The purpose of this study was to develop a multitarget, multicolor fluorescence in situ hybridization (FISH) assay for the detection of urothelial carcinoma (UC) in urine specimens. Urinary cells obtained from voided urine specimens of 21 patients with UC and 9 normal donors were analyzed with nine different centromere enumeration probes and a single locus-specific indicator probe to determine an optimal set of FISH probes for UC detection. The four probes with the greatest sensitivity for UC detection were then labeled with a unique fluorophore and combined into a single probe set. The probes with the greatest combined sensitivity for UC detection were CEP3, CEP7, CEP17, and the 9p21 (P16) LSI. This probe set was used to evaluate urine specimens acquired from 179 patients for prospective testing (46 with biopsy-proven UC). FISH slides were evaluated by scanning the slide for cells with nuclear features suggestive of malignancy and assessing the FISH signal pattern of these cells for polysomy (ie, gains of two or more different chromosomes). A receiver operator characteristic curve revealed that a cutoff of 5 cells with polysomy as the positive criterion for cancer resulted in an overall sensitivity of 84.2% for patients with biopsy-proven UC and a specificity of 91.8% among patients with genitourinary disorders but no evidence of UC. This study demonstrates that a multitarget, multicolor FISH assay containing centromeric probes to chromosomes 3, 7, and 17 and a locus-specific probe to band 9p21 has high sensitivity and specificity for the detection of UC in voided urine specimens.

The sensitivity of FISH for the detection of urothelial carcinoma is superior to that of cytology, and the specificity of FISH and cytology for urothelial carcinoma are not significantly different. Further prospective studies are required but FISH has the potential to improve significantly the management of urothelial carcinoma.

t(11;18)(q21;q21) and aneuploidy are recurrent chromosomal aberrations in mucosa-associated lymphoid tissue (MALT) lymphomas. To investigate their relationship and clinical significance, we developed a two-color fluorescence in situ hybridization (FISH) technique to detect t(11;18) and aneuploidy in nuclei isolated from paraffin-embedded tissue. Thirty-seven MALT lymphomas (all previously evaluated for t(11; 18) by reverse transcriptase-polymerase chain reaction), 1 large cell lymphoma (LCL) arising subsequent to MALT lymphoma, and 16 controls were tested by FISH using the t(11;18) probe set and multiple centromeric probes. t(11;18)(q21;q21) was present by FISH in 11 of 12 polymerase chain reaction-positive MALT lymphomas (92%). The LCL and its clonally identical antecedent MALT lymphoma both showed t(11;18). The LCL had trisomy 12, and a small subset of MALT lymphoma cells had trisomy 3 and/or 12. Only one other MALT lymphoma with t(11;18) showed aneuploidy (trisomy 3) in a small clone, whereas 15 of 25 t(11;18)-negative MALT lymphomas (60%) showed trisomy of chromosomes 18 (n ‫؍‬ 12), 3 (n ‫؍‬ 8), 7 (n ‫؍‬ 2), and/or 11 (n ‫؍‬ 1). t(11;18) and aneuploidy are primarily mutually exclusive events, suggesting different pathogenetic pathways in the development of MALT lymphomas. Both t(11;18) and aneuploidy were seen disproportionately in lung, and both were associated with recurrent disease. Extranodal marginal zone B-cell lymphoma of mucosaassociated lymphoid tissue (MALT lymphoma), nodal marginal zone B-cell lymphoma (NMZL), and splenic marginal zone B-cell lymphoma (SMZL) are all considered low-grade B-cell malignant lymphomas. Because of the similarities in morphology and immunophenotype, it was initially suggested that these neoplasms were different manifestations of the same disease process, with the postulated cell of origin being the marginal zone B cell. The theory of a unified disease process was supported by cytogenetic data demonstrating that certain cytogenetic abnormalities, including trisomies of chromosomes 3, 7, 12, and 18, were recurrent findings in MALT lymphomas, NMZLs, and SMZLs, 1,2 whereas they were not commonly identified in other B-cell malignant lymphomas.3 However, these findings were primarily based on fluorescence in situ hybridization (FISH) studies using centromeric probes that did not allow for detection of translocations or of anomalies involving chromosomes other than those specifically being tested.Concurrently, the t(11;18)(q21;q21) was emerging as the most frequent structural chromosomal abnormality in MALT lymphomas, based on karyotypic data. 4 -9 This translocation results in the fusion of two genes, API2 and MALT1 (also referred to as MLT), at the 11q21 and 18q21 breakpoints, respectively.10 The API2 gene is a member of a five-gene family in humans that codes for proteins involved in apoptosis regulation, and the MALT1 gene codes for a paracaspase (caspase-like protein).11 The API2-MALT1 fusion protein is thought to induce nuclear factor-B, resulting in transcription activa...

Our study reveals that UroVysion is the most sensitive and specific assay among those tested for the detection of urothelial carcinoma. Telomerase testing had good specificity but poor sensitivity. The BTA stat and hemoglobin dipstick tests had good sensitivity but relatively poor specificity. UroVysion is a promising new assay for the detection of urothelial carcinoma in urine specimens. However, further studies are needed to explore the role of the various assays in the treatment of patients with superficial urothelial carcinoma.

Purpose In 1998, the US Food and Drug Administration (FDA) approved human epidermal growth factor receptor 2 (HER2) testing guidelines to determine eligibility for HER2-directed therapy (HDT) in breast cancer. ASCO and the College of American Pathologists published immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) HER2 testing guidelines in 2007 (AC2007) and updated these guidelines in 2013 (AC2013). We compared the HER2 FISH amplification frequency using these three guidelines. Methods Patient samples that were sent to the Mayo Clinic cytogenetics laboratory for FISH testing (n = 2,851; from November 2013 to October 2014) were analyzed. Frequency of HER2 FISH amplification was examined and impact of AC2013 assessed. Results IHC results were available for 1,922 patient samples (67.4%), 137 of which were from Mayo Clinic. Distribution was 2.4% IHC 0, 7.9% IHC 1+, 84.8% IHC 2+, and 2.5% IHC 3+. Among IHC 2+ patients, HER2 FISH positivity was 11.8% (FDA), 9.4% (AC2007), and 24.1% (AC2013). Overall, 11.8% (n = 339) were positive with a FISH ratio ≥ 2.0, 1.3% (n = 35) with a FISH ratio ≥ 2.0 despite a HER2 signal < 4.0, and 3.0% (n = 86) with HER2 signal ≥ 6.0 despite FISH ratio < 2.0. Among 405 patients (14.2%) who were initially considered FISH-equivocal (ratio < 2.0 with HER2 signal ≥ 4.0, but < 6.0; AC2013), use of an alternative chromosome 17 probe reassigned 212 (7.4% overall) patients to FISH-positive and 36 (1.3% overall) patients to FISH-negative, whereas 157 (5.5% overall) patients remained equivocal. Final HER2 positivity with AC2013 (23.6%) was increased (P < .001) compared with FDA (13.1%) and AC2007 (11%) guidelines. Conclusion In a reference laboratory cohort that was highly enriched for IHC 2+ patient samples, AC2013 guidelines led to a larger number of FISH-equivocal patients. Approximately one half of these FISH-equivocal patients (7.4% overall) became HER2-positive upon alternative FISH probe testing. However, these patients would not have participated in the pivotal HDT trials. Clinical utility data on HDT benefit in these patients and other special subsets are needed.

A comprehensive, blinded, pathology evaluation of HER2 testing in HER2-positive/negative breast cancers was performed among three central laboratories. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) analyses were performed on 389 tumor blocks from three large adjuvant trials: N9831, BCIRG-006, and BCIRG-005. In 123 cases, multiple blocks were examined. HER2 status was defined according to FDA-approved guidelines and was independently re-assessed at each site. Discordant cases were adjudicated at an on-site, face-to-face meeting. Results across three independent pathologists were concordant by IHC in 351/381 (92 %) and FISH in 343/373 (92 %) blocks. Upon adjudication, consensus was reached on 16/30 and 18/30 of discordant IHC and FISH cases, respectively, resulting in overall concordance rates of 96 and 97 %. Among 155 HER2-negative blocks, HER2 status was confirmed in 153 (99 %). In the subset of 102 HER2-positive patients from N9831/BCIRG-006, primary blocks from discordant cases were selected, especially those with discordant test between local and central laboratories. HER2 status was confirmed in 73 (72 %) of these cases. Among 118 and 113 cases with IHC and FISH results and >1 block evaluable, block-to-block variability/heterogeneity in HER2 results was seen in 10 and 5 %, respectively. IHC−/FISH− was confirmed for 57/59 (97 %) primary blocks from N9831 (locally positive, but centrally negative); however, 5/22 (23 %) secondary blocks showed HER2 positivity. Among 53 N9831 patients with HER2-normal disease adjudicated as IHC−/FISH—(although locally positive), there was a non-statistically significant improvement in disease-free survival with concurrent trastuzumab compared to chemotherapy alone (adjusted hazard ratio 0.34; 95 % CI, 0.11–1.05; p = 0.06). There were similar agreements for IHC and FISH among pathologists (92 % each). Agreement was improved at adjudication (96 %). HER2 tumor heterogeneity appears to partially explain discordant results in cases initially tested as positive and subsequently called negative.Electronic supplementary materialThe online version of this article (doi:10.1007/s10549-013-2444-y) contains supplementary material, which is available to authorized users.

Purpose: A complete set of subtelomeric fluorescent DNA probes, except the acrocentric p-arms, was developed in 1996, was optimized in 1998, and is commercially available. These and other fluorescence in situ hybridization (FISH) probes have been used to detect anomalies of the subtelomere regions among groups of patients with idiopathic mental retardation (MR), developmental delay (DD), and/or nonspecific dysmorphic features (NDF), and individuals with multiple miscarriages (MM) who were karyotypically normal by standard G-banding techniques.Methods: A total of 425 patients were analyzed, of whom 372 had idiopathic MR/DD/NDF and 53 were involved in MM. An effort was made to select individuals for this study who were either normal karyotypically or who had subtle chromosomal anomalies that were inconclusive by banded chromosome analysis, although this was not always possible. Results: Anomalies involving the subtelomere regions were detected at a frequency of 6.8% in the MR/DD/NDF group. The cryptic or subtle anomalies are estimated to be about 3.4%. It was necessary to use M-FISH, chromosome, and locus specific FISH probes to clarify some of the abnormalities. No abnormalities were detected in the MM group. Deletion variants were present for 2qter, 7pter, and Xpter/Ypter subtelomeric regions ranging from Ͻ1 to 9.6%. Conclusions: The subtelomeric FISH probes are instrumental in the detection of subtelomeric anomalies in a significant proportion, although no more than 50% are subtle, of patients with idiopathic MR/DD/NDF. In some cases, however, it was necessary to use other FISH probes to clarify the nature of these abnormalities. No subtelomeric abnormalities were detected in our group of 53 MM patients, suggesting a relatively low frequency of occurrence in this patient population. Genet Med 2003:5(1):28 -34.

Our study reveals that UroVysion is the most sensitive and specific assay among those tested for the detection of urothelial carcinoma. Telomerase testing had good specificity but poor sensitivity. The BTA stat and hemoglobin dipstick tests had good sensitivity but relatively poor specificity. UroVysion is a promising new assay for the detection of urothelial carcinoma in urine specimens. However, further studies are needed to explore the role of the various assays in the treatment of patients with superficial urothelial carcinoma.