ArticleThe Journal of molecular diagnostics : JMD2018
Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer.
Article in The Journal of molecular diagnostics : JMD, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.Scientific reports · 2024Pooled it
- Real-world clinical utility of tumor whole-genome sequencing in solid cancers.Nature medicine · 2026Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- Clinical Implementation of Expanded Solid Tumor Fusion Detection With Whole-Transcriptome Sequencing at an Academic Cancer Center.JCO precision oncology · 2025Article
- Transforming Cancer Care: Genomic Profiling, AI, and Next-Generation Drug Delivery Systems.Current genomics · 2025Review
- Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice.Nature protocols · 2024Review
- Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care.JCO precision oncology · 2022Review
- Study protocol of the GLOW study: maximising treatment options for recurrent glioblastoma patients by whole genome sequencing-based diagnostics-a prospective multicenter cohort study.BMC medical genomics · 2022Article
- Correlation Between Genetic Abnormalities in Induced Pluripotent Stem Cell-Derivatives and Abnormal Tissue Formation in Tumorigenicity Tests.Stem cells translational medicine · 2022Article
- Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers.Nature communications · 2022Article
- Integration of Genomic Profiling and Organoid Development in Precision Oncology.International journal of molecular sciences · 2021Review
- Metastatic pediatric sclerosing epithelioid fibrosarcoma.Cold Spring Harbor molecular case studies · 2021Review
- The Application of Control Materials for Ongoing Quality Management of Next-Generation Sequencing in a Clinical Genetic Laboratory.Medicina (Kaunas, Lithuania) · 2021Review
- Identification of targetable BRAF ΔN486_P490 variant by whole-genome sequencing leading to dabrafenib-induced remission of aCold Spring Harbor molecular case studies · 2019Article
- "Somatic" and "pathogenic" - is the classification strategy applicable in times of large-scale sequencing?Haematologica · 2019Article
- Sequencing and curation strategies for identifying candidate glioblastoma treatments.BMC medical genomics · 2019Article
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Authors and funding
23 authors.
Funding
Abstract
We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, insertions/deletions, copy number variants, structural variants, and RNA gene fusions was analyzed. New York State's Department of Health next-generation DNA sequencing guidelines were expanded for establishing performance validation applicable to whole-genome and transcriptome sequencing. Whole-genome sequencing laboratory protocols were validated for the Illumina HiSeq X Ten platform and RNA sequencing for Illumina HiSeq2500 platform for fresh or frozen and formalin-fixed, paraffin-embedded tumor samples. Various bioinformatics tools were also tested, and CIs for sensitivity and specificity thresholds in calling clinically significant somatic aberrations were determined. The validation was performed on a set of 125 tumor normal pairs. RNA sequencing was performed to call fusions and to confirm the DNA variants or exonic alterations. Here, we present our results and WGTS standards for variant allele frequency, reproducibility, analytical sensitivity, and present limit of detection analysis for single nucleotide variant calling, copy number identification, and structural variants. We show that The New York Genome Center WGTS clinical assay can provide a comprehensive patient variant discovery approach suitable for directed oncologic therapeutic applications.
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