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. 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
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| Haplotype calling || Haplotype estimation for WGS was performed, but it is unclear which method was used. Probably the methodology is similar to that used in [https://www.nature.com/articles/ejhg201751 ''Mitt et al.''], in which case they used SHAPEIT2. Otherwise Eagle2 (as for microarray data) which is 6 times faster. || In general, the difference between haplotyping and PGx allele matching it not clear (maybe right to say that PGx allele matching is a subset of general haplotyping?).
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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.''])
