ArticleThe Journal of molecular diagnostics : JMD2014
Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens.
Article in The Journal of molecular diagnostics : JMD, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers.
What it found
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Who cites it
149 citing papers in PubMed, 279 citations in OpenAlex.
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- Global DNA methylomes reveal oncogenic-associated 5-hydroxylmethylated cytosine (5hmC) signatures in the cell-free DNA of cancer patients.medRxiv : the preprint server for health sciences · 2025Article
- Complete loss of lineage defining antigens in two cases of B-cell malignancies following CAR-T therapy.Journal of hematopathology · 2024Review
- Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for DetectingCancers · 2024Article
- Large-scale analysis of whole genome sequencing data from formalin-fixed paraffin-embedded cancer specimens demonstrates preservation of clinical utility.Nature communications · 2024Article
- Sulfatide imaging identifies tumor cells in colorectal cancer peritoneal metastases.Cancer & metabolism · 2024Article
- Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors.Journal of neuro-oncology · 2024Article
- Genomic Correlates of Prostate-Specific Membrane Antigen Expression and Response toJCO precision oncology · 2024Article
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- Novel, clinically relevant genomic patterns identified by comprehensive genomic profiling in ATRX-deficient IDH-wildtype adult high-grade gliomas.Scientific reports · 2023Article
- Adoption of Universal Testing in Endometrial Cancers for Microsatellite Instability Using Next-Generation Sequencing.JCO precision oncology · 2023Article
- Diagnosis of Ovarian Carcinoma Homologous Recombination DNA Repair Deficiency From Targeted Gene Capture Oncology Assays.JCO precision oncology · 2023Article
- Congenital pleuropulmonary blastoma in a newborn with a variant of uncertain significance in DICER1 evaluated by RNA-sequencing.Maternal health, neonatology and perinatology · 2023Article
- Infantile ZFTA Fusion-Positive Tumor of the Posterior Fossa: Molecular Tumor Board.JCO precision oncology · 2023Article
- Multiregional Sequencing Analysis Reveals Extensive Genetic Heterogeneity in Gastric Tumors from Latinos.Cancer research communications · 2022Article
- Blood-based liquid biopsies for prostate cancer: clinical opportunities and challenges.British journal of cancer · 2022Review
- A Validation Framework for Somatic Copy Number Detection in Targeted Sequencing Panels.The Journal of molecular diagnostics : JMD · 2022Article
89 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
20 authors at 3 institutions in 1 country.
Funding
Abstract
Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500× average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 previously characterized clinical tumor specimens from 10 different cancer types, including 41 formalin-fixed paraffin-embedded tissue samples. Mixing studies indicated reliable mutation detection in samples with ≥ 10% tumor cells. In clinical samples with ≥ 10% tumor cells, UW-OncoPlex correctly identified 129 of 130 known mutations [sensitivity 99.2%, (95% CI, 95.8%-99.9%)], including single nucleotide variants, small insertions and deletions, internal tandem duplications, gene copy number gains and amplifications, gene copy losses, chromosomal gains and losses, and actionable genomic rearrangements, including ALK-EML4, ROS1, PML-RARA, and BCR-ABL. In the same samples, the assay also identified actionable point mutations in genes not previously analyzed and novel gene rearrangements of MLL and GRIK4 in melanoma, and of ASXL1, PIK3R1, and SGCZ in acute myeloid leukemia. To best guide existing and emerging treatment regimens and facilitate integration of genomic testing with patient care, we developed a framework for data analysis, decision support, and reporting clinically actionable results.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.