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Imputation Matching Comparison

Roberta Estes

In a future article, I’ll be writing about the process of uploading files to DNA.Land and the user experience, but in this article, I want to discuss only one topic, and that’s the results of imputation as it affects matching for genetic genealogy. DNA.Land is one of three companies known positively to be using imputation (DNA.Land, MyHeritage and LivingDNA), and one of two that allows transfers and does matching for genealogy

This is the second in a series of three articles about imputation.

Imputation, discussed in the article, Concepts – Imputation, is the process whereby your DNA that is tested is then “expanded” by inferring results you don’t have, meaning locations that haven’t been tested, by using information from results you do have. Vendors have no choice in this matter, as Illumina, the chip maker of the DNA chip widely utilized in the genetic genealogy marketspace has obsoleted the prior chip and moved to a new chip with only about 20% overlap in the locations previously tested. Imputation is the methodology utilized to attempt to bridge the gap between the two chips for genetic genealogy matching and ethnicity predications.

Imputation is built upon two premises:

1 – that DNA locations are inherited together

2 – that people from common populations share a significant amount of the same DNA

An example of imputation that DNA.Land provides is the following sentence.

I saw a blue ca_ on your head.

There are several letters that are more likely that others to be found in the blank and some words would be more likely to be found in this sentence than others.

A less intuitive sentence might be:

I saw a blue ca_ yesterday.

DNA.Land doesn’t perform DNA testing, but instead takes a file that you upload from a testing vendor that has around 700,000 locations and imputes another 38.3 million variants, or locations, based on what other people carry in neighboring locations. These numbers are found in the SNPedia instructions for uploading DNA.Land information to their system for usage with Promethease.

I originally wrote about Promethease here, and I’ll be publishing an updated article shortly.

In this article, I want to see how imputation affects matching between people for genetic genealogy purposes.

Genetic Genealogy Matching

In order to be able to do an apples to apples comparison, I uploaded my Family Tree DNA autosomal file to DNA.Land.

DNA.Land then processed my file, imputed additional values, then showed me my matches to other people who have also uploaded and had additional locations imputed.

DNA.Land has just over 60,000 uploads in their data base today. Of those, I match 11 at a high confidence level and one at a speculative level.

My best match, meaning my closest match, Karen, just happened to have used her GedMatch kit number for her middle name. Smart lady!

Karen’s GedMatch number provided me with the opportunity to compare our actual match information at DNA.Land, then also at GedMatch, then compare the two different match results in order to see how much of our matching was “real” from portions of our tested kits that actually match, and what portion of our DNA matches as a result of the DNA.Land imputation.

At DNA.Land, your match information is presented with the following information:

Please note that you can click on any graphic to enlarge.

DNA.Land provides what they believe to be an accurate estimate of recent and anciently shared SNA segments.

The match table is a dropdown underneath the chromosome graphic at far right:

For this experiment, I copied the information from the match table and dropped it into a spreadsheet.

DNALand Match Locations

My match information is shown at DNA.Land with Karen as follows:

Matching segments are identified by DNA.Land as either recent or ancient, which I find to be over-simplified at best and misleading or inaccurate at worst. I guess it depends on how you perceive recent and ancient. I think they are trying to convey the concept that larger segments tend to me more recent, and smaller segments tend to be older, but ancient in the genetics field often refers to DNA extracted from exhumed burials from thousands of years ago.  Furthermore, smaller segments can be descended from the same ancestor as larger segments.

GedMatch Match

Since Karen so kindly provided her GedMatch kit number, I signed in to GedMatch and did a one-to-one match with this same kit.

Since all of the segments are 3 cM and over at DNA.Land, I utilized a GedMatch threshold of 3 cM and dropped the SNP count to 100, since a SNP count of 300 gave me few matches. For this comparison, I wanted to see all my matches to Karen, no matter how few SNPs are involved, in an attempt to obtain results similar to DNA.Land. I normally would not drop either of these thresholds this low. My typical minimum is 5cM and 500 SNPs, and even if I drop to 3cM, I still maintain the 500 SNP threshold.

Let’s see how the data from GedMatch and DNA.Land compares.

In my spreadsheet, below, I pasted the segment match information from DNA.Land in the first 5 columns with a red header. Note that DNA.Land does not provide the number of shared SNPs.

At right, I pasted the match information from GedMatch, with a green header. We know that GedMatch has a history of accurately comparing segments, and we can do a cross platform comparison. I originally uploaded my FTDNA file to DNA.Land and Karen uploaded an Ancestry file. Those are the two files I compared at GedMatch, because the same actual matching locations are being compared at both vendors, DNA.Land (in addition to imputed regions) and GedMatch.

I then copied the matching segments from GedMatch (3cM, 100 SNPs threshold) and placed them in the middle columns in the same row where they matched corresponding DNA.Land segments. If any portion of the two vendors segments overlapped, I copied them as a match, although two are small and partial and one is almost negligible. As you can see, there are only 10 segments with any overlap at all in the center section. Please note that I am NOT suggesting these are valid or real matches.  At this point, it’s only a math/match exercise, not an analysis.

The match comparison column (yellow header) is where I commented on the match itself. In some cases, the lack of the number of SNPs at DNA.Land was detrimental to understanding which vendor was a higher match. Therefore, when possible, I marked the higher vendor in the Match Comparison column with the color of their corresponding header.

Analysis

Frankly, I was shocked at the lack of matching between GedMatch and DNA.Land. Trying to understand the discrepancy, I decided to look at the matches between Karen, who has been very helpful, and me at other vendors.

I then looked at our matches at Ancestry, 23andMe, MyHeritage and at Family Tree DNA.

The best comparison would be at Family Tree DNA where Karen loaded her Ancestry file.  Therefore, I’m comparing apples to apples, meaning equivalent to the comparison at GedMatch and DNA.Land (before imputation).

It’s impossible to tell much without a chromosome browser at Ancestry, especially after Timber processing which reduces matching DNA.

DNA.Land categorized my match to Karen as “high certainty.” My match with Karen appears to be a valid match based on the longest segment(s) of approximately 30cM on chromosome 8.

Predicted vs Actual

One additional piece of information that I gathered during this process is the predicted relationship.

Vendor Total cM Total Segments Longest Segment Predicted Relationship
DNA.Land 162 to 3 cM 39 to 3 cM 17.3 & 12, split 3C
GedMatch 123 to 3 cM 27 to 3 cM 31.5 5.1 gen distant
Family Tree DNA 40 to 1 cM 12 to 1 cM 32 3-5C
MyHeritage No match No match No match No match
Ancestry 18.1 1 18.1 5-8C
23andMe 26 1 26 3-6C

Karen utilized her Ancestry file and I used my Family Tree DNA file for all of the above matching except at 23andMe and Ancestry where we are both tested on the vendors’ platform. Neither 23andMe nor Ancestry accept uploads. I included the 23andMe and Ancestry comparisons as additional reference points.

The lack of a match at MyHeritage, another company that implements imputation, is quite interesting. Karen and I, even with a significantly sized segment are not shown as a match at MyHeritage.

If imputation actually breaks some matching segments apart, like the chromosome 8 segment at DNA.Land, it’s possible that the resulting smaller individual segments simply didn’t exceed the MyHeritage matching threshold. It would appear that the MyHeritage matching threshold is probably 9cM, given that my smallest segment match of all my matches at MyHeritage is 9cM. Therefore, a 31 or 32 cM segment would have to be broken into 4 roughly equally sized pieces (32/4=8) for the match to Karen not to be detected because all segment pieces are under 9cM. MyHeritage has experienced unreliable matching since their rollout in mid 2016, so their issue may or may not be imputation related.

The Common Ancestor

At Family Tree DNA, Karen does not match my mother, so I can tell positively that she is related through my father’s line. She and I triangulate on our common segment with three other individuals who descend from Abraham Estes 1647-1720 .

Utilizing the chromosome browser, we do indeed match on chromosome 8 on a long segment, which is also our only match over 5cM at Family Tree DNA.

Based on our trees as well as the trees of our three triangulated Estes matches, Karen and I are most probably either 8th cousins, or 8th cousins once removed, assuming that is our only common line. I am 8th cousins with the other three triangulated matches on chromosome 8. Karen’s line has yet to be proven.

Imputation Matching Summary

I like the way that DNA.Land presents some of their features, but as for matching accuracy, you can view the match quality in various ways:

  1. DNA.Land did find the large match on chromosome 8. Of course, in terms of matching, that’s pretty difficult to miss at roughly 30cM, although MyHeritage managed. Imputation did split the large match into two, somehow, even though Karen and I match on that same segment as one segment at other vendors comparing the same files.
  2. Of the 39 DNA.Land total matches, other than the chromosome 8 match, two other matches are partial matches, according to GedMatch. Both are under 7cM.
  3. Of DNA.Land’s total 39 matches, 35 are entirely wrong, in addition to the two that are split, including two inaccurate imputed matches at over 5cM.
  4. At DNA.Land, I’m not so concerned about discerning between “real” and “false” small segment matches, as compared to both FTDNA and GedMatch, as I am about incorrectly imputed segments and matches. Whether small matches in general are false positives or legitimate can be debated, each smaller segment match based on its own merits. Truthfully, with larger segments to deal with, I tend to ignore smaller segments anyway, at least initially. However, imputation adds another layer of uncertainty on top of actual matching, especially, it appears, with smaller matches. Imputing entire segments of incorrect DNA concerns me.
  5. Having said that, I find it very concerning that MyHeritage who also utilizes imputation missed a significant match of over 30cM. I don’t know of a match of this size that has ever been proven to be a false match (through parental phasing), and in this case, we know which ancestor this segment descends from through independent verification utilizing multiple other matches. MyHeritage should have found that match, regardless of imputation, because that match is from portions of the two files that were both tested, not imputed.

Summary

To date, I’m not impressed with imputation matching relative to genetic genealogy at either DNA.Land or MyHeritage.

In one case, that of DNA.Land, imputation shows matches for segments that are not shown as matches at either Family Tree DNA or GedMatch who are comparing the same two testers’ files, but without imputation. Since DNA.Land did find the larger segment, and many of their smaller segments are simply wrong, I would suggest that perhaps they should only show larger segments. Of course, anyone who finds DNA.Land is probably an experienced genetic genealogist and probably already has files at both GedMatch and Family Tree DNA, so hopefully savvy enough to realize there are issues with DNA.Land’s matching.

In the second imputation case, that of MyHeritage, the match with Karen is missed entirely, although that may not be a function of imputation. It’s hard to determine.  MyHeritage is also comparing the same two files uploaded by Karen and I to the other vendors who found that match, both vendors who do and don’t utilize imputation.

Regardless of imputing additional locations, MyHeritage should have found the matching segment on chromosome 8 because that region does NOT need to be imputed. Their failure to do so may be a function of their matching routine and not of imputation itself. At this point, it’s impossible to discern the cause. We only know, based on matching at other vendors, that the non-match at MyHeritage is inaccurate.

Here’s what DNA.Land has to say about the imputed VCF file, which holds all of your imputed values, when you download the file. They pull no punches about imputation.

“Noisey and probabilistic.” Yes, I’d say they are right, and problematic as well, at least for genetic genealogists.

Extrapolating this even further, I find it more than a little frightening that my imputed data at DNA.Land will be utilized for medical research.

Quoting now from Promethease, a medical reference site that allows the consumer to upload their raw data files, providing consumers with a list of SNPs having either positive or negative research in academic literature:

DNA.land will take a person’s data as produced by such companies and impute additional variants based on population frequency statistics. To put this in concrete terms, a person uploading a typical 23andMe file of ~700,000 variants to DNA.land will get back an (imputed) file of ~39 million variants, all predicted to be present in the person. Promethease reports from such imputed files typically contain about 50% more information (i.e. 50% more genotypes) than the corresponding reports from raw (non-imputed) data.

Translated, this means that your imputed data provides twice as much “genetic information” as your actual tested data. The question remains, of course, how much of this imputed data is accurate.

That will be the topic of the third imputation article. Stay tuned.

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