SNP profiling discriminates histology-related subgroups based on chromosomal instability status.

<p>Chromosomal instability status (CIN) according to the number of allele-specific copy number alterations (CNAs) and copy number neutral loss of heterozygosity (CNN LOH), using a human mapping 250K single nucleotide polymorphism (SNP) array with paired tumor DNA and normal DNA. CNAs were divided into three subgroups: CIN-high (≥9 arms with CNAs), CIN-low (1–8 arms with CNAs), and CIN-negative (0 CNAs). (A) Details of number of chromosomal arms with CNAs in each tumor of three histological subtypes (serous carcinomas, SC; clear cell carcinomas, CCC; endometrioid carcinomas, EC). Stage I/II and stage III/IV are colored differently. (B) Correlation between CIN status and histological subtypes. (C) Overview of CNAs by running SNP arrays with 57 ovarian cancer samples. Hierarchical clustering based on the Euclidean distance for dissimilarities is shown. The type A cluster includes tumors with a broad range and low frequency of CNAs, whereas the type B cluster includes tumors with a focal range and high frequency of CNAs. C, E, and S indicate clear cell carcinoma, endometrioid carcinoma, and serous carcinoma, respectively.</p

Clustering by expression arrays and clinicopathological characteristics.

<p>Sensitive*: Complete response or Partial response.</p><p>Resistant**: Stable disease or Progressive disease.</p><p>p-value (by Fisher's exact test).</p><p>Clustering by expression arrays and clinicopathological characteristics.</p

Integrated analyses reveal a poor-prognostic clear cell signature associated with high chromosomal instability.

<p>Comparison of clear cell carcinoma (CCC) clusters CCC-1 and CCC-2 by gene expression profiling. (A) <i>UGT1A6</i> and <i>UGT1A10</i> were significantly upregulated in CCC-1 compared with CCC-2. (B) The cluster of genes upregulated in CCC-1 compared with CCC-2. The cluster includes <i>STAT3</i> and <i>HIF2A</i>.</p

Correlation between clustering by expression arrays, genetic alterations and clinicopathological characteristics in CCC.

<p>Sensitive*: Complete response or Partial response.</p><p>Resistant**: Stable disease or Progressive disease.</p><p>Correlation between clustering by expression arrays, genetic alterations and clinicopathological characteristics in CCC.</p

Ratio of whole arm CNAs among all the CNAs in serous and clear cell carcinomas.

<p>Ratio of whole arm CNAs among all the CNAs in serous and clear cell carcinomas.</p