Cargando…

Machine learning-based somatic variant calling in cell-free DNA of metastatic breast cancer patients using large NGS panels

Next generation sequencing of cell-free DNA (cfDNA) is a promising method for treatment monitoring and therapy selection in metastatic breast cancer (MBC). However, distinguishing tumor-specific variants from sequencing artefacts and germline variation with low false discovery rate is challenging wh...

Descripción completa

Detalles Bibliográficos
Autores principales:	Jongbloed, Elisabeth M., Jansen, Maurice P. H. M., de Weerd, Vanja, Helmijr, Jean A., Beaufort, Corine M., Reinders, Marcel J. T., van Marion, Ronald, van IJcken, Wilfred F. J., Sonke, Gabe S., Konings, Inge R., Jager, Agnes, Martens, John W. M., Wilting, Saskia M., Makrodimitris, Stavros
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2023
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10300101/ https://www.ncbi.nlm.nih.gov/pubmed/37369746 http://dx.doi.org/10.1038/s41598-023-37409-1

Ejemplares similares

A Systematic Review of the Use of Circulating Cell-Free DNA Dynamics to Monitor Response to Treatment in Metastatic Breast Cancer Patients
por: Jongbloed, Elisabeth M., et al.
Publicado: (2021)

A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins
por: Makrodimitris, Stavros, et al.
Publicado: (2020)

Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA
por: Weerts, Marjolein J. A., et al.
Publicado: (2017)

The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction
por: van den Bent, Irene, et al.
Publicado: (2021)

Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads
por: Keukeleire, Pia, et al.
Publicado: (2023)

Cost-Effectiveness of Abemaciclib in Early Breast Cancer Patients: One Size Fits All or Tailoring to Patients’ Needs?
por: Jongbloed, Elisabeth M, et al.
Publicado: (2023)

Improving protein function prediction using protein sequence and GO-term similarities
por: Makrodimitris, Stavros, et al.
Publicado: (2019)

Automatic Gene Function Prediction in the 2020’s
por: Makrodimitris, Stavros, et al.
Publicado: (2020)

Metric learning on expression data for gene function prediction
por: Makrodimitris, Stavros, et al.
Publicado: (2020)

Circular RNA in Chemonaive Lymph Node Negative Colon Cancer Patients
por: van den Berg, Inge, et al.
Publicado: (2021)

An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics
por: Makrodimitris, Stavros, et al.
Publicado: (2023)

High-throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by methylated DNA sequencing (MeD-seq) of LpnPI digested fragments
por: Deger, Teoman, et al.
Publicado: (2021)

Ovarian Cancer Cell Line Panel (OCCP): Clinical Importance of In Vitro Morphological Subtypes
por: Beaufort, Corine M., et al.
Publicado: (2014)

A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer
por: van den Berg, Inge, et al.
Publicado: (2021)

Tumor-agnostic ctDNA levels by mFAST-SeqS in first-line HR-positive, HER2 negative metastatic breast cancer patients as a biomarker for survival
por: Verschoor, Noortje, et al.
Publicado: (2023)

Inhibiting CDK4/6 in Breast Cancer with Palbociclib, Ribociclib, and Abemaciclib: Similarities and Differences
por: Braal, C. Louwrens, et al.
Publicado: (2020)

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function
por: Villegas-Morcillo, Amelia, et al.
Publicado: (2020)

Nimbus: a design-driven analyses suite for amplicon-based NGS data
por: Brouwer, R W W, et al.
Publicado: (2018)

Benchmarking variational AutoEncoders on cancer transcriptomics data
por: Eltager, Mostafa, et al.
Publicado: (2023)

Integrative whole-genome and transcriptome analysis of HER2-amplified metastatic breast cancer
por: Verschoor, Noortje, et al.
Publicado: (2023)

Plasma ESR1 mutations and outcome to first-line paclitaxel and bevacizumab in patients with advanced ER-positive/HER2-negative breast cancer
por: Bos, M. K., et al.
Publicado: (2023)

Pharmacological CDK4/6 inhibition reveals a p53‐dependent senescent state with restricted toxicity
por: Wang, Boshi, et al.
Publicado: (2022)

High‐throughput isolation of circulating tumor DNA: a comparison of automated platforms
por: van Dessel, Lisanne F., et al.
Publicado: (2018)

Genomic Alterations Associated with Estrogen Receptor Pathway Activity in Metastatic Breast Cancer Have a Differential Impact on Downstream ER Signaling
por: Angus, Lindsay, et al.
Publicado: (2023)

Lost by Transcription: Fork Failures, Elevated Expression, and Clinical Consequences Related to Deletions in Metastatic Colorectal Cancer
por: Smid, Marcel, et al.
Publicado: (2022)

APOBEC3B Gene Expression in Ductal Carcinoma In Situ and Synchronous Invasive Breast Cancer
por: Sieuwerts, Anieta M., et al.
Publicado: (2019)

Detection of circulating tumour DNA after neoadjuvant chemoradiotherapy in patients with locally advanced oesophageal cancer
por: Eyck, Ben M, et al.
Publicado: (2022)

Somatic growth in single ventricle patients: A systematic review and meta‐analysis
por: Van den Eynde, Jef, et al.
Publicado: (2022)

Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity
por: Garinis, George A., et al.
Publicado: (2009)

Absence of Common Somatic Alterations in Genes on 1p and 19q in Oligodendrogliomas
por: Bralten, Linda B., et al.
Publicado: (2011)

Liquid Biopsies for Colorectal Cancer and Advanced Adenoma Screening and Surveillance: What to Measure?
por: Eikenboom, Ellis L., et al.
Publicado: (2023)

A short tutorial in analyzing NGS data of cancer genomes for somatic mutation calling
por: Vuong, Huy, et al.
Publicado: (2013)

FiNGS: high quality somatic mutations using filters for next generation sequencing
por: Wardell, Christopher Paul, et al.
Publicado: (2021)

BRCA1/2 NGS Somatic Testing in Clinical Practice: A Short Report
por: Pepe, Francesco, et al.
Publicado: (2021)

Germline and somatic variants in ovarian carcinoma: A next-generation sequencing (NGS) analysis
por: Andrikopoulou, Angeliki, et al.
Publicado: (2022)

mFast‐SeqS‐based aneuploidy score in circulating cell‐free DNA is a prognostic biomarker in prostate cancer
por: Isebia, Khrystany T., et al.
Publicado: (2023)

Genome‐wide aneuploidy detected by mFast‐SeqS in circulating cell‐free DNA is associated with poor response to pembrolizumab in patients with advanced urothelial cancer
por: Mendelaar, Pauline A. J., et al.
Publicado: (2022)

Turning up the heat does not affect quality of life
por: van Driel, Willemien J., et al.
Publicado: (2022)

NGS-Logistics: federated analysis of NGS sequence variants across multiple locations
por: Ardeshirdavani, Amin, et al.
Publicado: (2014)

Advantages and Challenges of Using ctDNA NGS to Assess the Presence of Minimal Residual Disease (MRD) in Solid Tumors
por: Larribère, Lionel, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_gs1rffmc8s8bj4bholj0mrmkjo