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NGS
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* Variants in homologous regions are hard to capture. Notably, the genes CYP2D6 and CYP2A6 are challenging.
* HLA-typing require special software, e.g. [https://software.broadinstitute.org/cancer/cga/polysolver Polysolver] for whole exome sequencing (WES) or [https://github.com/FRED-2/OptiType OptiType] for whole genome sequencing (WGS)
==Solutions==
[[PGx in Estonia|Solutions for PGx on NGS data]] are given by ''Reisberg et al.'' in their article [https://doi.org/10.1101/356204 Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions].
==Publications==