Louis Kessler’s Behold Blog

Kevin Borland is the author of Borland Genetics, a fantastic site where you can upload your Raw DNA data, match to others, and use tools to reassemble your ancestors’ DNA. I very recently wrote a blog post about Kevin’s site.

Kevin also has a blog in which he has been posting very interesting articles, usually of an analytic nature which are the type I really like. Yesterday, Kevin posted an excellent article: Help! My Segments Are So Sticky! in which he clearly explains how he calculated the probabilities of age ranges for 7 cM and 20 cM autosomal segments, where he used 25 years = 1 generation.

So Kevin gives another take on the segment age estimates done by Speed and Balding in their 2014 paper made available online by Doug Speed:
Relatedness in the post-genomic era: is it still useful?

In the Genetic Genealogy Tips & Techniques group on Facebook, Blaine Bettinger posted about Kevin’s article and said: “I would absolutely love to see Kevin address the differences between his calculations and the calculations in the Speed & Balding paper, how fun that would be!”

I’ve always felt that Table 2B from the Speed and Balding paper overestimates the age of segments for a given segment size. I wrote two articles on my blog in 2017 with alternative analyses and compared them to Speed and Balding:

• Revisiting Speed and Balding – 5 Nov 2017
• Another Estimate of Speed and Balding Figure 2B – 15 Nov 2017

And I further updated that with another calculation in my article:

• The Life and Death of a DNA Segment – 19 Aug 2019

Those articles received many comments, including one from Doug Speed, and much discussion on Facebook.

So I was very interested to see what Kevin’s analysis says. Let’s compare.

Using Kevin’s easy to follow method of calculation, I can first calculate the probability of no recombinations in x generations:

And then I simply subtract each column from the previous to give the probability that a segment is x generations old:

Now let’s plot this in the Speed and Balding chart format:

Lets compare this to the Speed and Balding Figure 2B chart that everyone quotes. I’ll cut off the left and right sides which have smaller and larger segments that we’re not comparing:

Speed and Balding uses ranges, so for Kevin’s chart above, I used values at the start, middle and end of each range. Speed and Balding uses Megabases (Mb)and Kevin uses centimorgans (cM), but they are close enough for practical purposes.

What we see is:

Speed and Balding, 1 – 2 Mb:  About 18% chance of <= 20 Generations
Kevin Borland, 1 – 2 cM:  Between 18% and 33% chance of <= 20 Generations

Speed and Balding, 2 – 5 Mb:  About 28% chance of <= 20 Generations
Kevin Borland, 2 - 5 cM:  Between 33% and 63% chance of <= 20 Generations

Speed and Balding, 5 – 10 Mb:  About 50% chance of <= 20 Generations
Kevin Borland, 5 - 10 cM:  Between 63% and 87% chance of <= 20 Generations

Speed and Balding, 10 – 20  Mb:  About 68% chance of <= 20 Generations
Kevin Borland, 10 – 20 cM: Between 87% and 98% chance of <= 20 Generations

So indeed, Kevin’s figures do corroborate with my own and indicate that Speed and Balding’s table likely are an overestimate to the age of segments of a certain size.

Disclaimer: I sort of knew after reading Kevin’s article that his estimates would be similar to mine, since I used the same calculations as Kevin in my Life and Death of a DNA Segment article, except that I used the Poisson distribution for the starting probability rather than the 1 cM = 99% estimate that Kevin used.

On Facebook, I was delivered a sponsored ad for getting health reports from your DNA raw data at a 55% discount from a company called Xcode Life.
@xcode_ls

I’ve always been much more interested in DNA for genealogical purposes than for health, but I had never heard of this company and it sounded interesting. Their “Mega Pack report was said to contain reports for Nutrition, Fitness, Health, Allergy, Skin, Precision Medicine, Methylation, Carrier Status, and Traits & Personality in 600+ categories.

I looked around on the internet for a coupon and saved an additional $10 and paid $89 for the package. They accept uploads from all the major companies. I uploaded my combined all-6 file with 1.6 million SNPs in it that was in 23andMe format and it was accepted.

The next morning, 13 hours later, I got an email stating my reports were ready. In the email, they gave me the coupon code REFVTB47WRMU5 worth $10 off any of their packages that I can give away. If you use it, I will also get $10.

The Reports

I downloaded my reports as a compressed zip file. After unzipping, there were 9 pdf files for the 9 reports ranging in size (for me) from the Methylation report at 10 pages up to the Carrier report at 84 pages.

Most of the reports start with a 2 page introduction, the first page on understanding your report and the 2nd page on how to read your report. Each report ends with a 1 page disclaimer.

The results follow on the next 2 to 4 pages and each trait is presented as one row of a table containing 2 or 3 possible results. They are color coded green for better than average, orange for average and red for not as good as average.

For example, the Personality Results have two possible results. These are a couple of mine with better than average results:

And here’s a couple with just average results:

And then there are those for negative traits:

Whereas the Nutrition, Skin, Health, Allergy and Fitness reports give mostly 3 possible outcome per trait, e.g.:

The remainder of these 6 reports summarize and explain each of the traits, giving a recommendation with the same color as your result. It then tells you which genes were analyzed for the trait, but does not tell you which SNPs were analyzed or what your SNP values were.

The other 3 reports each have their own format.

The Carrier report lists 402 different conditions in alphabetical order and tells you if you have potential pathogenic variants.

They write in bold red letters in the introduction that these are not to be used for medical purposes. And the disclaimer says only your physician is qualified to interpret this report and incorporate this information in treatment and advice. None-the-less, if anything shows up, it is likely worthwhile following up on it with your doctor.

Actual SNPs!

The other two reports had what I was more interested in. I wanted the actual SNPs identified indicating the value that I had for them and what they meant.

The Pharmacogenetics Report lists the gene variants I have that are associated with my reaction to 185 different drugs:

The rsid (Reference SNP cluster ID) is listed,as well as my result: the Genotype TT.  I can find the rsid: rs2395029 in my Raw Data File that I supplied to Xcode.Life and that will tell me where it is by chromosome and position:

So this SNP is on Chromosome 6, position 31,431,760 and yes, it does have the value TT.

I can then look up that rsid on Google and it will bring up lots of other information that can be found about the SNP:

such as SNPedia, which was recently purchased by MyHeritage that they are leaving as a free resource available to all., presumably to give them information for their health tests.

The Methylation Report lists about 60 SNPs from various genes that are associated with conditions such as cardiovascular disease, Alzheimer’s, cancer, depression. They list the normal value, the risk value, and then show your genome values (GENO), shading the line if you have one or two risk values.

Conclusion:

I wasn’t expecting to find too much of importance, as I am relatively healthy, and my 23andMe health test results didn’t come up with anything important. But the Xcode Life reports did identify 1 potential variant for a condition I have that would have helped me 5 years ago before I found out about it.

If you have some ailment but don’t know what’s causing it, a DNA-based health report like this one from Xcode Life might be a good screen. If something shows up, you can discuss the report with your doctor.

For me, I did this mostly for curiosity. Having the rsids of the SNPs of interest in the Pharmacogenetics and Methylation reports will allow you, as a genetic genealogist to map those SNPs onto your genome with a tool like DNA Painter, and track those SNPs though your ancestors.

There’s another website I recommend you upload your DNA raw data to called Borland Genetics.

See this video: Introducing Borland Genetics Web Tools

In a way, Borland Genetics is similar to GEDmatch in that they accept uploads of raw data and don’t do their own testing. Once uploaded, you can then see who you match to and other information about your match. Borland Genetics has a non-graphic chromosome browser that lists your segment matches in detail.    
   
But Borland Genetics has a somewhat different focus from all the other match sites. This site is geared to help you reconstruct the DNA of your ancestors and includes many tools to help you do so. And you can search for matches of your reconstructed relatives, and your reconstructed relatives will also show up in the match lists of other people.

Once you upload your raw data and the raw data from some tests done by a few of your relatives, you’re ready to use the exotically named tools that include:

• Ultimate Phaser
• Extract Segments
• Missing Parent
• Two-Parent Phase
• Phoenix (partially reconstructs a parent using raw data of a child and relatives on that parent’s side)
• Darkside (partially reconstructs a parent using raw data of a child and relatives that are not on that parent’s side)
• Reverse Phase (partially reconstructs grandparents using a parent, a child, and a “phase map” from DNA Painter) 

Coming soon is the ominously named: Creeper, that will be guided by an Expert System that use a bodiless computerized voice to instruct you what your next steps should be.

There’s also the Humpty Dumpty merge utility that can combine multiple sets of raw data for the same person, and a few other tools.

The above tools are all free at Borland Genetics and there’s a few additional premium tools available with a subscription. You can use them to create DNA kits for your relatives. Then you can then download them if you want to analyze them yourself or upload them to other sites that allow uploads of constructed raw data.

By comparison, GEDmatch has only two tools for ancestor reconstruction. One called Lazarus and one called My Evil Twin. Both tools are part of GEDmatch Tier 1, so you need a subscription to use them. Also, you can only use the results on GEDmatch, because GEDmatch does not allow you to download raw data.

Kevin Borland

The mastermind behind this site is Kevin Borland. Kevin started building the tools he needed for himself for his own genetic genealogy research a few years ago and then decided, since there wasn’t one already, to build a site for DNA reconstruction. See this delightful Linda Kvist interview of Kevin from Apr 16, 2020.

In March 2020, Kevin formally created Borland Genetics Inc.and partnered with two others to ensure that this work would continue forward.

If you are a fan of the BYU TV show Relative Race (and if you are a genealogist, you should be), then you should know that Kevin was the first relative visited by team Green in Season 2.  See him at the end of Season 2 Episode 1 starting about 32:24.

Creating Relatives

I have not been as manic as many genetic genealogists in getting relatives to test. I only have my own DNA and my uncle (my father’s brother) who I have tested. So with only two sets of raw data, what can I do with that at Borland Genetics?

Well, first I uploaded and created profiles for myself and my uncle.

The database is still very small, currently sitting at about 2500 kits. Not counting my uncle, I have 207 matches with the largest being 54 cM. My uncle has 86 matches with the largest being 51 cM. This is interesting because most sites have more matches for my uncle than for me, since he is 1 generation further back.  I don’t know any of the people either of us match with. None of them are likely to be any closer than 4th cousins.

My uncle and I share 1805.7 cM. The chromosome browser indicates we have no FIR (fully identical regions) so it’s very likely that despite endogamy, I’m only matching my uncle on my father’s side.

The chromosome browser suggest three Ultimate Phaser options for me to try:

To interpret the results of these, you sort of have to know what you’re doing.

So let me go instead to try create some relatives. For that I can first use the Phoenix tool.

It allows me to select either myself or my uncle as the donor. I select myself as the donor and press Continue.

Here I enter information for my father and press Continue

I now can select all my matches who I know are related on my father’s side. You’ll notice the fourth entry lists the “Source” as “Borland Genetics” which means it is a kit the person created, likely of a relative who never tested anywhere.

In my case, my uncle is the only one I know to be on my father’s side, so I select just him. I then scroll all the way down to the bottom of my match list to press Continue.

And while I’m waiting, I can click play to listen to some of Kevin’s music.  After only about 2 minutes (the time was a big overestimate) the music stopped and I was presented with:

I now can go to my father’s kit and see what was created for him. His kit type is listed as “Mono” because only one allele (my paternal chromosome) can be determined. The Coverage is listed as 25% because I used his full brother who shares 50% with him, and thus 25% with me.

His match list will populate as if he was a person who had tested himself.

I can download my father’s kit:

which gives me a text file with the results at every base pair:

The pairs of values are all the same because this is a mono kit. Also be sure to  use only those SNPs within the reconstructed segments list. There must be an option somewhere to just download the reconstructed segments, but I can’t see it. (Kevin??)

In a very similar manner (which I won’t show here because it is, well, similar), I can use the Darkside tool to create a kit for my Mother using myself as the child and my Uncle as the family member on the opposite side of the tree.

Reconstructing Ancestral Bits

Now I have kits for myself, my uncle, my father and my mother. Can I do anything else?

Well yes! I can use my analysis from DNA Painter to define my segments by ancestor.

I just happened to have the DNA Painter analysis done already, which I used Double Match Triangulator for. Using DMT, I created a DNA Painter file from my 23andMe data for just my father’s side:

I labelled them based on the ancestor I identified, e.g. FMM = my father’s mother’s mother. I downloaded the segments from DNA Painter and clicked “Choose File” in Borland Genetics and it gave me my 5 ancestors with the same labeling to choose from.

I select “FF”, click on “Extract Selected Segments” and up comes a screen to create a Donor Profile for my paternal grandfather!

Wowzers! I have now just created a DNA profile for a long-dead ancestor, and I can do the same for 4 more of my ancestors on my father’s side.

Just a couple of days ago, I think I was asking Kevin for this type of analysis. Only today when writing this post, did I see that he already had it.

Summary

I only have my own and my uncle’s raw data to work with, yet I can still do quite a bit. For people who have parents, siblings and dozens of others tested … well I’m enviously drooling at the thought of what you can do at Borland Genetics with all that.

There is a lot more to the Borland Genetics site than I have discussed here. There are projects you can create or join. Family tree information. Links to WikiTree. You can send messages to other users. There are advanced utilities you can get through subscription.

The site is still under development and Kevin is regularly adding to it. Kevin started a Borland Genetics channel on YouTube, and over the past 2 years he made an excellent 20 episode series of You Tube videos on Applied Genetics. And he runs the Borland Genetics Users Group on Facebook, now with 738 members.  – I don’t know how he finds the time.

So now, go and upload your raw data kits to Borland Genetics, help build up their database of matches, and try out all the neat analysis it can do for you.