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Autosomal, Whole Genome Sequencing, and Chromosome Painting


Findings to date

Looking at the reliability of autosomal (atDNA) testing and how it compares with other testing methodologies, such as Whole Genome Sequencing and Chromosome Painting.

1. atDNA testing is reliable when reported by continent.
2. atDNA testing within regions of a continent is less accurate.
3. Test results differ among atDNA, Whole Genome, and Chromosome Painting.
4. Ancestry estimates influenced by level of statistical confidence.

Discussion

A consensus of atDNA test companies reveals few differences in estimating my ancestry percentages by continent. But differences exist between these estimates and two other methodologies -- whole-genome sequencing (WGS) and chromosome painting. Additionally, limitations exist in the usefulness of estimates made within a continent and the level of confidence of their estimations.

atDNA and WGS Ancestry Estimates Compared.

Table 4 reports ancestry estimates at the continental level between the consensus atDNA tests and Nebula Genomics. The degree to which these differences are significant is arguable, but for my purpose, they are relatively consistent.

Continental Ancestry

atDNA companies, such as 23andMe and AncestryDNA typically use microarray-based atDNA DNA testing. These companies sequence around 700,000 positions in our genetic sequence. In contrast, Nebula's (WGS) sequences my genome at 0.4x coverage which corresponds to ~ 1.3 billion positions and results in one thousand times more data than tests using microarray-based genotyping.

Also, unlike tests that use microarray-based atDNA DNA testing DNA Microarrays, WGS discovers novel genetic variants. Moreover, reportedly, the Nebula Genomics WGS test results are more accurate for people that have no European ancestry, which is partly my case.

However, both atDNA companies and Nebula Genomics rely on the process of educated guessing known as imputation in their ancestry estimates. atDNA companies, such as 23andMe, Ancestry and My Heritage, use imputation to expand their test results by inferring results for what they haven’t tested based on the results they have tested. Also, Nebula's coverage at .4x is really a partial read of the genome (about 40%), which is supplemented by imputation to infer the sequence of gaps in the data for the remaining 60%.

Chromosome Painting Comparisons

Chromosome painting offers another means by which atDNA testing provides a way of looking at ancestry. The Chromosomes Painting in Figure 3 is a view of my ancestry composition. It shows the 46 chromosomes passed between generations in the form of 23 pairs. My interest is with the first 22 because they represent ancestries I match. Each of these autosomes pairs appear as one of the colored horizontal lines.

Figure 3. My Chromosomes Shown in Color by Ancestry
23andMe DNA company Chromosome Painting


The multi-colored chromosome painting reveals the genetic mixing of my ancestry from different populations. The populations appear in the horizontal lines color-coded by descent. The long, unbroken stretches of color are evidence of recent ancestry, while the short segments suggest those of many generations ago. More recent sources of ancestry will have segments of that ancestry on more chromosomes. Moreover, those segments will be longer than of my ancestors of many generations ago. Of course, a significant limitation is that companies base their chromosome painter results on different databases. Thus chromosome paintings may not be consistent from one company to another.

Continent Estimates Comparisons

My ancestry reported by all three technologies is depicted in Table 5.

Continental Ancestry

Within Continent Limitations of Estimates

Differences in estimates of my ancestry percentages increase when viewed within continents. As Estes warns, "Within continents, like Europe, Asia and Africa, there has been a lot of population movement and intermixing over time making the term 'ethnicity' almost meaningless." Dr. Rutherford's parallel this view. "By inference, we are to assume that significant proportions of our deep family came from those places. But to say that you are 20 percent Irish, 4 percent Native American or 12 percent Scandinavian is fun, trivial and has very little scientific meaning."

An example of this is my Iberian ethnic ancestry estimates from atDNA testing, whole genome sequencing, and chromosome paining in Table 6.

Ancestry

Confidence in Estimating Ancestry

A confidence level refers to the percentage of all possible sample values expected to include the actual population value. A confidence level of 90% is a common choice in social research and expressed 90% CI. It is a range of values at 90% certainty to contain the true mean average value of the studied population. The chromosome painting values reported in Figure 4 and Table 5 are speculative calculations with a level of confidence of 50% by the company.

Depending on the company's level of confidence, its estimate of ancestry can vary. Table 7 is a chromosome painting prediction of my ancestral origin by the company, 23andMe. It depicts the speculative level of confidence (50%), which is the default, but with an option for users to select different confidence levels, including the 90% Confidence Level.

To yield more in-depth answers about my genetic ancestors living far back in prehistory, I next turned to mtDNA Y-DNA testing. These tests reach far back in matrilineal and patrilineal genetic prehistory.

Chromosome Painting

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