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The purpose of non-small cell lung cancer is of the highest incidence of malignant tumors diagnosed due to the lack of effective early detection method, which are mostly late, in addition to surgery, there is no other effective treatment. After 5-year survival rate is only about 15%. Like other tumors, the incidence of non-small cell lung cancer, the development of a multi-stage, multi-gene regulation, disorder or tumor suppressor gene inactivation caused by a variety of tumor-associated gene expression. Therefore, to understand the genetic changes in the cancer process, need to study the whole genome abnormalities. Studies show a direct result of increasing and decreasing the copy number of chromosome regions that copy number variation (copy number variationCNV) is located in the section of the gene copy number changes, affecting the level of gene expression, leading to phenotypic differences. Chromosomal region where the tumor suppressor gene loss of heterozygosity (loss of heterzygosity LOH) in tumors of epithelial and mesenchymal sources of important events in the development process. The lung cancer study of genetic variation method including karyotype analysis, fluorescence in situ hybridization (fluorescent in situ hybridizationFISH), comparative genomic hybridization (comparative genomic hybridization CGH). CGH can only be detected by amplification or missing number of exceptions, but you can not find Allelic homozygosity (AH), which need to be studied in tumor cells is a very common DNA variations in a loss of heterozygosity, heterozygosity of the tumor suppressor gene absence would lead to tumorigenesis, genome-wide scan of LOH traditional methods including the microsatellite markers Act (polymorphic microsatellite markers) and restriction fragment length polymorphism (retriction the fragment length polymorphism, RFLP), but these two methods are very time-consuming and laborious. The SNP is the most common polymorphic genetic markers in the human genome. Affymectrix Genome-wide SNP 6.0 approximately 906,600 bits of the chip select point analysis of the genotype of the locus, while the chip can provide you point two alleles copy number (CN), to obtain the bit point of the zone where CN and LOH genome analysis to achieve very high resolution (lt; 10kb). The purpose of this study is to genome-wide scan of lung tumor tissue by using SNP chip to explore the amplification of lung tissue gene copy number, deletions, and loss of heterozygosity of genetic variation and lung cancer, designed to reveal lung squamous cell carcinoma the molecular mechanisms to improve early diagnosis and provide treatment method. In this study, using SNP chip detect CNV and LOH of 15 cases of lung squamous cell carcinoma genome-wide genetic variation information, further studies of genome-wide copy number amplification, deletions, and loss of heterozygosity of chromosome abnormalities squamous cell carcinoma of the lung from the genome-wide level abnormal molecular genetic mechanisms discussed. Method to extract the 15 cases of lung squamous cell carcinoma of the lung tissue and cancer lung tissues of paired and used for whole-genome DNA microarray, Affymetrix Genome-wide SNP 6.0. Chip hybridization signal intensity data using the Affymetrix proprietary software GTC3.0 analysis of SNP genotype and copy number of whole-genome CNV of LOH, homozygous deletion region. Results 1.Genome-wide SNP 6.0 chip the QC Call rate exceeded the quality control standards. 15 chip the QC Call rate lowest of 95.07%, 99.26%, 97.49% on average, the Contrast QC as low as 2.08 up to 3.75, average 2.73, MAPD minimum of 0.16 up to 0.28, an average of 0.22 good quality microarray hybridization. 2.15 cases of lung tissue analysis results in CN 2 fragments of 181, accounting for 1.26%, and the shortest fragment length 100kb, the longest to 3,995 kb. CN 4 fragments of 226, accounting for 1.57%, the shortest fragment length 100kb, the longest for 34,862 kb. CN 3 fragment of a total of 6,018, accounting for 41.9%, the shortest fragment length 100kb, the longest for 25,654 kb. CN fragment of a total of 7,837, accounting for 54.6%, the shortest fragment length 100kb, the longest for 86,897 kb. CNV in Loss 3.15 cases of lung cancer are mainly located in chromosome 4 (7.11%, 1001/14081), chromosome 3 (6.22%, 876/14081), on chromosome 5 (4.92%, 693/14081), No. 1 chromosome (4.06%, 572/14081), chromosome 10 (3.14%, 442/14081) on the chromosome, gain is mainly distributed in the 7th chromosome (4.99%, 702/14081), chromosome 2 (4.57%, 643 / 14081), chromosome 8 (4.09%, 576/14081), chromosome 1 (3.88%, 547/14081), chromosome 12 (3.49%, 491/14081), on chromosome. Minimum number of gain fragment C08-0342, a total of seven fragments is C08-0027, a total of 877 fragments; minimum number of loss fragment C08-0085, a total of four fragments, most C08-0027 total 1,628 a fragment. 4.15 cases of lung tissue analysis results have varying degrees of loss of heterozygosity, 15 cases of lung cancer detected in various samples containing different number of LOH sites. Detected in 15 cases of lung cancer a total 1,921,845 LOH sites, including the minimum number of LOH sites for C08-0142, a total of 54,274 LOH sites, the largest number of LOH sites C08-0027, a total of 400,078 LOH sites. Different chromosomes and the different LOH number of sites, its incidence in descending order to the first five chromosomes the Part X chromosome (28.1%, 540,105 / 1,921,845), on chromosome 1 (7.14%, 137,282 / 1,921,845). chromosome 5 (6.89% 132,347 / 1,921,845), chromosome 3 (6.19% 119,014 / 1,921,845), chromosome 4 (6.11? 7336/1921845). 15 cases of lung cancer on the X chromosome could be detected LOH sites, detected a total of 31,793 LOH sites. 5.15 cases of lung tissue analysis detected homozygous deletion region (CN = 0) of 92, respectively, at 1,2,3,4,5,6,7,8,9,10,12,13 14,15,16,17,18,19,21, X and Y chromosome, and its incidence in descending order of chromosome 4 (21.7%, 20/92), chromosome 5 (11.9% , 11/92), chromosome 3 (9.8%, 9/92), the Y chromosome (8.7%, 8/92), chromosome X chromosome (7.6%, 7/92), No. 19 (6.5%, 6/92), chromosome 17 (5.4%, 5/92), chromosome 1 (4.3%, 4/92), 8,10,15,18 chromosome (3.3%, 3/92) chromosome 7 (2.2%, 2/92), 2,6,9,12,13,14,16,21 chromosome (1.1%, 1/92). The smallest deletion fragments of chromosome 19 q13.1, length 101kb, and the the deletion fragments longest chromosome 3 p12.3 ~ p12.2, length to 7,146 kb. Conclusion (1) Genome-wide SNP 6.0 GeneChip and analysis software the Genome Typing the Console 3.0, both a detailed analysis of lung squamous cell chromosomal deletions, amplifications and LOH, homozygous deletion region; (2) Genome-wide SNP 6.0 gene microarray screening of multiple lung squamous cell carcinoma associated genes, indicating that multiple genes may be involved in squamous cell carcinoma of the lung, the development process; (3) found that the amplification and homozygous deletion and loss of heterozygosity regions may contain new cancer genes or tumor suppressor genes, new clues and directions for future research.
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