ArticleExperimental and molecular pathology2018
Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.
Article in Experimental and molecular pathology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT00432172 ("A Randomized Multicenter Phase II Trial to Evaluate the Effectiveness of Selective Neoadjuvant Treatment According to Immunohistochemical Subtype for HER2 Negative Breast Cancer Patients"), which is not on this map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
"A Randomized Multicenter Phase II Trial to Evaluate the Effectiveness of Selective Neoadjuvant Treatment According to Immunohistochemical Subtype for HER2 Negative Breast Cancer Patients"
Who cites it
22 citing papers in PubMed.
- Shallow Whole-Genome Sequencing to Assess Genomic Instability and Predict Treatment Response in Metastatic Castration-Resistant Prostate Cancer.JCO precision oncology · 2026Article
- Benchmarking copy number variation detection with low-coverage whole-genome sequencing.Briefings in bioinformatics · 2025Article
- PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis.Briefings in bioinformatics · 2025Article
- SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.Briefings in bioinformatics · 2024Article
- The reckoning of chromosomal instability: past, present, future.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2024Review
- Clonal Patterns Between Pouch Neoplasia and Prior Colorectal Neoplasia in Inflammatory Bowel Disease Patients: An Exploratory Cohort Study.Inflammatory bowel diseases · 2023Article
- Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers.Nature communications · 2023Article
- Application of informatics in cancer research and clinical practice: Opportunities and challenges.Cancer innovation · 2022Review
- Article
- High levels of chromosomal aberrations negatively associate with benefit to checkpoint inhibition in NSCLC.Journal for immunotherapy of cancer · 2022Article
- [The molecular pathology breviary: read depth and coverage in NGS analysis].Der Pathologe · 2022Article
- Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast.Nature communications · 2022Article
- Review
- LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations.iScience · 2021Article
- Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data.BMC genomics · 2021Article
- A practical guide to cancer subclonal reconstruction from DNA sequencing.Nature methods · 2021Review
- Copy Number Signatures and Clinical Outcomes in Upper Tract Urothelial Carcinoma.Frontiers in cell and developmental biology · 2021Article
- Landscape of G-quadruplex DNA structural regions in breast cancer.Nature genetics · 2020Article
- Artificial intelligence (AI) and big data in cancer and precision oncology.Computational and structural biotechnology journal · 2020Review
- A Novel Approach for the Genetic Analysis of Biliary Tract Cancer Specimens Obtained Through Endoscopic Ultrasound-Guided Fine Needle Aspiration Using Targeted Amplicon Sequencing.Clinical and translational gastroenterology · 2019Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
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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.