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.
Highlights
Esophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide
We evaluated whether a pool of normal control samples could be used as the normal referent in an loss of heterozygosity (LOH) study with the 10 K single nucleotide polymorphism (SNP) chip instead of matched germ-line DNA
To the left of the picture, columns show: microsatellite markers, cartoon of the chromosome, and SNPs examined in the 10 K SNP chip
Summary
Esophageal squamous cell carcinoma (ESCC) is a common malignancy worldwide. Genetic instabilities are characteristic of most human cancers. Genome-wide detection of chromosomal changes, including loss of heterozygosity (LOH) and copy number alterations (CNA), either gain or loss, are the focus of substantial attention in cancer research. LOH is frequently observed in a variety of human cancers, and regions with frequent LOH may contain tumor suppressor genes. Detection of LOH will likely remain a cornerstone for predicting tumor aggressiveness for many human tumors [1]. The discovery of large-scale genome-wide copy number variation has stimulated interest in elucidating the role of CNA in the development of malignancy. The 10 K single nucleotide polymorphism (SNP) array (GeneChip Mapping 10 K array, Affymetrix) offers a high-resolution genomic approach to screen chromosomal alterations systematically. Several studies on allelic imbalance or loss in cancers and cancer cell lines using the 10 K SNP array have been published [2,3,4,5,6,7,8,9,10,11,12]
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