The sampling technique to get DNA to test is an important factor to understanding what is being measured. We already are aware of epigenetics which affects what part of each DNA strand is activated in a particular cell; giving rise to the development of different cells. But there is also genomic mosaicism where different cells arise to have different genetic material over time or due to some outside influence. So what cells are collected can affect the results that are delivered. As an example that came to the fore front recently — why does a cheek swab perform as a sufficient check for the existence of the Covid19 virus (versus a blood sample or saliva one) versus the nasal swab done in a healthcare setting?
There are four main types of cell collection techniques used when measuring the DNA of a person.
So why does the collection technique matter? In almost all cases, the majority of the collected DNA to be measured is based on white blood cells. But what if the tester has had a bone marrow transplant (as often happens during a Leukemia treatment). The white blood cells after transplant have the DNA from the bone marrow donor; not the recipient being tested. So using a technique to minimize the white blood cell contribution (that is, a buccal swab) is advised. This is termed mosaicism when a mix of sources of DNA can occur that can confuse the test results. Genotyping and sequencing results focus on expecting a pure sample; not one with a possible mixed source.
It is common to find those under 5 and over 80 cannot deal with a saliva spit collection technique. And yet, many of the personal DNA microarray testing companies only offer that solution. A user (see reference below) describes a successful technique of using brushes (like buccal swabs) and rinsing them in a fake saliva (saline) solution when submitting to Ancestry. Basically, a home remedy to do the fourth type mentioned above that seems to work (that is, have enough DNA in the sample) when submitting where a spit sample is expected.
The vast majority of the personal / consumer microarray test market uses saliva collection. A few use wet buccal swabs. YSEQ is unique in using dry buccal swabs — which are much easier to transport before and after collection. Dante has started using Tasso blood collection kits off and on since 2022. They used the Plus wet vial collection when ordered and delivered back to the USA (during their 1 year partnership with FTDNA) and the M20 dry capillary tube collector elsewhere in the world. Recent entrant NucleusGenomics uses the fourth swab and rinse technique.
In all cases, one is sampling the somatic cells. And not the germ or sex cells that get passed down to the next generation. We mention this because variants can be introduced into somatic cells over time. Local clusters of somatic cells can have a common variant that others do not. Such as occurs in a cancerous tumor. Hence why biopsies are performed of such suspect masses. Luckily, such somatic variant cells are not often picked up in sampling based primarily on white blood cells or even epithelial skin cells. Unless a bone marrow transplant has occurred.
There are four main types of cell collection techniques used when measuring the DNA of a person.
- The main technique used in a medical setting is a blood draw. Although medical testing looks at all components of the blood, the main nuclei DNA component in blood comes only from white blood cells.
- The main technique used in personal / consumer genetic genealogy are saliva spit tubes. Spit tubes contain upwards of 50% of the DNA collected from white blood cells. The amount of white blood cells dependent on what disease is in the mouth at the time. Otherwise, it is mostly epithelial cells.
- A second popular technique for consumer genotyping and collection is buccal swabs. Buccal swabs tend to have 90% or more of the collected DNA from epithelial skin cells of the inner mouth.
- A fourth technique is assisted saliva which uses repeated application of a buccal swab to soak up saliva with epithelial and white blood cells and then "wring" the swab into a collection solution. Repeating enough times to collect enough molecular weight DNA for testing.
So why does the collection technique matter? In almost all cases, the majority of the collected DNA to be measured is based on white blood cells. But what if the tester has had a bone marrow transplant (as often happens during a Leukemia treatment). The white blood cells after transplant have the DNA from the bone marrow donor; not the recipient being tested. So using a technique to minimize the white blood cell contribution (that is, a buccal swab) is advised. This is termed mosaicism when a mix of sources of DNA can occur that can confuse the test results. Genotyping and sequencing results focus on expecting a pure sample; not one with a possible mixed source.
It is common to find those under 5 and over 80 cannot deal with a saliva spit collection technique. And yet, many of the personal DNA microarray testing companies only offer that solution. A user (see reference below) describes a successful technique of using brushes (like buccal swabs) and rinsing them in a fake saliva (saline) solution when submitting to Ancestry. Basically, a home remedy to do the fourth type mentioned above that seems to work (that is, have enough DNA in the sample) when submitting where a spit sample is expected.
The vast majority of the personal / consumer microarray test market uses saliva collection. A few use wet buccal swabs. YSEQ is unique in using dry buccal swabs — which are much easier to transport before and after collection. Dante has started using Tasso blood collection kits off and on since 2022. They used the Plus wet vial collection when ordered and delivered back to the USA (during their 1 year partnership with FTDNA) and the M20 dry capillary tube collector elsewhere in the world. Recent entrant NucleusGenomics uses the fourth swab and rinse technique.
In all cases, one is sampling the somatic cells. And not the germ or sex cells that get passed down to the next generation. We mention this because variants can be introduced into somatic cells over time. Local clusters of somatic cells can have a common variant that others do not. Such as occurs in a cancerous tumor. Hence why biopsies are performed of such suspect masses. Luckily, such somatic variant cells are not often picked up in sampling based primarily on white blood cells or even epithelial skin cells. Unless a bone marrow transplant has occurred.
External References
- Theda, C., Hwang, S.H., Czajko, A. et al. "Quantitation of the cellular content of saliva and buccal swab samples". Nature Sci Rep 8, 6944 (May 2018).
- Wong YT, Tayeb MA, et al. "A comparison of epithelial cell content of oral samples estimated using cytology and DNA methylation". Epigenetics. 2022 Mar;17(3):327-334.
- Cascella R, Stocchi L, Strafella C, et al. "Comparative analysis between saliva and buccal swabs as source of DNA: lesson from HLA-B*57:01 testing". Pharmacogenomics. 2015;16(10):1039-46. doi: 10.2217/pgs.15.59.
- Ku CW, Shivani D, Kwan JQT, et al. "Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19". Int J Infect Dis. 2021 Mar;104:255-261. doi: 10.1016/j.ijid.2020.12.080. Epub 2021 Jan 2.
- Charburn, Kerry, "https://blog.dnagenotek.com/8-facts-most-people-dont-know-about-dna-from-saliva", The Genetic Link blog, DNA GenoTek, 1 Feb 2019
- Sammi, "How to do a DNA test without Spit (using a spit-only collection method)", series of blog posts with videos attached: Original, updated, final (2021) (not tested by anyone in our group as of yet; suspect buccal swabs may work instead of the brushes mentioned)