ArticleThe Journal of molecular diagnostics : JMD2015
Assessing copy number alterations in targeted, amplicon-based next-generation sequencing data.
Article in The Journal of molecular diagnostics : JMD, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
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- Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2018Trial
- Molecular classification of anaplastic oligodendroglioma using next-generation sequencing: a report of the prospective randomized EORTC Brain Tumor Group 26951 phase III trial.Neuro-oncology · 2016Trial
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- Development and Application of MiMouse, a Comprehensive Genomic Profiling Panel for Credentialing Mouse Tumor Models.Cancer research communications · 2025Article
- MET Alterations in Cancer and MET-Targeted Therapy: Detection Strategies, Treatment Efficacy, and Emerging Technologies.Targeted oncology · 2025Review
- Transfer Learning for Error-Contaminated Poisson Regression Models.Statistics in medicine · 2025Article
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- The radiogenomic and spatiogenomic landscapes of glioblastoma and their relationship to oncogenic drivers.Communications medicine · 2025Article
- Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for DetectingCancers · 2024Article
- Integrative Drug Screening and Multiomic Characterization of Patient-derived Bladder Cancer Organoids Reveal Novel Molecular Correlates of Gemcitabine Response.European urology · 2024Article
- Implementing Massive Parallel Sequencing into Biliary Samples Obtained through Endoscopic Retrograde Cholangiopancreatography for Diagnosing Malignant Bile Duct Strictures.International journal of molecular sciences · 2024Article
- Integrative multi-region molecular profiling of primary prostate cancer in men with synchronous lymph node metastasis.Nature communications · 2024Article
- Targeted Next-Generation Sequencing Improves the Prognostication of Patients with Disseminated Appendiceal Mucinous Neoplasms (Pseudomyxoma Peritonei).Annals of surgical oncology · 2023Article
- Somatic mosaicism in inborn errors of immunity: Current knowledge, challenges, and future perspectives.Seminars in immunology · 2023Review
- Prospective, Multi-Institutional, Real-Time Next-Generation Sequencing of Pancreatic Cyst Fluid Reveals Diverse Genomic Alterations That Improve the Clinical Management of Pancreatic Cysts.Gastroenterology · 2023Article
- Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity.Nature communications · 2022Article
- Serial monitoring of genomic alterations in circulating tumor cells of ER-positive/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection.Molecular oncology · 2022Article
- Androgen deprivation‑induced OPHN1 amplification promotes castration‑resistant prostate cancer.Oncology reports · 2022Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
Abstract
Changes in gene copy number are important in the setting of precision medicine. Recent studies have established that copy number alterations (CNAs) can be detected in sequencing libraries prepared by hybridization-capture, but there has been comparatively little attention given to CNA assessment in amplicon-based libraries prepared by PCR. In this study, we developed an algorithm for detecting CNAs in amplicon-based sequencing data. CNAs determined from the algorithm mirrored those from a hybridization-capture library. In addition, analysis of 14 pairs of matched normal and breast carcinoma tissues revealed that sequence data pooled from normal samples could be substituted for a matched normal tissue without affecting the detection of clinically relevant CNAs (>|2| copies). Comparison of CNAs identified by array comparative genomic hybridization and amplicon-based libraries across 10 breast carcinoma samples showed an excellent correlation. The CNA algorithm also compared favorably with fluorescence in situ hybridization, with agreement in 33 of 38 assessments across four different genes. Factors that influenced the detection of CNAs included the number of amplicons per gene, the average read depth, and, most important, the proportion of tumor within the sample. Our results show that CNAs can be identified in amplicon-based targeted sequencing data, and that their detection can be optimized by ensuring adequate tumor content and read coverage.
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