Aldy 4: An efficient genotyper and star-allele caller for pharmacogenomics

Abstract

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 discovery, 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 utilizes combinatorial optimization for accurate star-allele calling across different sequencing technologies. Aldy 4 adds support for long reads and ships with 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 PacBio HiFi. We show that Aldy 4 is the most accurate star-allele caller with near-perfect accuracy in all evaluated contexts. We hope that Aldy remains an invaluable tool in the clinical toolbox even with the advent of long-read sequencing technologies. Aldy 4 is available at https://github.com/0xTCG/aldy.

Functional interpretation, cataloging, and analysis of 1,341 glucose-6-phosphate dehydrogenase variants

“…Variant phasing for G6PD was done using Aldy v.4.1. 31 , 32 When multiple phasing results were returned, we chose the haplotype that matched the more commonly observed LD structure. For example, for two heterozygotes Aldy considered that the variants c.202G>A and c.376A>G were either on the same or separate alleles, but in these instances we chose the haplotype option with these variants on the same allele because that is more commonly observed.…”

Functional interpretation, cataloging, and analysis of 1,341 known and new glucose-6-phosphate dehydrogenase variants

“…Variant phasing for G6PD was done using Aldy version 4.1. 31,32 When multiple phasing results were returned, we chose the haplotype that matched the more commonly observed LD structure. For example, for a small number of individual(s) Aldy considered that the variants c.202G>A and c.376A>G were either on the same or separate alleles, however in these instances we chose the haplotype option with these variants on the same allele because that is more commonly observed.…”

Design and performance of a long-read sequencing panel for pharmacogenomics

“…For clinical star (*)-allele calling, all samples were analyzed using Aldy4 with the custom setting ‘pacbio-targeted-hifi-twist’, details of which are described by Hari et al (22, 23). Results were compared to the reference calls from GeT-RM, who provide genetic testing reference materials for PGx.…”

“…Results from MultiQC and VCF files were processed using Rstudio (v 1.3.1056) and Python 3.9.12. Benchmarking was performed for the three GIAB samples using Hap.py v3.12.1 (https://github.com/Illumina/hap.py) and v4.2.1 of the NIST benchmarks (21) For clinical star (*)-allele calling, all samples were analyzed using Aldy4 with the custom setting 'pacbio-targetedhifi-twist', details of which are described by Hari et al (22,23). Results were compared to the reference calls from GeT-RM, who provide genetic testing reference materials for PGx.…”