Test Methods, Markers, Targets and Results

We use this page to describe the detail of genetic genealogy test Methods, Markers, Targets and Results. Each should be clearly understood if you want to understand a particular product offered to the genetic genealogist.

Test Methods

There are three main test methods that are used in genetic genealogy. These methods came in waves of introduction. There is the original 1st wave based on capillary electrophoresis (CE), the 2nd wave of chip microarray testing, and the newest 3rd wave of high throughput sequencing (HTS). The latter initially using 30x WGS testing based on short-read NGS techniques offered to consumers.

These three waves of test methods roughly define the three decades of genetic genealogy as well. CE dominating the first decade since the genetic genealogy start in 2000. Microarray the second decade just ended. And now HTS starting to take over as the mainstay for the third decade. We use the term "waves" instead of "generation" to avoid the confusion with the "generations" of sequencing technology as well as the genealogy term covering ancestors and descendants.

Test Targets

There are three main test targets based on what DNA is being analyzed. These are autosomal (aka atDNA) with xDNA combined; or atxDNA to be more accurate, Y chromosome (yDNA), and mitochondrial (mtDNA). Any test method may be utilized for one or more test targets.

The test methods and test targets can vary widely in depth, coverage, and what benefits they may provide to the genetic genealogist.

Most genetic genealogy companies today are only offering the 2nd wave chip microarray testing introduced by 23andMe back in 2007. FTDNA and YSEQ are the only ones still offering 1st wave CE products. But numerous new entrants as well as established players are in the HTS space. Older players may use HTS as an extension of their original yDNA testing focus. While newer players often provide a product for a wider market than just genealogy.

We introduce here a chart showing the intersection of test methods with test targets and the players with product in that space.

Targets / Method	1st Wave CE	2nd Wave Microarray	3rd Wave HTS sequencing
atxDNA	Legal Forensics Only	23andMe, Ancestry, FTDNA, MyHeritage, LivingDNA, etc	Dante, Nebula, Sequencing.com, YSEQ, FGC
yDNA	FTDNA, DNA Fingerprint / YSEQ, SMGF	not FTDNA	Dante, Nebula, Sequencing.com, YSEQ, FGC, FTDNA (limited)
mtDNA	FTDNA	not FTDNA	Dante, Nebula, Sequencing.com, YSEQ (limited), FTDNA

Key to understand is that microarray testing is not just atxDNA testing; although that is the main use and analysis provided by most vendors. The microarray testing method tests all the DNA just like HTS. But because it uses primers like CE, it can only target known variants

Different vendors have a focus on delivering data with different targets. Genetic genealogy vendors are utilizing medical laboratory equipment. All microarray testing and HTS equipment return results from ALL the DNA. It is just that some vendors strip data out and choose not to return all the results or provide the analysis of all the ==test targets==. Do not be naive about what is being tested with a particular test method and therefore what can be delivered from it based on the test targets. Many so called "experts" in the genetic genealogy field do not understand this basic concept. And think microarray testing can and does only deliver atxDNA results. Or that yDNA and mtDNA testing is limited to that offered by historic CE techniques.

Test Markers

There are two main types of genetic markers analyzed from test results: Single-Nucleotide Variants (SNVs) and Copy-Number Variants (CNVs).

SNVs

We use the SNV term to include any small base-pair variation (mostly of length of 5 or less). This included small Insertion-Deletions (InDels). This generalization is common even in the genetics industry. But more strictly, SNV only applies to a single base-pair change in the DNA.

You will often hear the term Single Nucleotide Polymorphism (SNP) instead of SNV. SNP is technically a more specific term as it relates to the frequency of an SNV as found in the general population. Early adopters of genetic genealogy did not pay close attention to this and you mostly see SNP mentioned where SNV is really meant. The two are used interchangeably in the genetic genealogy field. But just realize that SNP is a refinement of SNV. DNA knowledge and testing is still quickly evolving and so are the terms that apply to it.

SNVs are looked for everywhere. It is the SNVs in yDNA and mtDNA that give rise to the definition of haplogroups and the phylogenetic trees that are built from them. SNVs are delivered in the microarray test results and can also be extracted from sequencing results. SNVs in atxDNA are used both for developing matching segments between testers and the ethnicity pie charts (or more formally, ad-mixture analysis). There are about 5,000 to 10,000 InDels interspersed in the microarray file results often of around 600,000 values. But these are often ignored. They are important for medical analysis performed with microarray test result files.

It can be just as important to know the SNV was tested and returned the reference model result as it is to know the SNV was variant from it. So, in most cases, the result of the test is returned for that marker no matter how the result compares to a standard reference genome model. In reality, around 15% of microarray test results are variant from the standard reference and general population. And only around 1-2% of the billions of results in HTS are different from that same reference. Rarely will just the actual variants from the reference be reported.

Microarray tests test only known SNVs whereas HTS testing returns results of all the DNA. Thus HTS is often used for the discovery of previously unknown variants. Which is why genetic genealogy is quickly adapting to the 3rd wave HTS testing. So much so that advances in the understanding of yDNA variants are being discovered by non-professional genetic genealogists and ancient DNA researchers quicker than the medical and traditional scientific research communities.

CNVs

Although CNV is the more general term, genetic genealogy is really only looking at a more restricted form known as Simple Tandem Repeats (STRs). And then only on the (Y chromosome. yDNA STR was the early and only form of genetic genealogy testing before widespread testing of SNVs was possible. STRs are still generally measured via CE although increasingly being extracted from HTS testing when possible. NGS testing based on short-read segments cannot reliably extract the longer STR values. But third generation HTS using long-reads often can.

Luckily, with HTS SNV testing of the yDNA, the testing of STRs using CE has become less important. yDNA STR testing was the mainstay of the 1st wave genetic genealogy and still widely used and followed for these historical reasons. STR testing has less importance as the deep SNV testing of yDNA made possible by the 3rd wave HTS reaches closer into the genealogical time frame with more accurate prediction of genealogical time frame family lines than STRs.

Test Results

Based on the test targets and test markers, there are four main types of genetic genealogy test results that are historically analyzed. They tend to be analyzed separately by different tools and are shown below in general order of importance to this project. The distinction of yDNA test analysis methods and use is quickly disappearing as SNV overtakes and absorbs all STR testing value.

1. Autosomal with X (Allosome) SNP (atxDNA) test results with segment matching analysis,
2. Y (Allosome) SNP (yDNA SNP) testing with haplogroup analysis,
3. Y (Allosome) STR (yDNA STR) testing with haplotype comparisons, and
4. Mitochondrial SNP (mtDNA) testing with haplogroup analysis,

It is very important to understand the differences in these test results, test targets and test methods as the testing companies do not clarify their offering and often make claims contrary to what you might expect for the type of test performed. Each type of test is explained in more detail in the next sections. See the Glossary or simply click on the terms for further clarification.

That concludes our coverage of the various test aspects. You can either continue on or return to the parent genetic genealogy testing page.