Genetic testing

This article is about genetic testing for an individual human genome. See Microbiome for testing the bacterial flora

Genetic testing, also known as DNA testing, analyzes an individual's genome to identify variations in DNA sequence and chromosome structure. Personal genetic information can be used to provide insights into ancestry, carrier status for heritable diseases, prediction of disease risk, and other human traits. Due to the high costs of whole genome sequencing, various technologies (e.g. microarray testing) are commonly used to more efficiently target analysis of specific regions or variations . While genetic testing is used and regulated in a clinical context, Direct-To-Consumer (DTC) companies also offer products focused on providing ancestry and health insights.

Genomes and genetic information

An individual's "genome" is the genetic material within the cells of their body. All cells in the body contain a copy of this genome, which are nearly identical copies of an original genome inherited from their biological parents. This genome consists of DNA molecules consisting of long sequences of "bases": adenine (A), cytosine (C), guanine (G), and thymine (T). The identity and sequence of these bases is the genetic information of an organism, and a human genome contains roughly 3 billion bases distributed in 23 chromosome pairs.

Genetic information in an individual genome is nearly identical to another individual of the same species: any two humans are 99.9% identical. The individual base positions that differ between individuals, as well as larger architectural differences, are the "genetic variants" that characterize an individual's personal genetic information.

Biologically, the genome primarily functions through the creation of proteins synthesized from "genes" (specific regions of genetic sequence). Genetic variants with biological effects (e.g. on traits or disease) commonly occur due to their effect on protein-coding. The subset of all protein-coding regions, known as the "exome", represents just 2% of the genome. Most genetic variations occur outside these regions and have little or no functional consequence, representing random changes that have accumulated over generations.

Genetic testing providers

"Direct-to-consumer" (DTC) genetic testing providers have offered genetic testing directly to consumers since the early 2000s.

Micro-array testing

Genetic testing based on micro-array technology is still the most widely used and offered form of DTC genetic testing due to the comparatively low cost of performing these tests. They analyze the genome for a wide array of different known genetic variants (between 300,000 and 700,000 variants depending on the provider). These variants are selected to help understand a person's ancestry and/or health, depending on the provider chosen.

Besides the raw testing results, providers deliver varying kinds of analyses. Virtually all DTC providers deliver ancestry results, based both on public reference populations as well as other customers of the given provider. Some providers like 23andMe additionally deliver results on human traits (also called phenotypes). Some additionally offer health or well-being related predictions.

Common providers:

• 23andMe
• AncestryDNA
• FamilyTreeDNA
• MyHeritage

Whole exome/genome testing

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Whole exome sequencing analyses the DNA that encodes all ~17,000 proteins that the human genome encodes. Unlike micro-array based methods (see above), this allows to find novel variants that have not previously been described. While exome sequencing can provide a more detailed analyses of the protein-coding regions of the human genome, it is important to keep in mind that only ~2% of the human genome actually encode for proteins, leaving 98% of the DNA unanalysed. In contrast, the thousands of variations used in micro-arrays fall both within and outside of protein-coding regions.

Whole genome sequencing analyses nearly all of the human genome. Consequentially it is also the most expensive way to get DNA testing done. Prices can vary both between sequencing providers as well as sequencing depth, which is a proxy for how well and accurate the sequencing is. Generally, the larger the sequencing depth the higher the cost but also the possibility to reliably detect variants.

Common providers:

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Limitations

There are a number of limitations to DTC genetic testing: Most DTC genetic testing offers are not validated for clinical use and are not reviewed by the Food and Drug Administration in the US (or equivalent bodies in other countries), as such they are not designed to deliver medical advice. Additionally, some studies have found excessive false-positive rates in DTC genetic testing (up to 40% for some variants).

DTC genetic tests are not generally available everywhere, as some countries (in particular in Europe, e.g. France or Germany) do not allow for genetic testing without a prescription by a medical doctor. Regardless of this, for some of those countries US providers offer testing by shipping sample collection kits into these countries while doing the actual sample processing back in the US.

Genetic testing interpretation

While most DTC testing providers deliver their own interpretations of the results of the genetic test, there is a growing body of third-party tools that can use the raw data generated by DTC providers to deliver enhanced report

Tools:

• Genevieve, uses the ClinVar database to deliver insights
• SNPedia / Promethease, makes use of the crowdsourced literature database of SNPedia
• GWAS catalog, a catalog of published genome-wide association studies to look up impact of individual variants
• MyVariant, an API that aggregates raw data for interpretation from a variety of sources

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