2.4. Assignment of Star Alleles

In pharmacogenomics, haplotypes, which are combinations of inherited variants such as single-nucleotide polymorphisms (SNPs), insertions/deletions (INDELs), and structural variants (SVs), are identified as star alleles (*). Our focus was on 25 pharmacogenes that are classified with evidence levels A or A/B according to the Clinical Pharmacogenetics Implementation Consortium (CPIC) based on data from the 1000 Genomes Project (1KGP). The 25 pharmacogenes are as follows: IFNL3, GSTP1, CYP2D6, VKORC1, NUDT15, NAT2, UGT1A1, G6PD, CYP4F2, GSTM1, UGT2B15, TPMT, CYP2B6, CYP3A4, CYP3A5, CYP2C8, CYP2C9, NAT1, UGT1A4, CACNA1S, SLCO1B1, RYR1, CYP2C19, CFTR, and DPYD (Table S1). To assign star alleles to individuals from the phased VCF file of the 1KGP, we utilized PyPGx v0.20.0 [21] with the Human Genome version (hg19).