Correlation of DNA ploidy and histologic diagnosis from prostate core-needle biopsies: is DNA ploidy more sensitive than histology for the diagnosis of carcinoma in small specimens?

TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy

The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. TumorNext also detects gene fusions and structural variants, such as tandem duplications and inversions, in 15 frequently disrupted oncogenes and tumor suppressors. The assay uses a matched control and custom bioinformatics pipeline to differentiate between somatic and germline mutations, allowing precise variant classification. We tested 170 previously characterized samples, of which > 95% were formalin-fixed paraffin embedded tissue from 8 different cancer types, and highlight examples where lack of germline status may have led to the inappropriate prescription of therapy. We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. We analyzed 80 previously characterized formalin-fixed paraffin-embedded specimens and provide examples of hemizygous deletion detection in samples with known pathogenic germline mutations. Thus, the TumorNext combined approach of NGS and OncoScan potentially allows for the identification of the “second hit” in hereditary cancer patients.

The Combination of DNA Ploidy Status and PTEN/6q15 Deletions Provides Strong and Independent Prognostic Information in Prostate Cancer

PURPOSE

Aberrant DNA content has been discussed as a potential prognostic feature in prostate cancer.

EXPERIMENTAL DESIGN

We analyzed the clinical significance of DNA ploidy in combination with prognostic relevant deletions of PTEN and 6q15 in 3,845 prostate cancers.

RESULT

The DNA status was diploid in 67.8%, tetraploid in 25.6%, and aneuploid in 6.8% of tumors, and deletions of PTEN and 6q15 occurred in 17.8% and 20.3% of tumors. Abnormal DNA content and deletions were linked to high Gleason score, advanced tumor stage, and positive nodal stage (P < 0.0001 each). The risk of PSA recurrence increased from diploid to tetraploid and from tetraploid to aneuploid DNA status (P < 0.0001 each). However, 40% of patients with Gleason score ≥4+4 and 55% of patients with PSA recurrence had diploid cancers. This fraction decreased to 21% (Gleason ≥4+4) and 29% (PSA recurrence) if PTEN and/or 6q deletion data were added to ploidy data to identify cancers with an aberrant DNA status. The significance of combining both deletions and ploidy was further demonstrated in a combined recurrence analysis. Presence of deletions increased the risk of PSA recurrence in diploid (P < 0.0001), tetraploid (P < 0.0001), and aneuploid cancers (P = 0.0049), and the combination of ploidy data and deletions provided clinically relevant information beyond the CAPRA-S nomogram. Multivariate modeling including preoperatively and postoperatively available parameters identified the "combined DNA status" as a strong independent predictor of poor patient outcome.

CONCLUSIONS

The combinatorial DNA content analysis involving general (ploidy) and specific events (deletions) has the potential for clinical utility in prostate cancer. Clin Cancer Res; 22(11); 2802-11. ©2016 AACR.

Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection

The molecular characterization of tumors using next generation sequencing (NGS) is an emerging diagnostic tool that is quickly becoming an integral part of clinical decision making. Cancer genomic profiling involves significant challenges including DNA quality and quantity, tumor heterogeneity, and the need to detect a wide variety of complex genetic mutations. Most available comprehensive diagnostic tests rely on primer based amplification or probe based capture methods coupled with NGS to detect hotspot mutation sites or whole regions implicated in disease. These tumor panels utilize highly customized bioinformatics pipelines to perform the difficult task of accurately calling cancer relevant alterations such as single nucleotide variations, small indels or large genomic alterations from the NGS data. In this review, we will discuss the challenges of solid tumor assay design/analysis and report a case study that highlights the need to include complementary technologies (i.e., arrays) and germline analysis in tumor testing to reliably identify copy number alterations and actionable variants.

Touch imprint cytology of prostate core needle biopsy specimens: A useful method for immediate reporting of prostate cancer

Background:

Cytology plays an important role in the preoperative assessment of many cancers. It is used as a first-line pathological investigation in both screening and diagnostic purposes.

Aims:

To determine the diagnostic value and accuracy of touch imprint cytology (TIC) smear of prostate core needle biopsy (CNB) specimens in the diagnosis of prostate carcinoma.

Materials and Methods:

One hundred and twenty-one patients had ultrasound-guided transrectal prostate CNB. A total of 1210 TIC smears were prepared from all CNB specimens.

Results:

Diagnoses of 1210 TIC smears were compared with the histopathological findings of the CNB specimens. One hundred and seventy (14%) TIC smears were found positive for malignancy, 35 (2.9%) were diagnosed as suspicious for malignancy and 1005 (83.1%) were found negative for malignancy. Twenty-five of 35 suspicious imprints and 150 of 170 malignant smears were confirmed to be malignant on histopathological evaluation. Although 20 malignant TIC smears were defined as benign in standard histological preparations, 10 of them had definitive diagnosis of malignancy following extensive serial sectioning. Last of all, there were 10 false-positive cytology results. Moreover, 10 of the 35 suspected TIC smears were false negative when compared with the histopathological diagnosis. The sensitivity, specificity, positive predictive value and negative predictive value of touch imprint smear results were 100%, 98%, 90.2% and 100%, respectively.

Conclusions:

TIC smears can provide an immediate and reliable cytological diagnosis of prostate carcinoma. It may clearly help the rapid detection of carcinoma, particularly in highly suspected cases that had negative routine biopsy results for malignancy with abnormal serum prostate specific antigen (PSA) levels and atypical digital rectal examination.

Histopathology reporting of prostate needle biopsies. 2005 update

This report reviews the diagnostic and prognostic importance of the pathologic findings in prostate needle biopsies. The morphological findings of the needle biopsy may be placed into one of the following five categories: prostate cancer, atypical small acinar proliferation, high-grade prostatic intraepithelial neoplasia, inflammation, and benign prostatic tissue. While the prime goal of the biopsy is to diagnose prostatic adenocarcinoma, once carcinoma is detected, further descriptive information regarding the type, amount of cancer, and grade forms the cornerstone for contemporary management of the patient and for assessment of the potential for local cure and the risk for distant metastasis. The information provided in the needle biopsy report regarding the attributes of carcinoma is used depending on the individual patient's medical condition and preference and on the treating physician's evaluation to determine whether any form of treatment is indicated and, if so, the type of therapy.

The usefulness of cytodiagnosis and DNA cytometry on nasopharyngeal brush smears for the diagnosis of nasopharyngeal carcinoma

BACKGROUND

To assess the usefulness of combining cytodiagnosis and DNA cytometry on nasopharyngeal brush samples for the detection of nasopharyngeal carcinoma (NPC).

METHODS

DNA ploidy analysis was undertaken on 66 nasopharyngeal brush samples that had been previously evaluated cytologically.

RESULTS

Cytodiagnosis and ploidy analysis demonstrated a sensitivity of 66% and 55%, respectively. Both techniques had a specificity of 100% for NPC cases that were histologically confirmed. The negative predictive values for cytodiagnosis and ploidy analysis were 29% and 24%, respectively.

CONCLUSIONS

The sensitivity and specificity for cytodiagnosis were not improved by the addition of DNA ploidy analysis. Furthermore, combining the two techniques did not confer any significant advantage compared with the use of cytology and DNA ploidy alone. The relatively low negative predictive values are a significant limitation, and combining cytodiagnosis and ploidy analysis on nasopharyngeal brush samples cannot be recommended for the detection of NPC.

Predicting prostate carcinoma volume and stage at radical prostatectomy by assessing needle biopsy specimens for percent surface area and cores positive for carcinoma, perineural invasion, Gleason score, DNA ploidy and proliferation, and preoperative serum prostate specific antigen: a report of 454 cases

BACKGROUND

DNA ploidy analysis of prostate carcinoma is a generally accepted prognostic marker, particularly when tumors are extraprostatic at the time of surgery. In the past decade, the DNA content of prostate carcinoma frequently has been assessed in needle biopsy specimens based on the assumption that ploidy, in conjunction with serum prostate specific antigen (PSA) and Gleason score, provides valuable pretreatment information.

METHODS

Between 1995 and 1998, the authors identified a consecutive series of 454 prostate carcinomas, verified by needle biopsies and followed by radical retropubic prostatectomies (RRP). Based on the needle biopsies, DNA ploidy and MIB-I immunostaining were measured by digital image analysis (DIA). The authors also quantified the percent of nuclei in four categories from the DNA histograms. The DIA data were combined with the age of the patient at diagnosis, the serum PSA, Gleason score, percent cores and percent surface area positive for carcinoma, and status of perineural invasion in multivariate models using tumor volume and risk of extraprostatic extension (EPE) at RRP as the outcome variables.

RESULTS

Joint predictors of tumor volume at RRP were the percent cores positive for carcinoma (P < 0.0001), serum PSA (P < 0.0001), the percent surface area positive for carcinoma (P < 0.0001), and the percent nuclei classified by DNA quantification to be in the "S-phase" category (P = 0.03). Joint predictors of risk of EPE were the percent cores positive for carcinoma (P = 0.0004), a Gleason score of 7 (P < 0.0001), a Gleason score of 8 or 9 (P < 0.0001), serum PSA (P = 0.006) and perineural invasion (P = 0.02).

CONCLUSIONS

After adjusting for traditional prognostic markers, DNA ploidy interpretation and MIB-I quantitation of prostate carcinoma did not appear to jointly predict either outcome variable in the multivariate models. However, a quantitative measure related to both ploidy and proliferation, the percent of nuclei in the putative "S-phase" category from the DIA histograms, was found to jointly predict for tumor volume.

Minimal adenocarcinoma in prostate needle biopsy tissue

One of the major diagnostic challenges in prostate needle biopsy interpretation is definitive establishment of a malignant diagnosis based on a minimal or limited amount of carcinoma in needle biopsy tissue. Major and minor diagnostic criteria should be used for interpretation of small foci of carcinoma. The constellation of findings and a combination of the major and minor diagnostic criteria permit a definitive diagnosis of focal adenocarcinoma. The differential diagnosis of minimal prostatic adenocarcinoma in needle biopsy tissue is broad and includes many benign lesions. The benign entities most likelty to be misdiagnosed as minimal prostatic adenocarcinoma are atypical adenomatous hyperplasia (adenosis) and atrophy. High-grade prostatic intraepithelial neoplasia and a descriptive diagnosis of focal glandular atypia or atypical small acinar proliferation also should be considered before diagnosing minimal adenocarcinoma. The most valuable adjunctive study for the diagnosis of minimal adenocarcinoma is immunohistochemistry using antibody 34 beta E12, reactive against basal cell-specific high-molecular-weight cytokeratins. Most cases can be diagnosed based on H&E-stained sections without this immunostain. Most minimal carcinomas in prostate needle biopsy tissue are of intermediate histologic grade, and most are indicative of pathologically significant carcinoma in the whole prostate gland.

Polyploidy: occurrence in nature, mechanisms, and significance for the megakaryocyte-platelet system

OBJECTIVE

Polyploidy, the state of having greater than the diploid content of DNA, has been recognized in a variety cells. Among these cell types, the megakaryocytes are classified as obligate polyploid cells, developing a polyploid DNA content regularly during the normal life cycle of the organism, while other cells may become polyploid only in response to certain stimuli. The objective of this review is to briefly describe the different cell cycle alterations that may lead to high ploidy, while focusing on the megakaryocyte and the importance of high ploidy to platelet level and function.

MATERIALS AND METHODS

Relevant articles appearing in scientific journals and books published in the United States and in Europe during the years 1910-1999 were used as resources for this review. We selected fundamental studies related to cell cycle regulation as well as studies relevant to the regulation of the endomitotic cell cycle in megakaryocytes. Also surveyed were publications describing the relevance of high ploidy to high platelet count and to platelet reactivity, in normal situations and in a disease state.

RESULTS

Different cells may achieve polyploidy through different alterations in the cell cycle machinery.

CONCLUSIONS

While upregulation of cyclin D3 further augments ploidy in polyploidizing megakaryocytes in vivo, future investigation should aim to explore how normal megakaryocytes may initiate the processes of skipping late anaphase and cytokinesis associated with high ploidy. In humans, under normal conditions, megakaryocyte ploidy correlates with platelet volume, and large platelets are highly reactive. This may not apply, however, to the disease state.

Isolation and characterization of a novel human bladder cancer cell line: BK10

Molecular studies of bladder carcinomas have aided in determining causative genetic events and the prognosis of cancers endowed with certain abnormalities. In vitro bladder cancer characterization of key cytogenetic alterations is useful for study of molecular changes that may promote oncogenic events. In our laboratory, a novel human bladder cancer cell line, BK10, has been established in vitro and passaged for more than 20 mo. This new bladder cancer cell line (BK10) was derived from bladder tissue containing grade III-IV/IV transitional cell carcinoma. Bladder cancer tissue was obtained at the time of radical cystoprostatectomy extirpation. Cell cultures derived from this surgical sample exhibited an epithelial morphology and expressed epithelial cytokeratins. Immunostains of BK10 were negative for prostate specific antigen (PSA), fibronectin, smooth muscle actin alpha, and desmin. Karyotypic analysis revealed an aneuploid chromosomal content <4n> with many numerical and structural abnormalities previously linked to bladder oncogenesis. Translocations occurred in chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 19, 20, 21, 22, X and Y. G-banding analysis revealed rearrangements involving chromosomes 9q and 17p, and the location of the ab11 oncogene and the p53 gene, respectively. The availability of this bladder cancer cell line will provide a useful tool for the further study of bladder carcinoma oncogenesis and gene therapy.

Minimal criteria for the diagnosis of prostate cancer on needle biopsy

Increased clinical screening of men at risk for prostate cancer, and the realization of the benefits of performing multiple biopsies per prostate, have facilitated early detection of malignancy, while presenting the pathologist with a growing array of diagnostic findings. Interpretation of these findings requires discussion of the minimal criteria required for the diagnosis of cancer on needle biopsy within a wide spectrum of related histologic findings. This spectrum includes small acinar proliferations suspicious for but not diagnostic of cancer, benign mimics of cancer, the preinvasive entity of high-grade prostatic intraepithelial neoplasia, and various treatment effects. Clinical implications of these findings and other prognostic factors are detailed.