How to Test Your DNA (Even if You’ve Had a Stem Cell Transplant)
WHAT HAPPENS TO DNA WHEN SOMEONE HAS A STEM CELL TRANSPLANT?
Some people have had a stem cell transplant using their own stem cells. This type of transplant does not have any impact on DNA and DNA test results. Organ transplants also do not appear to impact DNA results, even though the organ has come from a different person whose DNA differs from you.
Those who have had stem cell transplants in which they’ve received a stem cell donation from another person run into challenges when having a DNA test on blood or saliva. After transplant, the white blood cells circulating through the body contain the DNA of the stem cell donor because the blood-producing cells of the bone marrow have been replaced by the donor’s. Red blood cells are essentially sacks of hemoglobin and don’t contain DNA, so only white blood cells are the issue.
If you test the DNA from a blood sample, you get results for the donor. A saliva or cheek swab on a stem cell recipient will often fail to give a DNA result because the DNA sample is a mixture of the original person and the donor. A sample from the mouth contains cheek tissue cells (with DNA from the recipient) and white blood cells (with DNA from the donor).
The DNA testing technology can be confused by this mixed sample of DNA and fail to return a result even after multiple attempts. Occasionally, the test succeeds, but with a potentially interesting outcome. You can read about a fascinating and interesting case I wrote about here in which a stem cell recipient’s consumer DNA test succeeded…but the DNA results were for the family member who donated to him!
WHAT CAN SOMEONE DO IF THEY’VE ALREADY HAD A STEM CELL TRANSPLANT?
Theoretically, there are now a few ways to try to get back a record of your DNA if you’ve already had a stem cell transplant. I have not heard of these being tried or tested approaches for stem cell recipients, so if you do try one and whether it succeeds or fails, please let me know!
First, try to find an artifact, in other words an item that may have traces of your DNA on it. Here are a few things laying around your house or in a stored box somewhere that may contain an old DNA sample for you. Remember, the DNA on the artifact must have come from you pre-transplant.
Potential artifacts:
old toothbrush
old letter with a stamp you’ve licked (maybe your spouse held on to old love letters?)
WHERE CAN ARTIFACTS BE TESTED?
A few companies are willing to attempt to extract DNA from an artifact you send them, for a fee. The two I am aware of at this point are:
There will be a fee for the DNA extraction. If extraction succeeds, the company will supply you with a computerized version of your DNA markers. Don’t use just any company you find on the Internet because they may not give you the right data file type. For genealogical purposes, you’ll need a VCF file based on SNPs tested on a genotyping microarray.
From what I’ve gathered via online reading and podcast listening, both of these companies only accept stamps at this time. Where can you learn more about DNA extraction from atypical samples?
Here’s one post by Denise May Levenick about Living DNA successfully extracting DNA from old letters.
Here’s a podcast from ExtremeGenes in which Blaine Bettinger, founder of DNA Central and writer of The Genetic Genealogist blog, talks about his experience sending in a letter attempting to extract DNA from a deceased ancestor. The DNA stamp discussion goes from around minute 10:30 to minute 22:00. As Blaine and Fisher talked about on the podcast linked to above (around minute 20), it’s not cheap to try to get DNA from a stamp ($575-ish American), but it may be worth the cost to you. totheletter DNA has been transparent with how things are going and post about it on their website. Unfortunately, the DNA extraction on Blaine’s submitted stamp didn’t result. As is to be expected, some samples work out and some don’t and the company is working on improving outcomes.
This interesting article by Sarah Zhang of the Atlantic talks about different ways DNA is being extracted from artifacts like parchment in old books and beeswax seals.
WHAT IF YOU CAN’T TRACK DOWN A STAMP YOU’VE LICKED?
For now, options for artifact testing is limited to stamps.
I remember reading somewhere in comments on a Facebook thread that a toothbrush was successfully used by someone to extract DNA to use for genealogical testing purposes, but I’ve not found a company that processes these on a consumer market basis (please contact me if you know this and I will update the post).
Hair is also not tested on the consumer market at this time; it appears to be only used in forensic analysis at the moment. But you would not need to track down an old hair sample in any event. Hairs freshly plucked from the scalp should work just fine since they are epithelial cells (like the cells that line the inside cheek).
If there is no way to get a pre-transplant stamp on you AND you are a biological parent, there is another avenue you might try — reverse engineering your DNA using your family members.
HOW CAN YOU REVERSE ENGINEER YOUR DNA USING YOUR FAMILY MEMBERS?
These methods were developed in order to study the passage of DNA from ancestors to their descendants, but you can use the same techniques on yourself. It will work best if you have a spouse and at least one child to test, or if you have multiple children or grandchildren available and willing to test. The more descendants you have, the better and more workable these approaches will be.
First, your descendants (or child and spouse) need to have their own DNA tests. Any of the major five companies described in this post by Leah Larkin would work, since what you need is the raw data file (computer files). Once the results of your children, spouse, and/or grandchildren are back, you can transfer their raw data to the free website GEDmatch.
Roberta Estes has blogged about how to do raw file transfers for each of the big companies on her website. Kitty Cooper has blogged about getting started with GEDmatch.
GEDmatch has become a bit controversial since it is now being used by law enforcement to lead to criminal arrests, like in the case of the Golden State Killer. Make sure you’re comfortable being a user of GEDmatch and learn about different privacy setting options available to you before you transfer data to it.
Lazarus
Using the results of your descendants, you may find it possible to patch together your DNA profile using the Lazarus tool at GEDmatch (and its companion site Genesis, which more recent 23andMe testers will need to use because of file type differences). Lazarus allows reconstruction of an ancestor’s DNA sequence using those of descendants. It’s written about in more detail by Israel Pikholz in this blog post here.
GEDmatch Phasing
Ann Turner shared an alternate idea to the Lazarus approach: using test results from your child and your child’s other biological parent (usually, your spouse) to make use of “phasing” options available at GEDmatch. Here’s how Ann described it in her own words:
Testing even one child along with a spouse should be useful. The child's kit can be phased against the spouse at GEDmatch. For example, if the stem cell recipient is the mother and the spouse is the father, then the child's M1 kit will represent the mother's alleles, with the added bonus of being phased and reducing a large number of false positive segments.
Additional children would add some additional matches. This is just a thought experiment on my part (no practical experience), but I actually think creating multiple semi-phased kits is better than a Lazarus kit. Say a SNP has two possible alleles, A and G. From child 1 you may learn that the parent has an A, and from child 2 your may learn that the parent has a G. When you combine them, the parent is heterozygous AG, a universal match to everyone in the database.
DOES THIS ACTUALLY WORK?
Will these approaches work for those who haven’t been able to test as a result of a past stem cell transplant? We do not know of any cases of stem cell recipients using these approaches at this point in time to attempt to get a usable data file for genealogical searching and matching. But since these approaches have worked for genealogists studying the DNA of deceased ancestors, they ought to work for anyone living as well.
It’s all theoretical until someone tries and succeeds the first time. I hope it will be you!
**This post was updated on 12/12/18 to include the ExtremeGenes podcast info, a recent blog post by Leah Larkin, and a quote by Ann Turner shared with permission. It was updated again on 2/20/2019 to include the link to the Atlantic article by Sarah Zhang and an update on Blaine Bettinger’s stamp DNA extraction.