Development and validation of a cell cycle progression signature for decentralized testing of men with prostate cancer.

Aim: The 46-gene Prolaris® cell cycle progression test provides information on the risk of prostate cancer progression. Here we developed and validated a 16-gene kit-based version. Methods: RNA was extracted from prostate cancer biopsy tissue. Amplification efficiency, minimum tumor content, repeatability, reproducibility and equivalence with the 46-gene test were evaluated. Results: Amplification efficiencies for all genes were within the acceptable range (90-110%), and samples with ≥50% tumor content were appropriate for the 16-gene test. Results were repeatable (standard deviation: 0.085) and reproducible (standard deviation: 0.115). Instrument, operator and kit lot had minimal impact on results. Cell cycle progression scores from the 46- and 16-gene tests were highly correlated (r = 0.969; bias = 0.217). Conclusion: The 16-gene test performs consistently and similarly to the 46-gene test.

Prostate cancer does not always require aggressive treatment, and some men with low risk of disease progression may chose active surveillance. One way to measure the risk of disease progression is the Prolaris^® cell cycle progression test, which is performed at a commercial testing facility and measures the expression of 46 genes. However, certain European countries would prefer to run this test at a centralized testing facility. To this end we developed a streamlined kit measuring 16 genes to be used in these testing facilities, and showed that the cell cycle progression scores derived from the kit test are robust and equivalent to those obtained with the larger 46-gene test.

Gene expression signature as an ancillary method in the diagnosis of desmoplastic melanoma.

Desmoplastic melanoma (DM) is a rare fibrosing variant of melanoma that can be difficult to diagnose. One of the diagnostic challenges is its distinction from a melanocytic nevus with desmoplasia. Here we investigate the use of a 23-gene signature, which has previously been shown to distinguish benign from malignant melanocytic neoplasms. We assessed 50 cases with a differential diagnostic consideration of DM that underwent gene expression testing. Hematoxylin and eosin-stained sections were reviewed, and the final cohort included 20 DMs, 5 nondesmoplastic melanomas, and 27 desmoplastic melanocytic nevi. Of the 20 DMs, the gene expression score was positive ("likely malignant") in 15 tumors, indeterminate in 1, and negative ("likely benign") in 4. None of the desmoplastic melanocytic nevi were positive. The gene expression score was negative in 24 of the melanocytic nevi and indeterminate in the remaining 3. Nine DMs were also analyzed cytogenetically by single-nucleotide polymorphism (SNP) array. The SNP array revealed chromosomal copy number aberrations consistent with melanoma in 7 DMs and failed to show any aberrations in 2. The results of SNP array analysis and gene expression testing were discordant in 4 cases. Our results document limitations in the sensitivity of both the gene expression signature and SNP array for the detection of DM. Nonetheless, our findings suggest a potential role of the gene expression signature as ancillary supportive evidence for the distinction of DM from desmoplastic nevus because positive scores were only seen in melanomas.

The impact of assessing specimen adequacy and number of needle passes for fine-needle aspiration biopsy of thyroid nodules.

Fine-needle aspiration biopsy (FNAB) of thyroid nodules is a safe, cost-effective procedure but the rates of inadequate cytology specimens range from approximately 1% to 15%. This study tests the hypothesis that ultrasonographically (US) guided FNAB and onsite assessment of cytology improves the adequacy rate of FNAB. A retrospective analysis was performed on 693 thyroid FNAB specimens obtained with and without ultrasound guidance and with or without onsite cytology assessment. Overall, 29 specimens (4%) were inadequate for diagnosis. Among 163 cystic nodules and 530 solid nodules, inadequacy rates were 15% (n = 24) and 1% (n = 5) respectively (p = 0.0001). An onsite assessment of cytology for adequacy was done in 550 cases (83%), which was more accurately performed by a cytopathologist (97%) than a cytotechnologist (93%, p = 0.015). With US-guided FNAB, 3% of the cytology specimens were inadequate, compared to a 7% rate when US was not done (p = 0.003). The mean number of needle punctures necessary for an adequate specimen was 3.8 +/- 0.06 (median, 3.0; range, 1-11), which was different among various types of doctors, ranging from 3.2 +/- 0.07 to 5.4 +/- 0.12 (p = 0.001 analysis of variance [ANOVA]). The fewest number of needle passes to achieve an adequate specimen were required by university endocrinologists and pathologists working together (average, 3.2 +/- 0.07; median, 3.0; range, 1-11). Sample inadequacy rate varied significantly among physician groups, ranging from 3% to 18% (p = 0.0001 ANOVA). Stepwise regression analysis showed that onsite assessment of cytology, US-guided FNAB (p = 0.16), and cystic nature of the nodule (p < 0.0001 for all) correlated with adequacy of the specimen. We conclude that US-guided FNAB with onsite evaluation of cytology specimens substantially increases the adequacy of cytology specimens and decreases the number of required needle passes, which ultimately reduces patient discomfort and diagnostic errors, thus raising the question as to whether this should eventually become the standard of care. We believe this is a goal that training programs should strive to achieve.