Array Comparative Genomic Hybridization

Microarray-based technology has provided a platform on which a large number of genomic aberrations can be assessed in a single experiment. CGI is focused on one application of the microarray technology, known as array comparative genomic hybridization or array-CGH, to detect DNA copy number changes (gain/loss) frequently observed in cancers. Targeted arrays in various stages of design and development include those for diagnostic and prognostic purposes in lymphomas, genitourinary cancers, gynecological cancers and leukemias.

Cancers of the genitourinary system (prostate, testis, penis, cervical, uterine, ovarian, vulva, kidney, bladder, and ureter cancers) account for close to 30% of all estimated new cancer cases in the USA with the three most prevalent being prostate, bladder, and kidney cancers. The estimated deaths caused by these in 2010 are expected to be 32,050, 14,680, and 13,040 respectively, comprising ~10% of all cancer-related deaths. Thus, although generally characterized by early stage detections and encouraging five-year survival rates, these cancers still represent major health risk and substantial medical cost burden to the public with their high rates of incidence. In women, the three most frequent genital system cancers are endometrial, ovarian, and then cervical with a total overall expected deaths in 2010 to be 26,000 with ovarian cancer accounting for over half. Developing sophisticated, state-of-the-art molecular assays that enable more accurate diagnosis and/or prognosis of these cancers will not only benefit the patients by offering more appropriate treatments but also effectively reduce the unnecessary medical cost associated with surgery, long-term follow-up surveillance, or adjuvant therapy after the treatment.

UroGenRA® is a CGI custom-designed oligonucleotide array for implementation within a clinical laboratory as an array-CGH-based diagnostic/prognostic tool for kidney, prostate, and bladder cancers. It was designed to detect gains and losses that frequently occur in these three cancer types and that have the potential to differentially diagnose and/or stratify patients to assist and guide clinical management. For kidney cancer, it is specifically designed to classify tumors into the four main types (three malignant, one benign) critical at several levels in patient management: diagnosis of image-guided needle biopsies of small incidentally discovered kidney masses providing rationale for surgical/non-surgical management, diagnosis in patients with larger neoplasms to stratify for risks of local or regionally advanced disease that can be factored in to treatment selection recommendations (i.e., extent of surgical intervention, less invasive options or ablation), in those with metastatic disease, where drug trials are currently based on post-surgical tumor diagnosis, and potentially in the diagnosis of the so-called morphologically “unclassified” renal cancers. Additionally within the predominant subtype, clear cell renal cell carcinoma, prognostication is feasible based on the presence/absence of gain and loss of certain genomic regions. For prostate cancer, UroGenRA®, has the potential to assess prostate core/needle biopsy genomic variability, to identify biomarker for inclusion in nomograms for assessment of risk of biochemical recurrence, to assess radiocurability and treatment options for intermediate risk patients, and to explore the genomic aberrations of circulating tumor cells. For bladder cancer, UroGenRA® has application in identifying tumors most likely to recur, and of muscle-invasive lesions those most likely to benefit from treatment.

UGenRA™ is a CGI custom-designed oligonucleotide array designed to detect gains and losses of genomic material in endometrial, ovarian, and cervical cancers. Endometrial hyperplasia is a precursor lesion of endometriod endometrial carcinoma (EEC) and since about 50% of women with atypical hyperplasia also have concurrent EEC, it is important to identify those precursor lesions more likely to progress to and those with frank cancer. UGenRA™ offers the opportunity to identify such specimens and potentially guide clinical management. Another potential application is to stratify those tumors likely to recur, permitting the identification of patients most likely to benefit from adjuvant therapy. Risk-stratification of stage III/IV ovarian cancer patients after cytoreductive surgery for front-line platinum taxane-based chemotherapy is a potential application for UGenRA™, and the design currently contains the sites of genomic gain/loss with such prognostic value. For any of the three cancers, genomic gain/loss associated with response to particular therapies can be assessed using UGenRA™, especially with the need of only small amounts of starting material and the ability to perform UGenRA™ on FFPE specimens.

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