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Research Article

Implementation of whole-exome sequencing for pharmacogenomics profiling and exploring its potential clinical utilities

Danyi Wang1 EMD Serono Research & Development Institute, Inc., Billerica, MA, USA, an affiliate of Merck KGaAUSA

Jayaprakasam Bolleddula1 EMD Serono Research & Development Institute, Inc., Billerica, MA, USA, an affiliate of Merck KGaAUSA

https://orcid.org/0000-0003-4700-7819

Anna Coenen-Stass2 Merck Healthcare KGaA, Darmstadt, Germany

Thomas Grombacher2 Merck Healthcare KGaA, Darmstadt, Germany

https://orcid.org/0000-0001-9855-7429

Jennifer Q Dong1 EMD Serono Research & Development Institute, Inc., Billerica, MA, USA, an affiliate of Merck KGaAUSA

Juergen Scheuenpflug2 Merck Healthcare KGaA, Darmstadt, Germany

Giuseppe Locatelli2 Merck Healthcare KGaA, Darmstadt, Germany

Zheng Feng1 EMD Serono Research & Development Institute, Inc., Billerica, MA, USA, an affiliate of Merck KGaAUSACorrespondence[email protected]

https://orcid.org/0000-0003-3858-2205

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Figures & data

Figure 1. Analysis workflow.

A total of 79 blood samples from phase I oncology clinical trials were included for pharmacogenomic analysis using both ImmunoID NeXT™ WES and PharmacoScan™ assay. An orthogonal analysis was carried out to assess the concordance between WES and array-based assay in the commonly targeted regions within 28 core ADME genes. The exclusive variants that were unique to each technique were identified and followed by genotype-to-phenotype annotation.

ADME: Absorption, distribution, metabolism and elimination; SNP: Single-nucleotide polymorphism; SNV: Single-nucleotide variant; WES: Whole-exome sequencing.

Figure 1. Analysis workflow. A total of 79 blood samples from phase I oncology clinical trials were included for pharmacogenomic analysis using both ImmunoID NeXT™ WES and PharmacoScan™ assay. An orthogonal analysis was carried out to assess the concordance between WES and array-based assay in the commonly targeted regions within 28 core ADME genes. The exclusive variants that were unique to each technique were identified and followed by genotype-to-phenotype annotation.ADME: Absorption, distribution, metabolism and elimination; SNP: Single-nucleotide polymorphism; SNV: Single-nucleotide variant; WES: Whole-exome sequencing.

Table 1. Comprehensive summary of exclusive variants identified by PharmacoScan™.

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Figure 2. Whole-exome sequencing exclusive variants prioritized based on annotations in the PharmGKB database.

Figure 3. Comparative summary of the exclusive variants identified from different platforms.

Overview of the exclusive performance of WES can also be observed from the image for CYP2A6, DPYD, TPMT.

NA: Genes for which no annotation data exist. ’0’: No variants detected by the technique; WES: Whole-exome sequencing.

Figure 3. Comparative summary of the exclusive variants identified from different platforms. Overview of the exclusive performance of WES can also be observed from the image for CYP2A6, DPYD, TPMT.NA: Genes for which no annotation data exist. ’0’: No variants detected by the technique; WES: Whole-exome sequencing.

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Data availability statement

Any requests for data by qualified scientific and medical researchers for legitimate research purposes will be subject to Merck’s (CrossRef Funder ID: 10.13039/100009945) Data Sharing Policy. All requests should be submitted in writing to Merck’s data sharing portal (https://www.merckgroup.com/en/research/our-approach-to-research-and-development/healthcare/clinical-trials/commitment-responsible-data-sharing.html). When Merck has a co-research, co-development, or co-marketing or co-promotion agreement, or when the product has been out-licensed, the responsibility for disclosure might be dependent on the agreement between parties. Under these circumstances, Merck will endeavor to gain agreement to share data in response to requests.

Implementation of whole-exome sequencing for pharmacogenomics profiling and exploring its potential clinical utilities

Table 1. Comprehensive summary of exclusive variants identified by PharmacoScan™.

Supplementary Table 4

Supplementary Table 1

Supplementary Table 2

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Implementation of whole-exome sequencing for pharmacogenomics profiling and exploring its potential clinical utilities

Figures & data

Table 1. Comprehensive summary of exclusive variants identified by PharmacoScan™.

Supplementary Table 4

Supplementary Table 1

Supplementary Table 2

Data availability statement

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