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NGS
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* Short read NGS requires a priori knowledge of likelihood of particular haplotypes. ''In silico'' haplotype estimation can e.g. be performed by [http://faculty.washington.edu/browning/beagle/beagle.html Beagle].
* 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) ==Publications=={| class="wikitable sortable"|-! Institution !! Article !! Comments|-| St. Jude Children’s Research Hospital || [https://doi:10.1002/cpt.411 Comparison of Genome Sequencing and Clinical Genotyping for Pharmacogenes] || WES and WGS can be used for PGx with additional CNV calling and HLA calling|-| National Human Genome Research Institute || [https://doi:10.1038/gim.2016.105 Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening] || Suggest developing tools for PGx based on WES and WGS|-| University of Washington || [https://doi.org/10.1097/FPC.0000000000000202 PGRNseq: A Targeted Capture Sequencing Panel for Pharmacogenetic Research and Implementation] || Targeted PGx panel with 84 genes|}