ArticleHuman genomics2015
Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma.
Article in Human genomics, 2015. 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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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- CNAScope: pan-cancer copy number aberration database with functional annotation and interactive visualization.Nucleic acids research · 2026Article
- Emerging Biomarkers for Managing Barrett's Esophagus.Gastrointestinal endoscopy clinics of North America · 2026Review
- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- The Ubiquitin-Conjugating Enzyme E2 O (UBE2O) and Its Therapeutic Potential in Human Leukemias and Solid Tumors.Cancers · 2024Review
- Single-nuclei sequencing of uterine serous carcinoma reveals racial differences in immune signaling.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Correlation between NGS panel-based mutation results and clinical information in colorectal cancer patients.Heliyon · 2024Article
- High-resolution genomic profiling and locus-specific FISH in subcutaneous and visceral adipose tissue of obese patients.Frontiers in genetics · 2023Article
- Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8.The Journal of clinical endocrinology and metabolism · 2021Article
- The Positive Correlations between the Expression of Histopathological Ubiquitin-Conjugating Enzyme 2O Staining and Prostate Cancer Advancement.Pharmaceuticals (Basel, Switzerland) · 2021Article
- Clinical-grade whole-genome sequencing and 3' transcriptome analysis of colorectal cancer patients.Genome medicine · 2021Article
- Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC).Journal of cellular and molecular medicine · 2019Article
- A muscle-specific UBE2O/AMPKα2 axis promotes insulin resistance and metabolic syndrome in obesity.JCI insight · 2019Article
- Germline and somatic variations influence the somatic mutational signatures of esophageal squamous cell carcinomas in a Chinese population.BMC genomics · 2018Article
- A UBE2O-AMPKα2 Axis that Promotes Tumor Initiation and Progression Offers Opportunities for Therapy.Cancer cell · 2017Article
- Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapy.Scientific reports · 2017Article
- Integrated molecular analysis reveals complex interactions between genomic and epigenomic alterations in esophageal adenocarcinomas.Scientific reports · 2017Article
- Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis.PloS one · 2017Article
- Genetic alterations in hepatocellular carcinoma: An update.World journal of gastroenterology · 2016Review
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundEsophageal adenocarcinoma (EA) is among the leading causes of cancer mortality, especially in developed countries. A high level of somatic copy number alterations (CNAs) accumulates over the decades in the progression from Barrett's esophagus, the precursor lesion, to EA. Accurate identification of somatic CNAs is essential to understand cancer development. Many studies have been conducted for the detection of CNA in EA using microarrays. Next-generation sequencing (NGS) technologies are believed to have advantages in sensitivity and accuracy to detect CNA, yet no NGS-based CNA detection in EA has been reported.
resultsIn this study, we analyzed whole-exome (WES) and whole-genome sequencing (WGS) data for detecting CNA from a published large-scale genomic study of EA. Two specific comparisons were conducted. First, the recurrent CNAs based on WGS and WES data from 145 EA samples were compared to those found in five previous microarray-based studies. We found that the majority of the previously identified regions were also detected in this study. Interestingly, some novel amplifications and deletions were discovered using the NGS data. In particular, SKI and PRKCZ detected in a deletion region are involved in transforming growth factor-β pathway, suggesting the potential utility of novel biomarkers for EA. Second, we compared CNAs detected in WGS and WES data from the same 15 EA samples. No large-scale CNA was identified statistically more frequently by WES or WGS, while more focal-scale CNAs were detected by WGS than by WES.
conclusionsOur results suggest that NGS can replace microarrays to detect CNA in EA. WGS is superior to WES in that it can offer finer resolution for the detection, though if the interest is on recurrent CNAs, WES can be preferable to WGS for its cost-effectiveness.
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