296
edits
Changes
→Challenges and solutions
| [[Allele definition|Multiple allele matches]] || Made hierarchy of alleles based on the biochemical function (No function > Decreased Function > Other functional statuses) || Probably this can be seen as a variant of the best solution to the [[Unknown function|unknown function problem]]: Look for the most serious consequence, and if no allele with serious consequence was found, assume Normal function.
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| Haplotype calling || (Eagle2, most likely) In case there were more than one star allele match per haplotype, they matched all possible star allele diplotypes, and picked the diplotype with the most serious clinical consequence || Haplotype estimation for WGS was performed, but it is unclear which method was used (Eagle2 as for microarrays, probably). Probably the methodology is similar to that used in [https://www.nature.com/articles/ejhg201751 ''Mitt et al.''], in which case they used SHAPEIT2.
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| CYP2D6 calling || Combination of Genome STRiP and normal allele matching (favorable comparison to Astrolabe used by PharmCAT) || Did not understand exactly how they did it (maybe check out reference by [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5292679/ ''Gaedigk et al.''])
