The Chip Micro-Array (or even DNA Microarray), is a DNA test technique most used by traditional genetic genealogy test companies providing ethnicity reports and match lists across the autosomes. It is used to return around 600,000 alleles on the diploid autosomes, X and often some Y and mtDNA values as well. The microarray is a very cost-effective way to return hundreds of thousands of known SNP values and can often handle 12 to 24 different samples (testers) DNA at the same time. This technique works to identify ancestral versus derived values for already known SNPs. Not to discover new SNPs as happens with (full or next-generation) Sequencing. The genetics industry also calls it a Genotyping Assay or also a BioChip. Illumina's technique of using micro-beads that are pre-doped leads to the term micro-bead arrays or simply bead arrays as well. The technique of the microarray was invented in the 1980's at Stanford University by Patrick Brown.
Each genetic genealogy testing company has their own custom microarray with their defined SNP markers they test for. The overlap of SNPs tested by different chips from different companies (and even versions within the same company) is often large but can vary quite a bit. Leading to problems with doing segment match analysis on test results from different companies. This was first pointed out by Felix Chandrashakar on y-str.org when he developed some early analysis tools and much later picked up by ISOGG when they tried to understand the problems GEDMatch and MyHeritage were having incorporating different test companies using the new array products. The Illumina OmniExpress (r) and GlobalScreening (r) array chips have been popular as well as the Affymetrix GeneChip (r).
There is no standard, defined file format to represent the results although a somewhat defacto standard has emerged. Many term it the RAW File Format from the link name given in result pages. There is some basis for this as the files are similar to RAW VCF files in a simple TSV format. In fact, traditional sequencing tools can read and write these files. The biggest caveat being that these microarray file format (or RAW)) have both ancestral and derived values. A standard VCF only has derived.
Many lay persons in the consumer genetic genealogy market shorten the term "DNA Microarray Testing to extract a genotype" to simply "genotyping" instead of Microarray Testing. This is a bit of a misnomer as there are other forms of genotyping than just microarray testing. As mentioned earlier, genotyping assay is a term used in the genetics industry from which this use likely derives.
Each genetic genealogy testing company has their own custom microarray with their defined SNP markers they test for. The overlap of SNPs tested by different chips from different companies (and even versions within the same company) is often large but can vary quite a bit. Leading to problems with doing segment match analysis on test results from different companies. This was first pointed out by Felix Chandrashakar on y-str.org when he developed some early analysis tools and much later picked up by ISOGG when they tried to understand the problems GEDMatch and MyHeritage were having incorporating different test companies using the new array products. The Illumina OmniExpress (r) and GlobalScreening (r) array chips have been popular as well as the Affymetrix GeneChip (r).
There is no standard, defined file format to represent the results although a somewhat defacto standard has emerged. Many term it the RAW File Format from the link name given in result pages. There is some basis for this as the files are similar to RAW VCF files in a simple TSV format. In fact, traditional sequencing tools can read and write these files. The biggest caveat being that these microarray file format (or RAW)) have both ancestral and derived values. A standard VCF only has derived.
Many lay persons in the consumer genetic genealogy market shorten the term "DNA Microarray Testing to extract a genotype" to simply "genotyping" instead of Microarray Testing. This is a bit of a misnomer as there are other forms of genotyping than just microarray testing. As mentioned earlier, genotyping assay is a term used in the genetics industry from which this use likely derives.
External References
- NIH NHGR Micro-array Technology article
- Wikipedia Microarray article
- Illumina page on available Chip / Bead / Screen microarrays