ArticleGenome medicine2016
Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue.
Article in Genome medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 55 citations in OpenAlex.
- Circulating tumor DNA predicts efficacy of a dual AKT/p70S6K inhibitor (LY2780301) plus paclitaxel in metastatic breast cancer: plasma analysis of the TAKTIC phase IB/II study.Molecular oncology · 2022Trial
- Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression.The Journal of pathology · 2026Article
- Chromosomal instability as a predictive biomarker for recurrence risk following transurethral resection of NMIBC.Frontiers in oncology · 2026Article
- Identification of actionable targets using DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded tissues followed by shallow whole-genome sequencing.The Journal of pathology · 2026Article
- Feasibility of Low-Pass Whole Genome Sequencing for Detecting Somatic Copy Number Alterations in Formalin-Fixed Uveal Melanoma Specimens.Translational vision science & technology · 2025Article
- The Added Value of Genome-Wide Copy Numbers to Objectively Resolve Clonality of Multiple Tumors With Pulmonary Involvement and Ambiguous or Inconclusive Mutational Diagnosis.JTO clinical and research reports · 2025Article
- Benchmarking copy number variation detection with low-coverage whole-genome sequencing.Briefings in bioinformatics · 2025Article
- Low-coverage whole-genome sequencing for differentiating cervical cancer from cervical intraepithelial neoplasia and benign diseases.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- Novel liquid biopsy CNV biomarkers in malignant melanoma.Scientific reports · 2024Article
- Association between copy number alterations estimated using low-pass whole genome sequencing of formalin-fixed paraffin-embedded prostate tumor tissue and cancer-specific clinical parameters.Scientific reports · 2023Article
- Oral cancer prediction by noninvasive genetic screening.International journal of cancer · 2023Article
- High levels of chromosomal aberrations negatively associate with benefit to checkpoint inhibition in NSCLC.Journal for immunotherapy of cancer · 2022Article
- Improvement in the risk assessment of oral leukoplakia through morphology-related copy number analysis.Science China. Life sciences · 2021Article
- Association of Copy Number Variation Signature and Survival in Patients With Serous Ovarian Cancer.JAMA network open · 2021Article
- Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data.BMC genomics · 2021Article
- Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer.Scientific reports · 2021Article
- Loss of SMAD4 Is Sufficient to Promote Tumorigenesis in a Model of Dysplastic Barrett's Esophagus.Cellular and molecular gastroenterology and hepatology · 2021Article
- Copy Number Signatures and Clinical Outcomes in Upper Tract Urothelial Carcinoma.Frontiers in cell and developmental biology · 2021Article
- The Paratuberculosis Paradigm Examined: A Review of Host Genetic Resistance and Innate Immune Fitness inFrontiers in veterinary science · 2021Review
- MYC Copy Number Detection in Clinical Samples Using a Digital DNA-Hybridization and Detection Method.Methods in molecular biology (Clifton, N.J.) · 2021Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.
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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.