Genomic amplification in retinoblastoma narrowed to 1.2 Mb on chromosome 6p containing a novel kinesin-like gene, RBKIN

Abstract

Cutaneous melanoma is the most serious form of skin cancer and one of the most common cancers in young adults. Its incidence is increasing at a significant rate, and the long-term survival rate for patients with melanoma has not improved markedly since the 1970s. Our laboratory identified unexpected subtypes of human cutaneous melanoma and observed a unique pattern of gene expression in highly invasive melanomas 1. However, the study design for this initial report did not allow a direct correlation of gene expression profiles with disease progression or response to therapy. We have begun to address the relationship between gene expression profile and clinical outcome by collecting and analyzing a set of melanoma tumor biopsy samples with known clinical outcome. We have supplemented this set of samples with a melanoma tissue microarray. The examination of gene expression patterns of melanoma tumors will provide a unique opportunity to study a homogeneous group of patients and determine whether gene expression patterns can assist in predicting disease progression or therapeutic response.

Genomic gains on chromosome 1q in retinoblastoma: Consequences on gene expression and association with clinical manifestation

“…Possibly, gains in these samples were missed by CGH because the resolution of this technique, both spatial and quantitative, is inferior to that of QMPCR. 30,31 None of the tumors analyzed here showed high-level amplification of one or more specific markers on 1q32. This is also true for the results of QMPCR analysis of 1q21, a region that was included in QMPCR analysis because of the results of expression analysis after SAM.…”

“…In this respect, our results confirm previous reports. 30,31 We cannot exclude the possibility that some tumors identified as having gains by QMPCR may have no 1q gains. However, we controlled for stochastic and systematic errors, which are potential sources of false-positive results, by redundant measurements of some loci and by analysis of samples with known copy numbers of chromosome 1q, respectively.…”

Defining a 0.5-Mb Region of Genomic Gain on Chromosome 6p22 in Bladder Cancer by Quantitative-Multiplex Polymerase Chain Reaction

“…15 These STS's span 16 Mb between 6p21.3-6p23.1 and the PCR product from each primer pair is 200 bp or more. As before, we used the STS marker P4HA1 (WI-7221) on human 10q21 as an internal control.…”

“…Each set of PCR reactions also included the validated retinoblastoma external controls (RB1950 copy number 3.9, consistent with isochromosome 6p, and RB1925 copy number 2.1, consistent with no copy number gain) described previously. 15 The reactions were carried out in triplicate for each STS marker in every tumor. All forward primers for the STS markers were labeled with the fluorescent dye Cy5.0 (Integrated DNA Technologies Inc.).…”

“…recently identified a novel candidate oncogene, RBKIN, at this location in retinoblastoma (RB). 15 The identification of RBKIN was facilitated by the use of QM-PCR to systematically define a minimal critical region within the area of gain previously identified by CGH. 16 In the present study, we have used an identical strategy to define a minimal region of recurrent gain within subregions of chromosome band 6p22 in a series of 59 primary urothelial carcinomas of the bladder.…”