scholarly journals Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

10.3791/51718 ◽  
2015 ◽  
Author(s):  
Joo Wook Ahn ◽  
Michael Coldwell ◽  
Susan Bint ◽  
Caroline Mackie Ogilvie
Keyword(s):  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Array Comparative Genomic Hybridization ◽  
Array Cgh ◽  
Copy Number Variants ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Comparative Genomic Hybridization Array ◽  
Genomic Copy Number ◽  
Genomic Copy

Pituicytoma: Characterization of a Unique Neoplasm by Histology, Immunohistochemistry, Ultrastructure, and Array-Based Comparative Genomic Hybridization

2010 ◽  
Vol 134 (7) ◽  
pp. 1063-1069 ◽  
Author(s):  
Joanna J. Phillips ◽  
Anjan Misra ◽  
Burt G. Feuerstein ◽  
Sandeep Kunwar ◽  
Tarik Tihan
Keyword(s):  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Secretory Granules ◽  
Comparative Genomic ◽  
Sellar Region ◽  
Genomic Hybridization ◽  
Genetic Changes ◽  
Genomic Copy Number ◽  
Genomic Copy

Abstract The pituicytoma is a rare neoplasm whose histogenesis is debated partly because of the diversity of tissue types present in the sellar region. In this article we illustrate the characteristic histologic, immunohistologic, and ultrastructural features of this unique neoplasm. Furthermore, we use array-based comparative genomic hybridization to demonstrate a unique pattern of genomic copy number aberrations in pituicytomas. Tumors were composed of bipolar, spindle cells that were immunopositive for S100, vimentin, and Bcl-2 and immunonegative for synaptophysin, chromogranin, and glial fibrillary acidic protein. Ultrastructural analysis was remarkable for absence of secretory granules. Array comparative genomic hybridization demonstrated genomic copy number imbalances, including losses on chromosome arms 1p, 14q, and 22q and gains on 5p. This pattern of genetic changes only partially overlaps with the genomic alterations reported in pituitary adenomas. In summary, our data suggest that pituicytomas are a unique subset of tumors of the sellar region.

scholarly journals Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas

Blood ◽  
2006 ◽  
Vol 107 (6) ◽  
pp. 2477-2485 ◽  
Author(s):  
Weiyi Chen ◽  
Jane Houldsworth ◽  
Adam B. Olshen ◽  
Gouri Nanjangud ◽  
Seeta Chaganti ◽  
...  
Keyword(s):  
B Cell ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Array Comparative Genomic Hybridization ◽  
Array Cgh ◽  
B Cell Lymphoma ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Copy Number Changes ◽  
Large B Cell

Abstract To identify, in high-resolution regions of DNA, the copy number changes associated with outcome in patients with diffuse large B-cell lymphoma (DLBCL), a disease with an approximately 50% mortality rate, we performed array comparative genomic hybridization (array-CGH) on specimens from 64 patients with newly diagnosed DLBCL treated with anthracycline-based chemotherapy. For the entire cohort, 55 commonly gained/lost regions, ranging in size from less than 1 Mbp to entire chromosomes, were identified using 1- to 2-Mbp and 2- to 4-Mbp resolution BAC arrays. Copy number changes of 9 minimal regions significantly correlated with overall survival, of which 6 were 10 Mbp or smaller. On multivariate analysis, loss of chromosomes 2 (2.4-4.1 Mbp) and 16 (33.8-35.6 Mbp) were found to be prognostic indicators of poor survival, independent of clinical features routinely used to predict outcome. Loss of chromosome 1 (78.2-79.1 Mbp) was predictive of good outcome. For a subset of 55 specimens classified according to cell-of-origin expression signature subtype, gain of chromosome 12 (45.4-53.8 Mbp) was found to be significantly associated with the germinal center B-cell-like DLBCL subtype. Overall, array-CGH identified relatively small genomic regions associated with outcome, which, along with follow-up expression studies, may reveal target genes important in DLBCL clinical behavior. (Blood. 2006;107:2477-2485)

scholarly journals Computational Methods for the Analysis of Array Comparative Genomic Hybridization

2006 ◽  
Vol 2 ◽  
pp. 117693510600200 ◽  
Author(s):  
Raj Chari ◽  
William W. Lockwood ◽  
Wan L. Lam
Keyword(s):  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Array Cgh ◽  
Profile Analysis ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Comparative Genomic Hybridization Array ◽  
Software Packages ◽  
Cancer Genomes ◽  
Rapid Accumulation

Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.

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