ArticlePloS one2015
Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
33 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.
- Artificial intelligence-based non-small cell lung cancer transcriptome RNA-sequence analysis technology selection guide.Frontiers in bioengineering and biotechnology · 2023Pooled it
- Identifying Locally Recurrent Versus Second Primary Breast Cancer: Genomic Versus Clinical Criteria from Carolina Breast Cancer Study Phase III.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026Trial
- A randomized phase II/III study of paclitaxel/carboplatin/metformin versus paclitaxel/carboplatin/placebo as initial therapy for measurable stage III or IVA, stage IVB, or recurrent endometrial cancer: An NRG oncology/GOG study.Gynecologic oncology · 2025Trial
- Rapid Clearance Profile of Plasma Circulating Tumor HPV Type 16 DNA during Chemoradiotherapy Correlates with Disease Control in HPV-Associated Oropharyngeal Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2019Trial
- LCCC 1025: a phase II study of everolimus, trastuzumab, and vinorelbine to treat progressive HER2-positive breast cancer brain metastases.Breast cancer research and treatment · 2018Trial
- Phase II trial of palbociclib in patients with metastatic urothelial cancer after failure of first-line chemotherapy.British journal of cancer · 2018Trial
- Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer.The Journal of clinical investigation · 2018Trial
- Improved Tumor Purity Metrics in Next-generation Sequencing for Clinical Practice: The Integrated Interpretation of Neoplastic Cellularity and Sequencing Results (IINCaSe) Approach.Applied immunohistochemistry & molecular morphology : AIMMTrial
- Racial differences in endometrial cancer genomics and outcomes using UNCseqGynecologic oncology reports · 2025Article
- Genomic Analysis Reveals Racial and Age-Related Differences in the Somatic Landscape of Breast Cancer and the Association with Socioeconomic Factors.Cancer research · 2025Article
- VOYAGER: an international consortium investigating the role of human papilloma virus and genetics in oral and oropharyngeal cancer risk and survival.medRxiv : the preprint server for health sciences · 2025Article
- Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients.The pharmacogenomics journal · 2023Article
- Characterization of driver mutations in Chinese non-small cell lung cancer patients using a novel targeted sequencing panel.Journal of thoracic disease · 2022Article
- UNMASC: tumor-only variant calling with unmatched normal controls.NAR cancer · 2021Article
- Next-Generation Sequencing in Clinical Practice: Is It a Cost-Saving Alternative to a Single-Gene Testing Approach?PharmacoEconomics - open · 2021Article
- Genomic profiling of endometrial cancer and relationship with volume of endometrial cancer disease spread.Gynecologic oncology reports · 2021Article
- Brain Tumor Microenvironment and Angiogenesis in Melanoma Brain Metastases.Frontiers in oncology · 2020Article
- Histone deacetylase 11 inhibition promotes breast cancer metastasis from lymph nodes.Nature communications · 2019Article
- Role of cytokines in combinatorial immunotherapeutics of non-small cell lung cancer through systems perspective.Cancer medicine · 2019Review
- Identification of Clonal Hematopoiesis Mutations in Solid Tumor Patients Undergoing Unpaired Next-Generation Sequencing Assays.Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors at 1 institution in 1 country.
Funding
Abstract
The recent FDA approval of the MiSeqDx platform provides a unique opportunity to develop targeted next generation sequencing (NGS) panels for human disease, including cancer. We have developed a scalable, targeted panel-based assay termed UNCseq, which involves a NGS panel of over 200 cancer-associated genes and a standardized downstream bioinformatics pipeline for detection of single nucleotide variations (SNV) as well as small insertions and deletions (indel). In addition, we developed a novel algorithm, NGScopy, designed for samples with sparse sequencing coverage to detect large-scale copy number variations (CNV), similar to human SNP Array 6.0 as well as small-scale intragenic CNV. Overall, we applied this assay to 100 snap-frozen lung cancer specimens lacking same-patient germline DNA (07-0120 tissue cohort) and validated our results against Sanger sequencing, SNP Array, and our recently published integrated DNA-seq/RNA-seq assay, UNCqeR, where RNA-seq of same-patient tumor specimens confirmed SNV detected by DNA-seq, if RNA-seq coverage depth was adequate. In addition, we applied the UNCseq assay on an independent lung cancer tumor tissue collection with available same-patient germline DNA (11-1115 tissue cohort) and confirmed mutations using assays performed in a CLIA-certified laboratory. We conclude that UNCseq can identify SNV, indel, and CNV in tumor specimens lacking germline DNA in a cost-efficient fashion.
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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.