ArticleScientific reports2019
Development and validation of a targeted gene sequencing panel for application to disparate cancers.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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
18 citing papers in PubMed.
- PRICE: a personalized recursive intelligent cost effectiveness analysis framework for rare disease diagnosis.BMC medical informatics and decision making · 2025Article
- Functional genomics and tumor microenvironment analysis reveal prognostic biological subtypes in Mantle cell lymphoma.Nature communications · 2025Article
- The landscape of germline variants in breast and colorectal cancer susceptibility genes in patients with pituitary tumours.Journal of neuro-oncology · 2025Article
- Increasing pathogenic germline variant diagnosis rates in precision medicine: current best practices and future opportunities.Human genomics · 2025Review
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- FGFR1 variation in the divergent settings of congenital hypopituitarism and pituitary tumours.Pituitary · 2025Article
- Increased Prevalence of Germline Pathogenic CHEK2 Variants in Individuals With Pituitary Adenomas.The Journal of clinical endocrinology and metabolism · 2024Article
- Circadian rhythm and circulating cell-free DNA release on healthy subjects.Scientific reports · 2023Article
- Cell-free DNA-based liquid biopsies in neurology.Brain : a journal of neurology · 2023Review
- Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases.Cells · 2023Review
- Comprehensive comparison of theranostic nanoparticles in breast cancer.American journal of clinical and experimental immunology · 2022Review
- Cancer Type Classification in Liquid Biopsies Based on Sparse Mutational Profiles Enabled through Data Augmentation and Integration.Life (Basel, Switzerland) · 2021Article
- Genomic Sub-Classification of Ovarian Clear Cell Carcinoma Revealed by Distinct Mutational Signatures.Cancers · 2021Article
- Shifting Gears in Precision Oncology-Challenges and Opportunities of Integrative Data Analysis.Biomolecules · 2021Review
- The MURAL collection of prostate cancer patient-derived xenografts enables discovery through preclinical models of uro-oncology.Nature communications · 2021Article
- Review
- Contextualizing Genes by Using Text-Mined Co-Occurrence Features for Cancer Gene Panel Discovery.Frontiers in genetics · 2021Article
- HGNChelper: identification and correction of invalid gene symbols for human and mouse.F1000Research · 2020Article
Corrections and comments
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Authors and funding
25 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour's molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.
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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.