Difference between revisions of "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]. | * 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. | * 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 or [https://github.com/FRED-2/OptiType OptiType] for whole genome sequencing | + | * 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 | ||
| + | |} | ||
Revision as of 08:56, 14 August 2018
Next Generation Sequencing (NGS) is an interesting technology for PGx
A nice overview of the Requirements for comprehensive pharmacogenetic genotyping platforms was published by Volker Lauschke et al. They claim that rare variants account for 30-40% of functional variability in PGx. However they argue that pre-emptive PGx should only include validated variants, and rare variants should be investigated only when the patient experience unexpected drug response.
Challenges
- Short read NGS requires a priori knowledge of likelihood of particular haplotypes. In silico haplotype estimation can e.g. be performed by Beagle.
- Variants in homologous regions are hard to capture. Notably, the genes CYP2D6 and CYP2A6 are challenging.
- HLA-typing require special software, e.g. Polysolver for whole exome sequencing (WES) or OptiType for whole genome sequencing (WGS)
Publications
| Institution | Article | Comments |
|---|---|---|
| St. Jude Children’s Research Hospital | 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 | Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening | Suggest developing tools for PGx based on WES and WGS |
| University of Washington | PGRNseq: A Targeted Capture Sequencing Panel for Pharmacogenetic Research and Implementation | Targeted PGx panel with 84 genes |
