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Tuesday, June 1, 2021

Resolving Complex Pathogenic Alleles using HiFi Long-range Amplicon Data and a New Clustering Algorithm

Many genetic diseases are mapped to structurally complex loci. These regions contain highly similar paralogous alleles (>99% identity) that span kilobases within the human genome. Comprehensive screening for pathogenic variants amongst paralogous sequences is incomplete and labor intensive using short-reads or optical mapping. In contrast, long-range targeted amplification and PacBio HiFi sequencing fully and directly resolves and phases a wide range of pathogenic variants without assembly or inference. To capitalize on the accuracy of HiFi amplicon data we designed a new amplicon analysis tool, pbAA. pbAA uses a new sequence clustering algorithm to rapidly deconvolve (separate) a mixture of haplotypes, enabling precise diplotyping, and disease allele classification. In this experiment, we analyzed two sets of gene-pseudogene systems, GBA and CYP, that are the second and eighth most common carrier disease alleles, respectively. Samples tested…

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Tuesday, June 1, 2021

Full-Length Sequencing of CYP2D6Variants with PacBio HiFi Reads

CYP2D6 is a highly polymorphic gene with more than 130 named variants, including deletions, duplications, single nucleotide polymorphisms, and other types of variation (Butler, 2018; Black et al., 2011). These variants affect the rate of metabolism in human individuals of approximately 25% of common prescription drugs (Owen et al., 2019;). PacBio SMRT sequencing is a proven tool for the interrogation of CYP2D6 variants (Qiao et al., 2016; Buermans et al., 2017).  Now with HiFi sequencing, we have developed a streamlined end-to-end workflow for the more accurate detection of highly polymorphic CYP2D6 loci. This study also evaluates the advantage of HiFi reads for the sequencing of full-length CYP2D6 genes with…

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