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An Efficient Genotyper and Star-allele Caller for Pharmacogenomics by Ananth Hari; Qinghui Zhou; Nina Gonzaludo; John Harting; Stuart A. Scott; Xiang Qin; Steve Scherer; S. Cenk Sahinalp; Ibrahim Numanagić is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is An Efficient Genotyper and Star-allele Caller for Pharmacogenomics about?

High-throughput sequencing provides sufficient means for determining genotypes of clinically important pharmacogenes that can be used to tailor medical decisions to individual patients. However, pharmacogene genotyping, also known as star-allele calling, is a challenging problem that requires accurate copy number calling, structural variation identification, variant calling, and phasing within each pharmacogene copy present in the sample. Here we introduce Aldy 4, a fast and efficient tool for genotyping pharmacogenes that uses combinatorial optimization for accurate star-allele calling across different sequencing technologies. Aldy 4 adds support for long reads and uses a novel phasing model and improved copy number and variant calling models. We compare Aldy 4 against the current state-of-the-art star-allele callers on a large and diverse set of samples and genes sequenced by various sequencing technologies, such as whole-genome and targeted Illumina sequencing, barcoded 10x Genomics, and Pacific Biosciences (PacBio) HiFi. We show that Aldy 4 is the most accurate star-allele caller with near-perfect accuracy in all evaluated contexts, and hope that Aldy remains an invaluable tool

Who reads An Efficient Genotyper and Star-allele Caller for Pharmacogenomics?

Author

Ananth Hari; Qinghui Zhou; Nina Gonzaludo; John Harting; Stuart A. Scott; Xiang Qin; Steve Scherer; S. Cenk Sahinalp; Ibrahim Numanagić

Publisher

Cold Spring Harbor Laboratory

Published

2023

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)