Design and Validation of a Whole-Genome SequencingBased Assay for Population Health
oregon; chiles; genomics; isb
Introduction: Next-generation sequencing (NGS) is rapidly emerging as a key methodology in the clinical laboratory for a wide array of clinical uses, including heritable disease testing, somatic tumor profiling, and microbiology. Whereas current clinical methods are largely focused on targeted gene panels, the low cost and high throughput of modern sequencing platforms are making it possible to use whole-genome sequencing (WGS) for routine clinical applications. Here we developed a clinical WGS-based lab developed test (LDT) for heritable disease gene testing and pharmacogenomics (PGx) and performed extensive validation across a large cohort of blood and saliva specimens. Methods: DNA was isolated from both whole blood (EDTA) and saliva (Oragene collection) using the Qiagen QIAsymphony DSP Midi Kit. Whole genome libraries were prepared from 300 to 500 ng gDNA with the Illumina DNA PCR-Free Tagmentation kit. Sequencing (30X) was performed on the Illumina NovaSeq 6000. Pharmacogenetic genotyping and variant detection analysis (82 genes) were performed using standard analysis pipelines on the Illumina Dynamic Read Analysis for GENomics (DRAGEN) platform. Interpretation of heritable disease gene variants as well as PGx star allele assignment were performed by experts utilizing the Fabric Genomics interpretation platform as well as a novel in-house developed platform for clinical reporting. Results: WGS was performed on a combined retrospective and prospective validation cohort of 119 whole blood and 69 saliva specimens that were orthogonally tested via single gene or small panel tests at commercial laboratories. Validation was performed across a set of 77 actionable disease genes and resulted in 100% agreement in called pathogenic and likely pathogenic single nucleotide variants, indels, and copy number variants when compared to the reference method. Genotyping from WGS across a panel of PGx genes (CYP2C19, CYP2C9, VKORC1, and CYP4F2) in the 119 whole blood and 69 saliva gDNA samples resulted in 100% concordance with the reference method (MALDI-TOF mass spectrometry). Conclusions: WGS exhibited equivalent performance with targeted gene panel testing across a large cohort of clinical specimens. The comprehensive nature of a WGS backbone for clinical testing has the added benefit of facilitating expanded reanalysis of new actionable genes, rapid redeployment for use in other clinical contexts, as well as for use by researchers in supporting novel genomic discoveries. Given the anticipated upcoming reductions in cost for WGS, a singular clinical genome-based platform will likely represent a viable streamlined option for supporting clinical genetic/genomic testing across the clinical spectrum.
Earle A. Chiles Research Institute
Welle, John; Piening, Brian; Wagner, Josiah; Lucas-Beckett, I; Ward, Thomas; Cosgrove, B; Shull, Eric; Rattray, R; Pukay, Marina; Ricks, Milena; Childers, K; Linehan, J; Campbell, M; Gordon, Ora; and Bifulco, Carlo, "Design and Validation of a Whole-Genome SequencingBased Assay for Population Health" (2022). Articles, Abstracts, and Reports. 7001.