ArticleBreast cancer research : BCR2019
Targeted mutation detection in breast cancer using MammaSeq™.
Article in Breast cancer research : BCR, 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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18 citing papers in PubMed, 41 citations in OpenAlex.
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- Detection of genetic mutations in patients with breast cancer from Saudi Arabia using Ion AmpliSeq™ Cancer Hotspot Panel v.2.0.Biomedical reports · 2022Article
- A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology.Nature cancer · 2022Article
- Association of Pathway Mutations With Survival in Taiwanese Breast Cancers.Frontiers in oncology · 2022Article
- Comprehensive comparison of theranostic nanoparticles in breast cancer.American journal of clinical and experimental immunology · 2022Review
- Multi-Gene Testing Overview with a Clinical Perspective in Metastatic Triple-Negative Breast Cancer.International journal of molecular sciences · 2021Review
- Identifying Genomic Alterations in Patients With Stage IV Breast Cancer Using MammaSeq: An International Collaborative Study.Clinical breast cancer · 2021Article
- EARN: an ensemble machine learning algorithm to predict driver genes in metastatic breast cancer.BMC medical genomics · 2021Article
- Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.Scientific reports · 2020Article
- Plasma DNA as a "liquid biopsy" incompletely complements tumor biopsy for identification of mutations in a case series of four patients with oligometastatic breast cancer.Breast cancer research and treatment · 2020Article
- Targeted next generation sequencing identifies somatic mutations in a cohort of Egyptian breast cancer patients.Journal of advanced research · 2020Article
- TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use.BMC bioinformatics · 2020Article
- Immuno-Oncology Biomarkers for Personalized Immunotherapy in Breast Cancer.Frontiers in cell and developmental biology · 2020Review
- Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer.Cancer management and research · 2020Review
- A Research Roadmap: Connected Health as an Enabler of Cancer Patient Support.Journal of medical Internet research · 2019Article
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Authors and funding
15 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundBreast cancer is the most common invasive cancer among women worldwide. Next-generation sequencing (NGS) has revolutionized the study of cancer across research labs around the globe; however, genomic testing in clinical settings remains limited. Advances in sequencing reliability, pipeline analysis, accumulation of relevant data, and the reduction of costs are rapidly increasing the feasibility of NGS-based clinical decision making.
methodsWe report the development of MammaSeq, a breast cancer-specific NGS panel, targeting 79 genes and 1369 mutations, optimized for use in primary and metastatic breast cancer. To validate the panel, 46 solid tumors and 14 plasma circulating tumor DNA (ctDNA) samples were sequenced to a mean depth of 2311× and 1820×, respectively. Variants were called using Ion Torrent Suite 4.0 and annotated with cravat CHASM. CNVKit was used to call copy number variants in the solid tumor cohort. The oncoKB Precision Oncology Database was used to identify clinically actionable variants. Droplet digital PCR was used to validate select ctDNA mutations.
resultsIn cohorts of 46 solid tumors and 14 ctDNA samples from patients with advanced breast cancer, we identified 592 and 43 protein-coding mutations. Mutations per sample in the solid tumor cohort ranged from 1 to 128 (median 3), and the ctDNA cohort ranged from 0 to 26 (median 2.5). Copy number analysis in the solid tumor cohort identified 46 amplifications and 35 deletions. We identified 26 clinically actionable variants (levels 1-3) annotated by OncoKB, distributed across 20 out of 46 cases (40%), in the solid tumor cohort. Allele frequencies of ESR1 and FOXA1 mutations correlated with CA.27.29 levels in patient-matched blood draws.
conclusionsIn solid tumor biopsies and ctDNA, MammaSeq detects clinically actionable mutations (OncoKB levels 1-3) in 22/46 (48%) solid tumors and in 4/14 (29%) of ctDNA samples. MammaSeq is a targeted panel suitable for clinically actionable mutation detection in breast cancer.
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