Development of an extensive workflow for comprehensive clinical pharmacogenomic profiling: lessons from a pilot study on 100 whole exome sequencing data

Abstract

This pilot study is aimed at implementing an approach for comprehensive clinical pharmacogenomics (PGx) profiling. Fifty patients with cardiovascular diseases and 50 healthy individuals underwent whole-exome sequencing. Data on 1800 PGx genes were extracted and analyzed through deep filtration separately. Theoretical drug induced phenoconversion was assessed for the patients, using sequence2script. In total, 4539 rare variants (including 115 damaging non-synonymous) were identified. Four publicly available PGx bioinformatics algorithms to assign PGx haplotypes were applied to nine selected very important pharmacogenes (VIP) and revealed a 45–70% concordance rate. To ensure availability of the results at point-of-care, actionable variants were stored in a web-hosted database and PGx-cards were developed for quick access and handed to the study subjects. While a comprehensive clinical PGx profile could be successfully extracted from WES data, available tools to interpret these data demonstrated inconsistencies that complicate clinical application.

A Follow-Up Study on the Thai Pharmacogenomics Database-1 (TPGxD-1): Validating CYP2D6 Allele Calls Using Contemporary Bioinformatics Tools

“…Earlier research that compared several bioinformatics algorithms for calling alleles found that the all PGx speci c bioinformatic tools worked well together 4,6 . A study, however, found that command-line-based programs had higher accuracy than web-based PGx haplotype tools like PharmaKU 10 . This could be why there is a high level of similarity among all four different tools, which are all command-line-based algorithms, in this study.…”

“…These discrepancies in calling genotype may be due to algorithm differences, as each tool employs unique algorithms and methodologies for aligning sequencing reads, identifying variants, and translating genotypes to star alleles 10 . In addition, reference database updates 27 , indel and SVs handling, quality thresholds and lters, and phasing and haplotype reconstruction.…”

PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting

“…Whole exome sequencing (WES) has been evaluated for CYP2D6 SV/CNV detection, but there are inherent technical challenges, including difficulties with coverage and SV/CNV calling that preclude clinical implementation of WES‐based CYP2D6 determination 91–95 . In addition, CYP2D6 calling from WES data is inconsistent among star‐allele calling tools, indicating limited clinical application for WES 96 . Specialized software has been developed and successfully used for CYP2D6 calling from targeted next‐generation sequencing (NGS) captures that include baits for CYP2D6 and CYP2D7 97,98 ; however, the software requires customization to the specific capture and significant adjustment to apply to other captures.…”

“…[91][92][93][94][95] In addition, CYP2D6 calling from WES data is inconsistent among star-allele calling tools, indicating limited clinical application for WES. 96 Specialized software has been developed and successfully used for CYP2D6 calling from targeted next-generation sequencing (NGS) captures that include baits for CYP2D6 and CYP2D7 97,98 ; however, the software requires customization to the specific capture and significant adjustment to apply to other captures.…”

Editorial: Integration of computational genomics into clinical pharmacogenomic tests: how bioinformatics may help primary care in precision medicine area

“…In order to select the most appropriate bioinformatic tools for variant calling, it is essential to have a comprehensive understanding of the available PGx dedicated tools and their main features. Furthermore, common bioinformatics algorithms, such as SIFT, Polyphen2, FATHMM, CAD, etc., may require pre-filtration of variants for specific markers (Tafazoli et al, 2022). However, these tools often overlook variants that result in "increased or decreased function," which are crucial for determining ultrarapid and intermediate metabolizer phenotypes.…”