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Keywords de novo variants Mendelian disease long-read sequencing HiFi sequencing Introduction De novo variants, which are present in affected probands but not (constitutively) present in the parents, underlie a substantial fraction of Mendelian disorders.1,2,3,4,5,6 These disorders are typically highly penetrant and are often encountered as cases of severely affected probands with unaffected parents.
Abstract Pharmacogenomics is central to precision medicine, informing medication safety and efficacy. Pharmacogenomic diplotyping of complex genes requires full-length DNA sequences and detection of structural rearrangements. We introduce StarPhase, a tool that leverages PacBio HiFi sequence data to diplotype 21 CPIC Level A pharmacogenes and provides detailed haplotypes and supporting visualizations for HLA-A, HLA-B, and CYP2D6.
FS received support from Illumina, Genentech, PacBio, and Oxford Nanopore Technologies. JH, XC, CL, SZ, PB, ME, SK, GH, and ZK are PacBio employees and shareholders. HC, TH, CR, and TF are employees of Twist. FJS and MM are supported by NIH grants (1U01HG011758-01). SIH S10 grant 1S10OD028587. We would like to thank Luis F. Paulin for his fruitful discussion on the de novo SVs calling. We would like to thank Barbara Bock for her help on gene annotations.
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