Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6-CYP2D7 hybrid allele genotyping

We optimized the PCR-free nanopore Cas9-targeted sequencing (nCATS) method combined with adaptive sequencing and developed a new comprehensive long read genotyping (CoLoRGen) pipeline to generate complete allele-specific consensus sequences of complex regions, such as the CYP2D6-CYP2D7 locus. In reference samples, our genotyping assay confirms the presence of CYP2D6-CYP2D7 large structural variants, single nucleotide variants (SNVs), and small insertions and deletions (INDELs) that go undetected by most current assays. Moreover, our results provide direct evidence that the CYP2D6 reference genotype of the NA12878 DNA should be updated to include the CYP2D6-CYP2D7 *68 hybrid and several additional SNVs.