ArticleNPJ genomic medicine2016
Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care.
Article in NPJ genomic medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Patient-derived organoids across cancers reveal conserved tumor heterogeneity and actionable therapeutic vulnerabilities.Science advances · 2026Article
- EXaCT-2: an augmented and customizable oncology-focused whole exome sequencing platform.NPJ precision oncology · 2026Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- Enhancing Clinical Applications by Evaluation of Sensitivity and Specificity in Whole Exome Sequencing.International journal of molecular sciences · 2024Article
- Non-small cell lung cancer organoids: Advances and challenges in current applications.Chinese journal of cancer research = Chung-kuo yen cheng yen chiu · 2024Article
- Validation and Implementation of a Somatic-Only Tumor Exome for Routine Clinical Application.The Journal of molecular diagnostics : JMD · 2024Article
- The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis.Nature communications · 2024Article
- Molecular and modular intricacies of precision oncology.Frontiers in immunology · 2024Review
- The importance of escalating molecular diagnostics in patients with low-grade pediatric brain cancer.Cold Spring Harbor molecular case studies · 2023Article
- Immunogenomic Landscape of Neuroendocrine Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- Salivary gland cancer organoids are valid for preclinical genotype-oriented medical precision trials.iScience · 2023Article
- Whole-genome characterization of myoepithelial carcinomas of the soft tissue.Cold Spring Harbor molecular case studies · 2022Article
- Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management.Biomedicines · 2022Review
- Comparative genomics of primary prostate cancer and paired metastases: insights from 12 molecular case studies.The Journal of pathology · 2022Article
- Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology.Diagnostics (Basel, Switzerland) · 2022Review
- The genomic landscape of metastatic clear cell renal cell carcinoma after systemic therapy.Molecular oncology · 2022Article
- Recent Major Transcriptomics and Epitranscriptomics Contributions toward Personalized and Precision Medicine.Journal of personalized medicine · 2022Review
- MutaXome: A Novel Database for Identified Somatic Variations ofCancer informatics · 2022Article
- Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer.Prostate cancer and prostatic diseases · 2021Article
- Circulating tumor cell heterogeneity in neuroendocrine prostate cancer by single cell copy number analysis.NPJ precision oncology · 2021Article
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
We describe Exome Cancer Test v1.0 (EXaCT-1), the first New York State-Department of Health-approved whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation sequencing (Illumina) of tumour and matched constitutional control DNA. We present a detailed clinical development and validation pipeline suitable for simultaneous detection of somatic point/indel mutations and copy-number alterations (CNAs). A computational framework for data analysis, reporting and sign-out is also presented. For the validation, we tested EXaCT-1 on 57 tumours covering five distinct clinically relevant mutations. Results demonstrated elevated and uniform coverage compatible with clinical testing as well as complete concordance in variant quality metrics between formalin-fixed paraffin embedded and fresh-frozen tumours. Extensive sensitivity studies identified limits of detection threshold for point/indel mutations and CNAs. Prospective analysis of 337 cancer cases revealed mutations in clinically relevant genes in 82% of tumours, demonstrating that EXaCT-1 is an accurate and sensitive method for identifying actionable mutations, with reasonable costs and time, greatly expanding its utility for advanced cancer care.
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Registered trials
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