CIC rearranged sarcomas: A single institution experience of the potential pitfalls in interpreting CIC FISH results.

AIM: The aim of this study was to establish how reliable FISH CIC analysis using an IVD (in vitro diagnostic) commercial probe is. METHODS AND RESULTS: A series of 19 CIC-DUX4 sarcomas were evaluated. The samples presenting CIC-DUX4 fusion transcript detected by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Sanger sequencing and/or Next Generation Sequencing were selected for Fluorescent in Situ Hybridization (FISH) CIC analysis with CIC break-apart IVD probe and compared to molecular analysis. CIC FISH analysis showed 26% of false negatives. CONCLUSION: Our results indicate that, in the setting of CIC-DUX4 fusion positive small round cell sarcomas, CIC FISH using IVD commercial probe may lead to false-negative results. This novel study evaluates the diagnostic use of a commercial IVD CIC probe for FISH.

Identification of fetal aneuploidy with dual-probe fluorescence in situ hybridization analysis in circulating trophoblasts after enrichment using a high-sensitivity microfluidic platform.

OBJECTIVE: To evaluate a microfluidics-based positive selection technology for isolating circulating trophoblasts (CTs) from peripheral blood of women whose pregnancies are affected by aneuploidy and to evaluate fetal karyotype using fluorescence in situ hybridization (FISH). METHOD: Ten 18-ml samples of peripheral blood were collected consecutively from pregnant women whose fetus was affected by aneuploidy. A preservation buffer was added, and the specimens were shipped overnight to the testing laboratory at ambient temperature. The specimen was infused into the fully automated microfluidics-based LiquidScan® instrument without pre-processing. This instrument contains microfluidic chips, which are coated with antibodies (anti-huEpCAM and a proprietary antibody mixture) specific to CT surface epitopes. FISH analysis was performed on the enriched cells. RESULTS: Fetal aneuploidy evaluated included trisomy 21 (n = 3), trisomy 18 (n = 1), trisomy 13 (n = 1), monosomy X (n = 3), and triploidy (n = 1). CTs for analysis by FISH were identified in all samples. The average number of mononucleate cells per 1 ml of whole blood was 2.11 (range 0.38-4.63) overall and was 2.67 (range 1.13-4.63) using the proprietary combination of antibodies. FISH results were concordant with the aneuploidy based on other testing in all cases. Multinucleate cells were searched for and identified in the last seven samples (average number: 0.84/1 ml). CONCLUSIONS: Our study demonstrates that the LiquidScan® , a high-sensitivity microfluidic platform, can enrich circulating trophoblasts (mononucleate and multinucleate). FISH can then be used to detect fetal aneuploidy.

Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization for detecting chromosome abnormalities in myelodysplastic syndromes: A retrospective study.

ABSTRACT: This study aimed to compare interphase fluorescence in situ hybridization (iFISH) and multiplex ligation dependent probe amplification (MLPA) for identifying genetic changes in myelodysplastic syndromes (MDS).The frequencies of cytogenetic changes in MDS patients treated at the Institute of Hematology and Blood Disease Hospital (China) in 2009 to 2018 were assessed by iFISH based on bone marrow samples. Then, the effectiveness of MLPA in detecting these anomalies was evaluated.Specimens from 287 MDS patients were assessed. A total of 36.9% (103/279) of MDS cases had chromosomal abnormalities detected by iFISH; meanwhile, 44.1% (123/279) harbored ≥1 copy-number variation (CNV) based on MLPA: +8 (n=46), -5 (n = 39), -7 (n = 27), del 20 (n = 32) and del 17 (n = 17). Overall, 0 to 4 aberrations/case were detected by MLPA, suggesting the heterogeneous and complex nature of MDS cytogenetics. There were 29 cases detected by MLPA, which were undetected by FISH or showed low signals. Sixteen of these cases had their risk classification changed due to MLPA detection, including 9 reassigned to the high-risk IPSS-R group. These findings demonstrated that MLPA is highly efficient in assessing cytogenetic anomalies, with data remarkably corroborating FISH findings (overall consistency of 97.1%). The sensitivities of MLPA in detecting +8, -5, -7, del 20 and del 17 were 92.3%, 97.1%, 100%, 100%, and 90%, respectively, with specificities of 95.8%, 97.6%, 97.7%, 97.6%, and 97%, respectively.MLPA represents a reliable approach, with greater efficiency, accuracy, and speed than iFISH in identifying cytogenetic aberrations in MDS.

Targeted next generation sequencing (NGS) to classify melanocytic neoplasms.

This study piloted a pan-solid-tumor next generation sequence (NGS)-based laboratory developed test as a diagnostic aid in melanocytic tumors. 31 cases (4 "epithelioid" nevi, 5 blue nevi variants, 7 Spitz tumors [3 benign and 4 malignant] and 15 melanomas) were evaluated. All tumors [median diameter 7 mm (range 4-15 mm); median thickness 2.25 mm (range 0.25-12 mm)] yielded satisfactory results. The number of small nucleotide variants/tumor was significantly different between melanoma (median 18/tumor, range 4-71) and all other lesions (median 8/tumor, range 3-17) (P < 0.004) and malignant (median 16/tumor, range 4-71) vs benign lesions (median 7/tumor, range 3-14) (P = 0.01). BRAF, MET, NTRK1, and ROS fusions only occurred in benign Spitz tumors; EML4 fusion, BRAF, MAP2K1 and TERT mutations occurred in malignant Spitz tumors and/or melanoma. Amplifications and NRAS and NF1 mutations only occurred in melanoma. Most melanomas contained >1 pathogenic alteration. Developed NGS-based criteria correctly classified all malignant lesions in this series. 10/12 cases showed concordance with FISH; consensus diagnosis agreed with NGS classification in FISH-non-concordant cases. This pilot study suggests that NGS may be an effective diagnostic adjunct comparable to FISH, but further studies with larger numbers of cases are needed.

Low ALK FISH positive metastatic non-small cell lung cancer (NSCLC) patients have shorter progression-free survival after treatment with ALK inhibitors.

ALK FISH assay guides clinical decision to initiate therapy with ALK inhibitors in patients with stage IV non-small cells lung cancer (NSCLC). In this single institution retrospective study, we investigated the association between the strength of ALK positivity and progression-free survival (PFS) We screened 4,829 patients tested for ALK rearrangement by FISH from 01/06/2012 to 06/30/2018 and included 66 stage IV NSCLC ALK positive patients, who were ALK inhibitor naïve, received an ALK inhibitor, and been followed at least 10 months to the study. The median PFS for cases high positive cases [≥=50% positive nuclei; n = 49] and low positive cases [16-49% positive nuclei; n = 17] is 16 months and 4 months respectively, and the hazard ratio is 2.89 [95 CI 1.34-6.2] (p = 0.0068). When cases are stratified according to cut-off ≥=30% positive nuclei, the median PFS for cases above (n = 55) and below the cut-off (n = 11) is 12 and 3 months, respectively and the hazard ratio is 9.60 [95 CI 2.63-35.04] (p < 0.0001) Patients with low FISH positive results have shorter PFS. Although a biological reason is plausible, false positivity may be a contributing factor. For low positive results, confirmation of the FISH result with an orthogonal technology is warranted.

Cholangioscopy Biopsies Improve Detection of Cholangiocarcinoma When Combined with Cytology and FISH, but Not in Patients with PSC.

BACKGROUND AND AIMS: Single-operator cholangioscopy (SOC) has been suggested to be a cost-effective strategy for the detection of cholangiocarcinoma (CCA). The aim of this study is to compare the performance characteristics of SOC-guided biopsies and transpapillary biopsies with standard sampling techniques for the detection of CCA. METHODS: A retrospective cohort study of patients undergoing SOC between 1/2007 and 10/2018 at a single academic center was performed. Demographic, procedural, and outcomes data were recorded and analyzed using STATA 14.0. Sensitivity comparison between diagnostic tests was performed using exact McNemar test exclusively among patients with CCA. Two-sided p value < 0.05 was considered statistically significant. RESULTS: Ninety-two patients were included; 36 (39.1%) with primary sclerosing cholangitis (PSC), 41 (44.6%) with CCA, and median follow-up was 15.1 months. In the overall cohort, brush cytology demonstrated a sensitivity of 44.7% and increased with the addition of FISH (56.8%; p = 0.12), FISH with SOC-guided biopsy (71.4%; p = 0.03), and FISH with transpapillary biopsy (64.5%; p = 0.01). However, in patients with PSC, there was no significant improvement in sensitivity with the addition of SOC-guided biopsy or transpapillary biopsy in addition to FISH when compared to brush cytology. There was no difference in the rates of overall adverse events (14% vs. 23.2%; p = 0.27) or infection (3% vs. 4%; p = 0.83) in patients with and without PSC. CONCLUSIONS: SOC-guided and transpapillary biopsies improve sensitivity for the detection of cholangiocarcinoma in combination with other ERCP-based techniques compared to brush cytology alone. However, while safe, these modalities do not significantly improve the sensitivity for the detection of malignancy in PSC patients.

A model for the impact of FFPE section thickness on gene copy number measurement by FISH.

Fluorescent in situ hybridization (FISH) assays to detect gene amplification such as HER2 or MET in tumors are used for prognosis evaluation and selection of targeted therapies. Although FISH guidelines recommended 4~6 µm FFPE sections, many laboratories use 2~3 µm sections, which is a common practice for H&E staining and immunohistochemistry. A former study concluded that section thickness did not affect FISH results. We found, however, that thinner FFPE sections may lead to false negative results for gene amplification. A mathematic model was constructed and cell-line based controls with known gene copy number were prepared, and the model had a reasonable fit with the experimental data. The model revealed that even when counting the apparently full-sized nuclear images, many of them have partial volumes, which leads to under-estimation of gene copy number. Therefore, improperly thinner sections are prone to give false negative results, and thicker sections give a better approximation to the true value. The discrepancy between this and the former study was discussed. In summary, the model applies generally to FISH/ISH detection of gene copy number, and section thickness is an important parameter to control for precision medicine research, assay development, clinical trials and daily practice in pathology laboratory.

Real-world testing and treatment patterns in chronic lymphocytic leukemia: A SEER patterns of care analysis.

BACKGROUND: Laboratory testing and treatments for chronic lymphocytic leukemia (CLL) have changed dramatically within the last decade. The authors evaluated changes in patterns of real-world testing and treatment over time by comparing 2 population-based cohorts. METHODS: The National Cancer Institute-sponsored Patterns of Care study was conducted among patients with CLL who were sampled from 14 Surveillance, Epidemiology, and End Results (SEER) program registries. Demographics, testing, and treatment data were abstracted from medical records within 24 months of diagnosis. RESULTS: A total of 1008 patients diagnosed in 2008 and 1367 patients diagnosed in 2014 were included. There was a significant increase in fluorescence in situ hybridization (FISH) testing, immunoglobulin heavy-chain variable region gene (IgVH ) mutation analyses, and lymph node biopsies between 2008 and 2014. FISH testing was performed in the majority of, but not all, treated patients (53% in 2008, which increased to 62% in 2014). Some differences in the receipt of FISH testing by age and insurance status were observed over time (older patients and Medicare patients without private insurance were less likely to be tested in 2014). There were contrasting testing patterns noted by practice type and year, with nonteaching hospitals more likely to perform bone marrow biopsies in 2008, and teaching hospitals more likely to perform FISH and IgVH testing in 2014. There also were differences in treatments over time, with the use of bendamustine and rituximab being more common in 2014, at the expense of fludarabine, cyclophosphamide, and rituximab. CONCLUSIONS: There have been rapidly changing practices in the testing and treatment patterns of patients with CLL within the last decade.

Impact of QuickFISH in addition to antimicrobial stewardship on vancomycin use and resource utilization in cancer patients with coagulase-negative staphylococcal blood cultures.

OBJECTIVE: To evaluate the impact of rapidly identifying coagulase-negative staphylococci (CoNS) from positive blood cultures combined with an established antimicrobial stewardship (AS) programme at a tertiary cancer centre. METHODS: We compared cancer patients ≥18 years old who between 01/1/13 and 12/31/13 had one or more positive CoNS blood culture(s) identified by Staphylococcus QuickFISH® (a peptide nucleic acid fluorescence in situ hybridization assay) with cancer patients ≥18 years old who had CoNS identified by standard microbiological techniques between 01/01/11 and 12/31/11 (baseline). Positive blood culture results were reported to the clinician by microbiology staff; restricted antibiotics (e.g., vancomycin) required approval by the AS team. RESULTS: There were 196 baseline and 103 QuickFISH patients. Faster median time to organism identification (33 (IQR 27-46) versus 49 (IQR 39-63) hours, p < 0.001), more vancomycin avoidance (51/103 (50%) versus 60/196 (31%), p 0.002), shorter median antibiotic duration (1 (IQR 0-3) versus 2 (IQR 0-6) days, p 0.019), fewer central venous catheter (CVC) removals (14/78 (18%) versus 57/160 (36%), p 0.004), and reduced vancomycin level monitoring (16/52 (31%) versus 71/136 (52%), p 0.009) were observed in the QuickFISH group. QuickFISH implementation was predictive of a lower likelihood of antibiotic therapy prescription (OR 0.35, 95%CI 0.20-0.62, p < 0.001). Prior transplant (RR 1.47, 95%CI 1.13-1.92, p 0.004), neutropenia (RR 1.47, 95%CI 1.09-1.99, p 0.012), multiple positive blood cultures (RR 4.23, 95%CI 3.23-5.54, p < 0.001), and CVC (RR 1.60, 95%CI 1.02-2.53, p 0.043) were independent factors for antibiotic duration. CONCLUSIONS: QuickFISH implementation plus AS support leads to greater avoidance of vancomycin therapy and improved resource utilization in cancer patients with CoNS blood cultures.

Utility of Fluorescence In Situ Hybridization Panel for Myelodysplastic Syndrome in Evaluation of Cytopenia in a Pediatric Hospital: A 5-Year Retrospective Review and Utilization Management.

BACKGROUND: MDS FISH was routinely ordered together with chromosome analysis for patients with cytopenia in our hospital. The utility of MDS FISH in the pediatric population is unknown. OBJECTIVE: To analyze the utility of fluorescence in situ hybridization panel for myelodysplastic syndrome (MDS FISH) in the management of patients with cytopenia. METHODS: We performed a retrospective review over a 5-year period, from 2009 to 2014 to determine whether chromosome analysis (CA) plus MDS FISH added useful information compared to chromosome analysis alone. Both CA and MDS FISH were performed on 253 bone marrow biopsies from 182 patients. RESULTS: CA was highly correlated with MDS FISH (P < .0001) and detected all of the abnormalities seen by MDS FISH in 93.7% of the cases. CA is less expensive and detects additional chromosomal abnormalities not tested in the myelodysplastic syndrome panel. We propose MDS FISH should be ordered when CA fails to give adequate results.

[Internal quality control on HER2 status determination in breast cancers: Experience of a cancer center]. / Contrôle de qualité interne de la détermination du statut HER2 dans les cancers du sein : expérience d'un centre de lutte contre le cancer.

INTRODUCTION: The implementation of an internal quality control is mandatory to guarantee the accuracy of HER2 status in invasive breast cancers. OBJECTIVES: To evaluate the impact of our quality control assurance on HER2 status results in invasive breast carcinomas from 2008 to 2014. METHODS: HER2 status was determined by immunohistochemistry as the first-line indication, completed by fluorescence in situ hybridization (FISH) for scores 2+ by immunohistochemistry. Internal quality control of HER2 status relied on the standardization of pre-analytical phases, the use of external controls with a known number of HER2 gene copies determined by FISH and continued monitoring of concordance between immunohistochemistry and FISH. RESULTS: The proportion of HER2-positive cases corresponding to scores 3+ by immunohistochemistry and 2+ amplified by FISH varied from 10.6% to 13.8% (median of 11.3%). The proportion of scores 2+ amplified by FISH varied from 13.3% to 32.7% during period of study. The rate of concordance between FISH and immunohistochemistry for score 0/1+ and 3+ cases were≥97%. Eight among 12 discordant cases were false positive resulting from errors in interpretation of immunohistochemistry (score 2+ instead of 3+). DISCUSSION: Calibration of immunohistochemistry on FISH for HER2 status contributes to limit variability of immunohistochemistry results due to technical issues or interpretation. The implementation of an external control of score 3+ on each slide enables accurate interpretation of score 2+ and 3+ by immunohistochemistry.

Serum amyloid A expression in the breast cancer tissue is associated with poor prognosis.

BACKGROUND: Serum amyloid A (SAA), an acute-phase protein, is expressed primarily in the liver, and recently found also expressed in cancer tissues. However, its expression and prognostic value in breast cancer have not been described. RESULTS: SAA protein was found expressed in tumor cells in 44.2% cases and in TAM in 62.5% cases. FISH showed more frequent SAA mRNA expression in TAM than in tumor cells (76% versus 12%, p < 0.001), and a significant association between the frequencies of SAA mRNA expression in TAM and tumor cells (rs = 0.603, p < 0.001). The immunoreactivities of SAA protein in TAM and tumor cells were both associated with lymphovascular invasion and lymph node metastasis. Moreover, SAA-positivity in TAMs was associated with larger tumor-size, higher histological-grade, negative estrogen-receptor and progesterone-receptor statuses, and HER-2 overexpression. It was also linked to worse recurrence-free survival in a multivariable regression model. METHODS: Immunohistochemistry was applied on the tumor tissues from 208 breast cancer patients to evaluate the local SAA-protein expression with additional CD68 stain to identify the tumor-associated macrophage (TAM) on the serial tissue sections. Fluorescent in situ hybridization (FISH) was conducted on serial tissue sections from 25 of the 208 tumors to examine the expression and location of SAA mRNA. CONCLUSIONS: Our results suggested that the TAMs may be a pivotal and main source of SAA production in tumor microenvironment of breast cancer. SAA immunoreactivity in TAM is associated with worse recurrence-free survival, and is therefore a biomarker candidate for postoperative surveillance and perhaps a therapeutic target for breast cancer.

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.

Connect MM Registry: The Importance of Establishing Baseline Disease Characteristics.

BACKGROUND: Connect MM is the first and largest observational, noninterventional, prospective registry of patients newly diagnosed with multiple myeloma (NDMM) in the United States. It collects longitudinal data on patients within clinical practice including patients in clinical trials. PATIENTS AND METHODS: Of the 1513 patients enrolled, 1493 were protocol-eligible. RESULTS: Median age was 67 years, 81.9% (1223/1493) were Caucasian, and 57.2% (854/1493) were male. Of these patients, 26.5% (232/877) were International Staging System stage I, 34.9% (306/877) stage II, and 38.7% (339/877) stage III. Eastern Cooperative Oncology Group performance status of 0/1/2 were reported in 96.6% (1017/1053). Clonal plasma cells > 10% were found in 91.6% (1282/1399) of patients and M-component in 98.8% (1343/1359). Hypercalcemia was present in 7.3% (108/1481) of patients, serum creatinine > 2 mg/dL in 18.3% (271/1484), anemia in 45.1% (673/1493), and bone involvement in 76.7% (1143/1490). Of the 15 National Comprehensive Cancer Network (NCCN) recommended diagnostic tests, a median of 12 were performed. Lactate dehydrogenase assessment, serum free light chain ratio, and immunofixation were reported in 38.4% (574/1493), 62.1% (927/1493), and 66% (985/1493) of patients, respectively. Quantitative immunoglobulin, ß-2 microglobulin, and protein electrophoresis (serum or urine) were reported in 72.3% (1080/1493), 74.1% (1107/1493), and 78.0% (1164/1493) of patients, respectively. Bone marrow biopsy was reported in 92.2% (1376/1493), but conventional cytogenetic and fluorescence in situ hybridization analysis were reported in only 63.2% (944/1493) and 59.8% (893/1493) of patients, respectively. A high-risk cytogenetic profile (according to International Myeloma Working Group [IMWG] criteria) was found in 16.9% (253/1493). CONCLUSION: This analysis provides insight into the demographic and disease characteristics of NDMM patients in a range of clinical practices. Creating solid records of baseline patient disease characteristics using suggested NCCN diagnostic work-up and IMWG criteria provides a foundation for monitoring disease progression and response to treatment.

Immunohistochemistry, fluorescence in situ hybridization, and reverse transcription-polymerase chain reaction for the detection of anaplastic lymphoma kinase gene rearrangements in patients with non-small cell lung cancer: potential advantages and methodologic pitfalls.

CONTEXT: Echinoderm microtubule-associated protein-like 4 gene (EML4) and anaplastic lymphoma kinase gene (ALK) fusion was shown to be the driver of tumorigenesis in approximately 3% to 5% of patients with non-small cell lung cancer (NSCLC) and is associated with response to inhibition with crizotinib. However, no complete agreement regarding the best diagnostic test for identification of ALK rearrangements has been achieved yet. OBJECTIVE: To investigate the concordance, sensitivity, and specificity of immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and reverse transcription-polymerase chain reaction (RT-PCR) for detection of ALK rearrangements. DESIGN: Thirty-six prospectively tested patients with NSCLC who had adenocarcinoma and 10 ALK-positive samples were included in the study. All samples were tested by IHC (ALK1 clone, 5A4 clone, D5F3 clone), FISH (LSI ALK Break Apart and ALK FISH Probe), and multiplexed RT-PCR. RESULTS: Immunohistochemistry staining was successful in all samples.. Clone D5F3 showed the best sensitivity and specificity of 100%; clones ALK1 and 5A4 showed sensitivities of 91% with specificity of 100%. Both FISH probes showed concordance with sensitivity and specificity of 100%. Hybridization and RT-PCR were successful in 98% and 93.4% of samples, respectively, with sensitivity of 88% and specificity of 100%. Frequent artifacts leading to misinterpretation were observed with all 3 methodologies. CONCLUSIONS: All 3 methodologies showed good sensitivity, specificity, and concordance, when artifacts were characterized and excluded. However, all ambiguous cases have to be confirmed as ALK rearranged by at least 2 of the 3 methods.

Automated quantification of FISH signals in urinary cells enables the assessment of chromosomal aberration patterns characteristic for bladder cancer.

Targeting the centromeres of chromosomes 3, 7, 17 (CEP3, 7, 17) and the 9p21-locus (LSI9p21) for diagnosing bladder cancer (BC) is time- and cost-intensive and requires a manual investigation of the sample by a well-trained investigator thus overall limiting its use in clinical diagnostics and large-scaled epidemiological studies. Here we introduce a new computer-assisted FISH spot analysis tool enabling an automated, objective and quantitative assessment of FISH patterns in the urinary sediment. Utilizing a controllable microscope workstation, the microscope software Scan^R was programmed to allow automatic batch-scanning of up to 32 samples and identifying quadruple FISH signals in DAPI-scanned nuclei of urinary sediments. The assay allowed a time- and cost-efficient, automated and objective assessment of CEP3, 7 and 17 FISH signals and facilitated the quantification of nuclei harboring specific FISH patterns in all cells of the urinary sediment. To explore the diagnostic capability of the developed tool, we analyzed the abundance of 51 different FISH patterns in a pilot set of urine specimens from 14 patients with BC and 21 population controls (PC). Herein, the results of the fully automated approach yielded a high degree of conformity when compared to those obtained by an expert-guided re-evaluation of archived scans. The best cancer-identifying pattern was characterized by a concurrent gain of CEP3, 7 and 17. Overall, our automated analysis refines current FISH protocols and encourages its use to establish reliable diagnostic cutoffs in future large-scale studies with well-characterized specimens-collectives.

Detection of genetic abnormalities by using CVS and FISH prior to fetal reduction in sonographically normal appearing fetuses.

OBJECTIVE: To examine the ability of chorionic villus sampling (CVS) and fluorescence in situ hybridization (FISH) to detect aneuploidy before first trimester fetal reduction (FR) in sonographically normal-appearing fetuses. METHODS: A retrospective review of 470 patients referred to our unit for FR from January 2007-March 2011. Prenatal diagnosis was offered to all. FR was performed after next-day FISH results. Abnormalities were categorized by ultrasound, FISH, and/or karyotype. Sensitivity, specificity, positive predictive value, and negative predictive value of pre-FR FISH were calculated. RESULTS: Four hundred thirty-two of 470 patients seen were first trimester. 24/432 (5.2%) were excluded for abnormal ultrasound findings, including nuchal translucency (NT) > 3.0 mm, and 360 (88.2%) underwent CVS before FR. Ten fetuses were then excluded for euploid sex mosaicism. 10/350 (2.9%) patients with normal ultrasounds had abnormal FISH confirmed by karyotype. 9/350 (2.6%) patients with normal FISH had an abnormal karyotype necessitating follow up amniocentesis in which the clinically relevant discordancy was confirmed in one case (1/350, 0.3%). Pre-FR FISH had a 90% sensitivity, 99.4% specificity, 83.3% positive predictive value, and 99.7% negative predictive value. CONCLUSIONS: 3.1% of patients with normal-appearing fetuses prior to first trimester FR had a fetus with an abnormal karyotype of which FISH detected 90%. CVS with FISH prior to FR adds significant information that can guide reduction decisions.

MYC overexpression and poor prognosis in sporadic breast cancer with BRCA1 deficiency.

Breast cancer is a complex disease; the molecular mechanisms involved in sporadic breast carcinogenesis remain to be elucidated. The present study aimed to explore the deficiency of breast cancer susceptibility gene 1 (BRCA1), including protein loss expression, promoter hypermethylation and gene copy deletion, its correlationship with other tumor markers expression (TP53, MYC, etc.), and clinical significance in sporadic breast cancer. BRCA1 protein expression was negative in 226 of 374 (60.4%) cases of this study. Cases negative for BRCA1 protein were more often with pathological tumor-node-metastasis stage III, positive for lymph node metastasis and MYC overexpression than BRCA1-positive tumors. BRCA1 hypermethylation was detected in 16.4% (31 of 189) breast cancers, which correlated with BRCA1 negative, ER negative, MYC overexpression, and triple-negative phenotype. In addition, the percentage of cells with BRCA1 gene copy deletion was significantly increased in BRCA1-methylated tumors. Kaplan-Meier survival analysis showed that patients with BRCA1-negative expression showed a worse overall survival (OS) than those with BRCA1-positive expression, and patients with BRCA1-methylated tumors had a significantly worse disease-free survival than did patients with unmethylated tumors. Furthermore, BRCA1 hypermethylation showed an inverse association with OS in LN-positive or p53-negative subgroup patients. Importantly, uni- and multivariate Cox regression analyses revealed that BRCA1 was an independent prognostic indicator of OS in sporadic breast cancer. Thus, we found MYC overexpression and poor prognosis in sporadic breast cancer with BRCA1 deficiency. The targeting of BRCA1 deficiency in combination with MYC-pathways inhibitors may provide a promising strategy for sporadic breast cancer care, the triple-negative subtype in particular.

Chromosome analysis of nuclear power plant workers using fluorescence in situ hybridization and Giemsa assay.

The aim of this study was to evaluate the genotoxic effects of ionizing radiation in vivo in exposed Bulgarian nuclear power plant workers by using classical cytogenetic and molecular cytogenetic analyses of peripheral lymphocytes. Chromosome analysis using fluorescence in situ hybrydization (FISH) and Giemsa techniques was undertaken on 63 workers and 45 administrative staff controls from the Bulgarian Nuclear Power Plant. Using the Giemsa method, the frequencies of cells studied with chromosome aberrations, dicentrics plus rings and chromosome fragments in the radiation workers were significantly higher compared with the control group (P = 0.044, P = 0.014, and P = 0.033, respectively). A significant association between frequencies of dicentrics plus rings and accumulated doses was registered (P < 0.01). In the present study, a FISH cocktail of whole chromosome paints for chromosomes 1, 4 and 11 was used. A significant association between frequency of translocations and accumulated doses was also observed (P < 0.001). Within the control group, a correlation was found between age and the spontaneous frequency of translocations. No correlation was found between smoking status and frequency of translocations. When compared with the control group, workers with accumulated doses up to 100 mSv showed no increase in genome translocation frequency, whereas workers with accumulated doses from 101 to 200 mSv showed a statistically significant doubling of genome translocation frequency (P = 0.009). Thus, in cases of chronic exposure and for purposes of retrospective dosimetry, the genome frequency of translocations is a more useful marker for evaluation of genotoxic effects than dicentric frequency.

The utility of UroVysion fluorescence in situ hybridization in pancreatic fine-needle aspiration samples directed and obtained by endoscopic ultrasonography.

CONTEXT: The diagnosis of pancreatic adenocarcinoma can be challenging for the pathologist. Endoscopic ultrasound-guided, fine-needle aspiration (EUS-FNA) can be used to obtain samples of pancreatic masses. UroVysion fluorescence in situ hybridization (UFISH) has been reported to increase the sensitivity and to be very specific for the diagnosis of adenocarcinoma when combined with cytology in the diagnosis of biliary brushings and washings. OBJECTIVES: To determine the sensitivity and specificity of UFISH on tissues obtained from pancreatic lesions suggestive of adenocarcinoma obtained by EUS-FNA, compared against fine-needle aspiration (FNA) results. Additionally, to use patient follow-up data to evaluate UFISH results in FNA samples that showed significant atypia but did not meet the criteria for malignancy. DESIGN: Sixty consecutive cases of pancreatic EUS-FNA from our institution submitted for UFISH testing. RESULTS: Polysomic UFISH has a sensitivity of 93% and a specificity of 100% when compared against FNA results. Follow-up studies showed that adding UFISH to FNA increased the sensitivity for patients with true-positive results from 83% to 94% and increased specificity from 85% to 100%. For 7 patients with suspicious FNA results who had sufficient follow-up, UFISH was 100% sensitive and 100% specific. CONCLUSIONS: UFISH can be used to confirm the diagnosis of malignancy in pancreatic adenocarcinoma. Because of the high specificity, polysomic UFISH may help establish a diagnosis of malignancy when the FNA features are suggestive of, but not conclusive for, malignancy. The most common cause for a false-negative UFISH result was insufficient numbers of malignant cells.