Project description:We analyzed 155 squamous- cell lung cancer and 77 adenocarcinoma of the lung samples using 6.0 SNP-arrays all normal tissues that were used to infer copy number are provided
Project description:DNA from four 29 cases, 38 tumor samples (23 PB, 12 LN, 1 Tonsil, 1 colonic biopsy, 1 spleen) and 29 normal DNA from the same patients were analyzed with Affymetrix SNP 6.0 platform for copy number alterations study. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples, lymph nodes and other tissues like spleen, tonsil and colonic biopsy
Project description:Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors.
Project description:Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected a NET and a the corresponding lymph node and liver metastases as well as the derivative cell lines to screen for somatic mutations in the primary NET and to track the fate of genetic changes (by Affymetrix SNP 6.0 micorarray and targeted resequencing by 454 GS FLX) and during metastasis and in vitro progression. using Affymetrix SNP 6.0 Arrays.
Project description:Cytogenetic profiles of 50 meningiomas using high-density GeneChip Mapping 500K set and Genome-Wide Human SNP 6.0 Array in the tumor tissues and in the peripheral blood of the same patients. A total of two hundred 500k arrays (100 tumor samples and 100 blood samples) and 14 SNP6.0 arrays (7 tumour samples and 7 peripheral blood samples) were studied to explore the most common recurrent chromosomal abnormalities (gains and losses) in meningiomas. Our results confirm that del(22q) (52%) and del(1p) (16%) (common deleted regions: 22q11.21-22q13.3. and 1p31.2-p36.33) are the most frequent abnormalities. Additionally, recurrent monosomy 14 (8%), del(6p) (10%), del(7p) (10%) and del(19p) (6%) were also observed, while copy number variation (CNV) patterns consistent with recurrent chromosome gains, gene amplification was absent or rare. Based on their overall SNP profiles meningiomas could be classified into: i) diploid cases, ii) meningiomas with a single chromosome change (e.g. monosomy 22/del(22q) and iii) tumours with ≥2 altered chromosomes.
Project description:We analyzed copy numbers of 60 SCLC cell lines using 6.0 SNP-arrays. For a subgroup of 36 cell lines, previously published copy number data was utilized. CEL and SEG files are included for all cell lines, for which copy number data were not publicly available.
Project description:East-Asian (EA) patients with Non Small Cell Lung Cancer (NSCLC) are associated with a high proportion of non-smoking women, EGFR activating somatic mutations, and clinical responses to tyrosine kinase inhibitors. We identify copy number alterations specific to EA and Western European (WE) NSCLCs and conducted an integrative analysis using transcritomic data for identifying copy-number-driven candidate genes. Samples were hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.
