High-Resolution Single Nucleotide Polymorphism Array Analysis of Epithelial Ovarian Cancer Reveals Numerous Microdeletions and Amplifications

Abstract

Purpose: Genetic changes in sporadic ovarian cancer are relatively poorly characterized compared with other tumor types.We have evaluated the use of high-resolution whole genome arrays for the genetic profiling of epithelial ovarian cancer. Experimental Design: We have evaluated 31 primary ovarian cancers and matched normal DNA for loss of heterozygosity and copy number alterations using 500K single nucleotide polymorphism arrays. Results: In addition to identifying the expected large-scale genomic copy number changes, >380 small regions of copy number gain or loss (<500 kb) were identified among the 31 tumors, including 33 regions of high-level gain (>5 copies) and 27 homozygous deletions. The existence of such a high frequency of small regions exhibiting copy number alterations had not been previously suspected because earlier genomic array platforms lacked comparable resolution. Interestingly, many of these regions harbor known cancer genes. For example, one tumor harbored a 350-kb high-level amplification centered on FGFR1 and three tumors showed regions of homozygous loss 109 to 216 kb in size involving the RB1 tumor suppressor gene only. Conclusions: These data suggest that novel cancer genes may be located within the other identified small regions of copy number alteration. Analysis of the number of copy number breakpoints and the distribution of the small regions of copy number change indicate high levels of structural chromosomal genetic instability in ovarian cancer.

No evidence of clonal somatic genetic alterations in cancer-associated fibroblasts from human breast and ovarian carcinomas

“…It is reasonable to assume the presence of some adjacent non-neoplastic and nonfibroblast cells within the 5 mm distance of the epithelial compartment of the carcinoma, but this problem would be shared by all published results, including this work. Third, we used ultra high-resolution SNP arrays, which can simultaneously detect copy number alterations and LOH events with high precision and sensitivity 19,20 .In contrast to previous studies in ovarian cancer 15,16 and breast cancer 13,14 , our study did not find any evidence of frequent somatic genetic alterations in CAFs from either cancer type. The sole confirmed somatic genetic alteration was detected in an endometrioid ovarian cancer, which showed copy number loss of the entire chromosome 22.…”

“…It is reasonable to assume the presence of some adjacent non-neoplastic and nonfibroblast cells within the 5 mm distance of the epithelial compartment of the carcinoma, but this problem would be shared by all published results, including this work. Third, we used ultra high-resolution SNP arrays, which can simultaneously detect copy number alterations and LOH events with high precision and sensitivity 19,20 .…”

“…High-throughput microarray genotyping analysis was done for each tumor epithelia, corresponding stroma, and matched normal DNA using GeneChip Human Mapping 250K Arrays NspI and/or StyI (Affymetrix) following manufacturer's instructions and as described previously 19 . We analyzed 28 of ovarian and breast fresh frozen samples with both chips, and the primary breast CAFs on the NspI array only.…”

“…We hypothesized that the contradictory data may in part be a reflection of inherent technical limitations of the various methodologies used. Therefore, we took advantage of innovative SNP array-based technologies 19 to investigate in detail the genomic integrity of CAFs microdissected from fresh frozen primary human ovarian and breast cancers as well as short-term cultures of primary breast CAFs.…”

Electrical detection of single-base DNA mutation using functionalized nanoparticles

“…High throughput screening has identified altered genes in many spontaneous as well as hereditary cancers. 1,2 For example, mutations in base 12 of the K-ras gene are implicated in over 90% of pancreatic carcinomas, and it is also considered a prognostic indicator for lung cancer patients. 3 Specific mutations in such genes can thus be used as diagnostic indicators for the susceptibility of disease, aiding in early detection and treatment.…”