To genotype is to investigate the genetic constitution of an individual organism. Specifically, most often, to assess their variation from a known reference genome. Genotyping being the act of doing so.
Traditional genetic genealogy companies state they are providing genotyping services. In reality, they are performing microarray testing to extract a small subset of known variant locations in a persons genome. There are other forms of genotyping but none are used in genetic genealogy. The genotyping tests from microarray testing return all alleles whether they are ancestral or derived with respect to the reference genome. This is important because knowing what the ((allele) is can be more important than simply knowing what is different (or derived) from a reference genome. Because if the allele is not included, you cannot assume it was tested and ancestral. This is commonly misunderstood by those taking personal genetic tests.
As the technique of using microarray testing to find individual variants has been the only available method for the longest time, the word genotyping in the genetic genealogy community is often synonymous with any technique of variant discovery and testing. But this is a misnomer as "genotyping" is only the second wave of techniques used in genetic genealogy; albeit the most well known by those not invested in the concepts.
Key with this process is they are looking only for known variations. Most specifically and often, SNPs or simple, single base pair variation (and more properly termed SNP genotyping). This technique is not used to discover new possible variants among organisms. There are some simple InDels that are covered in genotyping tests.
Genotyping is implemented in genetic genealogy by microarray testing to read known variant locations. This is in contrast to sequencing which works to read each and every base pair in the human genome. And only later analyzing the base pairs for variance from one or more reference models. Possibly even years later after new variants are discovered to focus on.
Technically, that process of variant determination from a sequencing run could be called genotyping as well. But this is often not applied as sequencing use is so novel (in both genetic genealogy and the biological / medical fields as well). Illumina, that makes equipment for all these forms of testing, terms sequencing as the base of "whole genome genotyping" and microarray testing as "targeted genotyping". Technically, in its purest form, genotyping is the process to compare species with a known variation in characteristic between them to try and determine what underlying DNA variation may exist to cause the differences. The characteristic recognized may be a phenotype; but we digress.
Traditional genetic genealogy companies state they are providing genotyping services. In reality, they are performing microarray testing to extract a small subset of known variant locations in a persons genome. There are other forms of genotyping but none are used in genetic genealogy. The genotyping tests from microarray testing return all alleles whether they are ancestral or derived with respect to the reference genome. This is important because knowing what the ((allele) is can be more important than simply knowing what is different (or derived) from a reference genome. Because if the allele is not included, you cannot assume it was tested and ancestral. This is commonly misunderstood by those taking personal genetic tests.
As the technique of using microarray testing to find individual variants has been the only available method for the longest time, the word genotyping in the genetic genealogy community is often synonymous with any technique of variant discovery and testing. But this is a misnomer as "genotyping" is only the second wave of techniques used in genetic genealogy; albeit the most well known by those not invested in the concepts.
Key with this process is they are looking only for known variations. Most specifically and often, SNPs or simple, single base pair variation (and more properly termed SNP genotyping). This technique is not used to discover new possible variants among organisms. There are some simple InDels that are covered in genotyping tests.
Genotyping is implemented in genetic genealogy by microarray testing to read known variant locations. This is in contrast to sequencing which works to read each and every base pair in the human genome. And only later analyzing the base pairs for variance from one or more reference models. Possibly even years later after new variants are discovered to focus on.
Technically, that process of variant determination from a sequencing run could be called genotyping as well. But this is often not applied as sequencing use is so novel (in both genetic genealogy and the biological / medical fields as well). Illumina, that makes equipment for all these forms of testing, terms sequencing as the base of "whole genome genotyping" and microarray testing as "targeted genotyping". Technically, in its purest form, genotyping is the process to compare species with a known variation in characteristic between them to try and determine what underlying DNA variation may exist to cause the differences. The characteristic recognized may be a phenotype; but we digress.
External References
- European Bioinformatics Institute post on Functional Genomics course on Genotyping
- Illumina Genotyping Page
- 23andMe Blog post on Genotyping vs Sequencing
- 23andMe Video Blog Post on Genotyping vs Sequencing
- Helix blog post on Genotyping vs Sequencing