92. At this point, my paternal chromosome recombines, and I begin sharing the Foster segments. (see diagram 5)

Diagram 5

To complete the last part of the paternal chromosome, I color both green. Yegerlehner cousin 1C1R – SY begins matching us at point 21. Since neither of us have a recombination point there (point 21), our segments are extended to the beginning of the chromosome. (see diagram 6)

Diagram 6

The Maternal Chromosome

Jack and I each share part of the same segment with maternal cousin 1C2R – RS. My segment begins at recombination point 28 and continues past point 50. Jack’s segment begins before point 28 but ends at point 50. I extend Jack’s segment to the beginning of the maternal chromosome. On my maternal chromosome, I extend the McGraw segment to point 73.

Looking at points 0 through 28 and points 50 through 73, I observe the blue and grey bars on the Gedmatch one-to-one chromosome comparison as well as the yellow top bar. The Gedmatch colors tell me that from points 0 though 28, Jack and I match on only one chromosome. We have segment data from a paternal cousin which we both share. Logically, this indicates that Jack and I do not have matching segments on our maternal chromosome. If Jack has part of the McGraw segment, then I must have inherited the Leonard one. Similarly, from points 50 through 73, Jack and I do not share any segments in this part of the chromosome. I share part of the McGraw DNA so my brother must share the Leonard side. (see diagram 7)

Diagram 7

The last section of the maternal chromosomes is completed with a combination of shared segment data and more logic. From points 73 through 89, Jack and I must share the same maternal segment. Gedmatch indicates that we share a half-region, and we do not share our paternal chromosome. We also have distant cousins 5C1R – AF and 5C1R – MG who share segment data with us. Even though these are distant cousins, our maternal grandparents came from different regions of the country so it is unlikely there is intermingling of these two branches of our tree. The paper trail also verifies the match. Jack stops sharing the segment at recombination point 89. From points 89 through 92, I do not share any DNA with Jack. From 92 through 108, we already share our paternal segment, so we must have different maternal segments. I continue to share with maternal cousin 5C1R – AF on the Leonard branch of the family while Jack shares part of his maternal portion with a McGraw cousin. (see diagram 8)

Diagram 8

And voilà! Chromosome 13 is mapped, only 22 more to go!

Chromosome mapping with only two siblings is highly dependent on matches with accessible segment data. Sometimes it takes time to find that one cousin who will provide the segment data you need. Just be patient! All it takes is one spit at a time…and possibly a lot of tenacity, and a little bit of bribery.

Blaine Bettinger ‘s Visual Phasing blogs:

Part I

Part II

Part III

Part IV

Part V

©2017 Deborah Sweeney
Post originally found: https://genealogylady.net/2017/05/02/down-the-dna-rabbit-hole-visual-phasing-with-two-siblings/

Down the DNA Rabbit Hole

I spend much of my genealogy work these days trying to sort and analyze my DNA research. It is amazing how time consuming this aspect of genealogy can be. However, I find it very fulfilling as well as enlightening. Currently I am working on a project that I think will break down several brick walls. As much as I want to share (because I am excited!!!), I also need to find two good cases to use for my BCG portfolio.

For the last year, many people in the genetic genealogy community have been very excited over a technique using the autosomal DNA of three of more siblings to map their chromosomes. In the beginning, I was stymied by this technique as I have only one sibling. However, I have used the shared DNA of my close family relatives to supplement the “three-sibling technique.”

Why is chromosome mapping important? For me, I love the visual picture of the map. Additionally, and most importantly, the map shows valuable information that I can use when tracing unknown matches. Below is an example of a mapped chromosome.

The top color block shows a one-to-one comparison of my brother and myself from the gedmatch website. The dark blue blocks show where we share half of our DNA while the gray sections indicate where no DNA is shared at all. A small section of bright green between lines 28-31 denotes that my brother and I inherited identical DNA from both our parents. Remember each chromosome is a pair (we inherit one from each parent).

The middle block is a representation of the segments I inherited from each of my four grandparents. The third block paints the segments of my brother’s thirteenth chromosome. I was able to complete this chromosome map thanks to five first and second cousins as well as several more distant cousins who have tested their autosomal DNA. By tracking and comparing the locations of shared segments among the cousins, I was able to determine which segments of DNA my brother and I inherited. Tracking is easily done with a basic spreadsheet.

My known paternal matches on chromosome 13

For future research, the completed map becomes a valuable tool. Whenever a match shares a portion of this chromosome with me or my brother, I can identify which branch of the family the match comes from. I can also use future matches to test the validity of the chromosome map.

©2017 Deborah Sweeney
Post originally found: https://genealogylady.net/2017/04/18/down-the-dna-rabbit-hole/