Use cases: Population Genomics - Genome of Europe (GoE)
A 1+MG initiative aiming to deliver more than 500,000 whole genome sequences (WGS) as a reference database to represent genetic diversity across Europe. One objective of the GoE is to contribute to the 1+MG effort begun in 2018 where 24 signatory countries declared to make the data accessible for the genomes of at least 1,000,000 European citizens. This will require existing genomes to be made available for access and new genomes to be created by whole genome sequencing. The main goal of this effort is to create the reference dataset for genomic health programs in European countries.
GoE was created to have a large, European-wide collection of subgroup-specific reference datasets as “normal” or “reference” genomes. These can be used to a) document and quantify genetic diversity and heterogeneity across European populations to assist with b) interpreting potentially clinical or pathogenic genetic variants in comparison to disease-specific genomes as well as c) to recalibrate genetic risk profiles to ancestral backgrounds, which is important for developing population-specific polygenic risk scores and d) as a reference panel for imputations in lower resolution, but larger scale array genotyping efforts.
WGS contributions expected
- Contributions per country are expected to be proportional to the country’s population
- Minimum of 1,000 per population subgroup identified to support the detection of rare frequency variants and the comprehensive detection of common variants
- Ancestral composition: Member states provided the country of origin composition of their population as a proxy for ancestry. 40 ancestral subgroups were identified and included both country-specific subgroups outside of Europe (such as Turkey and Morocco) as well as groups that are not represented by a specific location (such as Roma). Countries that have their own national genome programs were excluded (such as the UK and China). The sequencing of these groups was distributed across the countries based on the country contributions, the minimum samples per subgroup and the proportion of subgroups in each country.
WGS technology and data requirements
Member countries were provided a questionnaire covering:
- Capacity for sequencing technology: most members have Illumina short read technology, some have MGI short read tech, and some have long read technology from companies including PacBio and Oxford Nanopore. Some countries were exploring gaining capacity in more modern technology as well.
- Existing WGS data that could be used for GoE
- Local funding for GoE support.
GoE Pilot Studies for GDI
- Exchange of synthetic whole genome sequencing data
- Exchange of real whole genome sequencing data
GoE Use Cases
- Look-ups of individual variants
- Creating a Principal Component Analysis of genetic variation
- Generating reference panels for ancestry-specific imputation
- Providing population distributions for polygenic risk scores
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