23andME v5 Chip And What You Should Know About It

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In 2017, 23andMe migrated from the Illumina OmniExpress chip that was used across multiple ancestry DNA companies. The current 23andme v5 chip, the Global Screening Array is a next-generation genotyping array for population-scale genetics, variant screening, pharmacogenomics studies, and precision medicine research. This version of the chip has around 6,50,000 SNPs suitable for both ancestry and health testing.

What Is The GSA?

According to Illumina, the GSA covers a multi-ethnic, genome wide markers with curated clinical research variants and markers that serve as quality control for precision medicine research. The content has been selected for high imputation accuracy specifically to the minor allele frequencies above 1%. All the 26 1000 Genomes Project populations have been considered. The balance between the health and ancestry markers is evident in that, variants with established associations with diseases, pharmacogenomic relevance have been included. The content is curated based on ClinVar, National Human Genome Research Institute (NHGRI), PharmGKB, Exome Aggregation Consortium (ExAc Database). In-built quality control markers enable sample identification for applications in large scale genomics and screening, which is very useful for companies with a huge customer demand like 23andMe.

What Is the Difference Between GSA and Omniexpress?

The Illumina Omniexpress chip, is the current chip version for other popular companies like Ancestry DNA and Family Tree DNA. However given the demand for third party re-analysis from companies like Xcode Life, and GSA’s compatibility with these tools, all other ancestry companies are likely to migrate to this version. While the OmniExpress chip was satisfactory for the European populations, it could not be applied to the other populations. The GSA is more inclusive of other world populations.

Do All Companies Cover The Same SNPs?

Because there are so few overlapping markers between the GSA and the OmniExpress this change will also present problems for companies and third-party websites that accept autosomal DNA transfers. A choice will need to be made as to whether to do comparisons using only the overlapping markers or whether to experiment with imputation. Xcode’s platform caters to all major genotyping platforms across the ancestry DNA testing companies.

Markers In the GSA Chip

Those of you who purchased the 23andMe kit after August 2017, will have reports based on Illumina’s latest v5 chip. Given that this chip is the most conducive with health-related traits, let’s take a look at a list of all traits that you can do from the raw data file:

CHIP NAME NO. OF SNPs Applications
23andMe Major categories
v1 HumanHap550+ 576,000
  • Ancestry re-analysis for South Asians
  • Immunoregulation and cognition
  • Drug metabolism and excretion
  • Somatic mutations in cancer
  • Methylation and MTHFR
  • Autoimmune disorders
  • Cardiovascular disease
  • Detoxification analysis
  • Transplant rejection
  • Alzheimer’s disease
  • Parkinson’s disease
  • Blood phenotypes
  • Disease defense
  • Skin conditions
  • Alcohol flush
  • Nutrition
  • BRCA1/2
  • Fitness
v2 HumanHap550+ 597,000
v3 HumanOmniExpress+ 992,000
v4 HTS iSelect HD 611,000
v5* Global Screening Array (GSA) ~650,000
Ancestry DNA
v1 OmniExpress Genotyping BeadChip 701,400
v2* OmniExpress Plus Genotyping BeadChip 669,000
Family Tree DNA
OmniExpress microarray chip 696,800**
Living DNA
Global Screening Array (GSA) ~650,000
MyHeritage
OmniExpress microarray chip 696,800**

 

*current chip

**Only for autosomal and the X chromosome