PGx in Estonia

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