ArticleScientific reports2019
Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer.
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 19 papers.
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Who cites it
19 citing papers in PubMed, 29 citations in OpenAlex.
- Impact of somatic PIK3CA mutations on clinical outcomes in HER2-positive breast cancer.Breast cancer research : BCR · 2026Article
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- Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics.Cancers · 2023Article
- Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome.NPJ genomic medicine · 2023Article
- Classification with 2-D convolutional neural networks for breast cancer diagnosis.Scientific reports · 2022Article
- TBX21 Methylation as a Potential Regulator of Immune Suppression in CMS1 Subtype Colorectal Cancer.Cancers · 2022Article
- Left sided breast cancer is associated with aggressive biology and worse outcomes than right sided breast cancer.Scientific reports · 2022Article
- Exome sequencing reveals a distinct somatic genomic landscape in breast cancer from women with germline PTEN variants.American journal of human genetics · 2022Article
- Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer.Annals of surgical oncology · 2022Article
- Disease characterization in liquid biopsy from HER2-mutated, non-amplified metastatic breast cancer patients treated with neratinib.NPJ breast cancer · 2022Article
- SAMHD1 as a prognostic and predictive biomarker in stage II colorectal cancer: A multicenter cohort study.Frontiers in oncology · 2022Article
- Genomic landscape of lung adenocarcinomas in different races.Frontiers in oncology · 2022Article
- Identification of putative actionable alterations in clinically relevant genes in breast cancer.British journal of cancer · 2021Article
- Article
- A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer.International journal of molecular sciences · 2020Article
- Immune Infiltration Landscape in Clear Cell Renal Cell Carcinoma Implications.Frontiers in oncology · 2020Article
- The current status of the clinical utility of liquid biopsies in cancer.Expert review of molecular diagnostics · 2019Review
- "Somatic" and "pathogenic" - is the classification strategy applicable in times of large-scale sequencing?Haematologica · 2019Article
- First Responder to Genomic Information: A Guide for Primary Care Providers.Molecular diagnosis & therapy · 2019Review
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Whole exome sequencing (WES), targeted gene panel sequencing and single nucleotide polymorphism (SNP) arrays are increasingly used for the identification of actionable alterations that are critical to cancer care. Here, we compared The Cancer Genome Atlas (TCGA) and the Genomics Evidence Neoplasia Information Exchange (GENIE) breast cancer genomic datasets (array and next generation sequencing (NGS) data) in detecting genomic alterations in clinically relevant genes. We performed an in silico analysis to determine the concordance in the frequencies of actionable mutations and copy number alterations/aberrations (CNAs) in the two most common breast cancer histologies, invasive lobular and invasive ductal carcinoma. We found that targeted sequencing identified a larger number of mutational hotspots and clinically significant amplifications that would have been missed by WES and SNP arrays in many actionable genes such as PIK3CA, EGFR, AKT3, FGFR1, ERBB2, ERBB3 and ESR1. The striking differences between the number of mutational hotspots and CNAs generated from these platforms highlight a number of factors that should be considered in the interpretation of array and NGS-based genomic data for precision medicine. Targeted panel sequencing was preferable to WES to define the full spectrum of somatic mutations present in a tumor.
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Registered trials
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