The Estonian Genome Centre at the University of Tartu has done a considerable job with Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations.
We here list the bioinformatic pipelines used for the biobank
| Technology | Methods | Comments |
|---|---|---|
| High density microarrays | HumanOmniExpress beadchip (OMNI, 8132 patients) and Global Screening Array (GSA, Illumina, 33157 patients), GenomeStudio (Illumina, genotyping, filtering for GSA), PLINK (filtering for all), zCall (genotyping rare variants for GSA) | 1308 of these patients were also Whole genome sequenced |
| Whole genome sequencing | TruSeq PCR-free prep, Illumina HiSeq X (150bp paired-end, 30x mean coverage), BWA-MEM (GRCh37 reference genome), Picard (mark PCR duplicates), GATK 3.4, bcftools (normalization and decomposition) | Quality filtering parameters are given in the article. The WGS samples (with some modifications) were also merged into a reference panel used for imputation (total 2279 Estonians and 1856 Finns) |
| Whole exome sequencing | Agilent SureSelect Human All Exon V5+UTRs target capture kit, HiSeq2500 (67x mean coverage) | Otherwise same bioinformatic pipeline as WGS |
We here list some of the challenges and solutions they identified:
| Challenge | Solution | Comments |
|---|---|---|
| Example | Example | Example |
| Example | Example | Example |
| Example | Example | Example |
| Example | Example | Example |