Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences

TLDR

Whole‑genome sequencing is a key component of precision medicine, yet accurately determining CYP2D6 activity is difficult because the gene is highly polymorphic and subject to complex structural variations that govern drug metabolism. The study aims to automate the identification of genetic variation in drug‑metabolism genes, and introduces Constellation, a probabilistic tool that assigns CYP2D6 activity scores from paired‑end WGS data. Constellation uses a probabilistic scoring system based on 2×100 bp paired‑end WGS, validated against a consensus reference comprising TaqMan genotyping, copy‑number variation assays, and Sanger sequencing. Compared to the reference, Constellation achieved 97 % analytic sensitivity and 95 % specificity, correctly identified all extreme metabolizer phenotypes, and is expected to extend to all ADMER genes at modest additional cost.

Abstract

An important component of precision medicine-the use of whole-genome sequencing (WGS) to guide lifelong healthcare-is electronic decision support to inform drug choice and dosing. To achieve this, automated identification of genetic variation in genes involved in drug absorption, distribution, metabolism, excretion and response (ADMER) is required. CYP2D6 is a major enzyme for drug bioactivation and elimination. CYP2D6 activity is predominantly governed by genetic variation; however, it is technically arduous to haplotype. Not only is the nucleotide sequence of CYP2D6 highly polymorphic, but the locus also features diverse structural variations, including gene deletion, duplication, multiplication events and rearrangements with the nonfunctional, neighbouring CYP2D7 and CYP2D8 genes. We developed Constellation, a probabilistic scoring system, enabling automated ascertainment of CYP2D6 activity scores from 2×100 paired-end WGS. The consensus reference method included TaqMan genotyping assays, quantitative copy-number variation determination and Sanger sequencing. When compared with the consensus reference Constellation had an analytic sensitivity of 97% (59 of 61 diplotypes) and analytic specificity of 95% (116 of 122 haplotypes). All extreme phenotypes, i.e., poor and ultrarapid metabolisers were accurately identified by Constellation. Constellation is anticipated to be extensible to functional variation in all ADMER genes, and to be performed at marginal incremental financial and computational costs in the setting of diagnostic WGS.