![]() ![]() The PGx genotyping pipeline using Stargazer is described in: Calling star alleles with Stargazer in 28 pharmacogenes with whole genome sequences. The most recent reference for Stargazer's genotyping algorithm is: If you use Stargazer in a published analysis, please report the program version and cite the appropriate article. However, Sean & Aparna are now developing and maintaining it. Steven graduated in June of 2019 and now works in industry, but had been instrumental in developing Stargazer. Stargazer was developed by Seung-been Lee (he goes by "Steven") during his PhD in the Nickerson lab at the University of Washington. We are continuously extending Stargazer to additional genes, so stay tuned! If you do not see your favorite PGx genes in the list, let us know and we will try to prioritize them when adding new genes.ĢC_CLUSTER, ABCB1, ABCG2, CACNA1S, CFTR, CYP17A1, CYP19A1, CYP1A1, CYP1A2, CYP1B1, CYP26A1, CYP2A13, CYP2A6, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP2F1, CYP2J2, CYP2R1, CYP2S1, CYP2W1, CYP3A4, CYP3A43, CYP3A5, CYP3A7, CYP4A11, CYP4A22, CYP4B1, CYP4F2, DPYD, G6PD, GSTM1, GSTP1, IFN元, NAT1, NAT2, NUDT15, POR, PTGIS, RYR1, SLC15A2, SLC22A2, SLCO1B1, SLCO1B3, SLCO2B1, SULT1A1, TBXAS1, TPMT, UGT1A1, UGT1A4, UGT2B15, UGT2B17, UGT2B7, VKORC1, XPC ![]() The latest version of Stargazer can call star alleles in 58 PGx genes shown below. You will see lots of abbreviations and acronyms shown below throughout this website (you've been warned).ġKGP, The 1000 Genomes Project AF, allele fraction AS, activity score CN, copy number DOI, digital object identifier GDF, GATK-DepthOfCoverage format indels, insertion-deletion variants NGS, next-generation sequencing PGx, pharmacogenomics SDF, SAMtools depth format SGE, Sun Grid Engine SNP, single nucleotide polymorphism SNV, single nucleotide variant SV, structural variant TS, targeted sequencing VCF, variant call format WGS, whole genome sequencing To date, over 100 star alleles have been defined for CYP2D6, some involving a gene hybrid with its nearby non-functional but highly homologous paralog CYP2D7.įor more details on how Stargazer works, please see the Documentation page. We purposely chose CYP2D6 as a starting point because 1) the enzyme it encodes metabolizes ~25% of prescription drugs, 2) its activity varies considerably among individuals due to the gene's highly polymorphic nature, and 3) it is one of the most complex genetic loci to genotype in the human genome. When building Stargazer, we used the clinically important CYP2D6 gene as a model for detection and interpretation of SVs in the context of other observed SNVs and indels. Stargazer can detect complex SVs including gene deletions, duplications, and hybrids by calculating paralog-specific copy number from read depth. Stargazer identifies star alleles by detecting SNVs, indels, and SVs. Stargazer can accept NGS data from both WGS and TS. Stargazer is a bioinformatics tool for calling star alleles (haplotypes) in PGx genes using data from NGS or SNP array. ![]()
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