Design considerations for array CGH to oligonucleotide arrays.

Background: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome.

Altered expression of a cell-cycle suppressor gene, Tob-1, in endometriotic cells by cDNA array analyses.

Objective: Interleukin (IL)-1beta, a product of activated peritoneal macrophages, is a central cytokine coordinating neovascularization and monocyte chemotaxis in endometriotic implants. To evaluate the effects of this cytokine on normal endometrial stromal cells and endometriotic stromal cells we performed cDNA expression array analyses before and after exposure to IL-1beta.

Design: Nested case-control study of women with and without laparoscopic evidence of endometriosis.

PIK3CA is implicated as an oncogene in ovarian cancer.

Ovarian cancer is the leading cause of death from gynecological malignancy and the fourth leading cause of cancer death among American women, yet little is known about its molecular aetiology. Studies using comparative genomic hybridization (CGH) have revealed several regions of recurrent, abnormal, DNA sequence copy number that may encode genes involved in the genesis or progression of the disease. One region at 3q26 found to be increased in copy number in approximately 40% of ovarian and others cancers contains PIK3CA, which encodes the p110alpha catalytic subunit of phosphatidylinositol 3-kinase (PI3-kinase).

Isolation of genomic fragments from polymorphic regions by representational difference analysis.

Representational difference analysis is an effective technique for isolating the differences between two nearly identical genomes. We have found the technique to be extremely valuable in our analyses of mouse germline mutations. We also present several technical improvements in the procedure that make it more efficient and reliable.

Recovery of probes linked to the jcpk locus on mouse chromosome 10 by the use of an improved representational difference analysis technique.

Representational difference analysis (RDA) is a subtractive hybridization technique by which the differences between two complex genomes can be isolated. An improved version of this technique was used to isolate DNA segments that map to a narrow genetic region adjacent to the jcpk locus on Chromosome 10 of the mouse. A mutation at this locus acts recessively and causes an early onset polycystic kidney disease.