ArticleBMC genomics2006
Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 52 citations in OpenAlex.
- Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network.European journal of medical research · 2014Pooled it
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- Upregulation of IBSP Expression Predicts Poor Prognosis in Patients With Esophageal Squamous Cell Carcinoma.Frontiers in oncology · 2019Article
- Underlying Causes and Therapeutic Targeting of the Inflammatory Tumor Microenvironment.Frontiers in cell and developmental biology · 2018Review
- Somatic mutations in ZFHX4 gene are associated with poor overall survival of Chinese esophageal squamous cell carcinoma patients.Scientific reports · 2017Article
- Chromosomal and Genomic Variations in Esophageal Squamous Cell Carcinoma: A Review of Technologies, Applications, and Prospections.Journal of Cancer · 2017Review
- Amplification and overexpression ofInternational journal of medical sciences · 2016Article
- An Old Story Retold: Loss of G1 Control Defines A Distinct Genomic Subtype of Esophageal Squamous Cell Carcinoma.Genomics, proteomics & bioinformatics · 2015Article
- Chromosomal aneuploidies and combinational fluorescence in situ hybridization probe panels are useful for predicting prognosis for esophageal squamous cell carcinoma.Journal of gastroenterology · 2015Article
- Three-dimensional mRNA measurements reveal minimal regional heterogeneity in esophageal squamous cell carcinoma.The American journal of pathology · 2013Article
- Identification of unique expression signatures and therapeutic targets in esophageal squamous cell carcinoma.BMC research notes · 2012Article
- A novel functional DEC1 promoter polymorphism -249T>C reduces risk of squamous cell carcinoma of the head and neck.Carcinogenesis · 2010Article
- Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma.BMC genomics · 2010Article
- Article
- Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.PloS one · 2009Article
- A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans.Experimental & molecular medicine · 2009Article
- ERCC1 and XRCC1 gene polymorphisms predict response to neoadjuvant radiochemotherapy in esophageal cancer.Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract · 2009Article
- Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China.Cancer research · 2009Article
- Telomere attrition in cancer cells and telomere length in tumor stroma cells predict chromosome instability in esophageal squamous cell carcinoma: a genome-wide analysis.Cancer research · 2009Article
- Prevalence of copy-number neutral LOH in glioblastomas revealed by genomewide analysis of laser-microdissected tissues.Neuro-oncology · 2008Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundEsophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide. Comprehensive genomic characterization of ESCC will further our understanding of the carcinogenesis process in this disease.
resultsGenome-wide detection of chromosomal changes was performed using the Affymetrix GeneChip 10 K single nucleotide polymorphism (SNP) array, including loss of heterozygosity (LOH) and copy number alterations (CNA), for 26 pairs of matched germ-line and micro-dissected tumor DNA samples. LOH regions were identified by two methods--using Affymetrix's genotype call software and using Affymetrix's copy number alteration tool (CNAT) software--and both approaches yielded similar results. Non-random LOH regions were found on 10 chromosomal arms (in decreasing order of frequency: 17p, 9p, 9q, 13q, 17q, 4q, 4p, 3p, 15q, and 5q), including 20 novel LOH regions (10 kb to 4.26 Mb). Fifteen CNA-loss regions (200 kb to 4.3 Mb) and 36 CNA-gain regions (200 kb to 9.3 Mb) were also identified.
conclusionThese studies demonstrate that the Affymetrix 10 K SNP chip is a valid platform to integrate analyses of LOH and CNA. The comprehensive knowledge gained from this analysis will enable improved strategies to prevent, diagnose, and treat ESCC.
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