Traditional Fluorescence In Situ Hybridization Research Articles

Efficient diagnosis of IDH-mutant gliomas: 1p/19qNET assesses 1p/19q codeletion status using weakly-supervised learning

Accurate identification of molecular alterations in gliomas is crucial for their diagnosis and treatment. Although, fluorescence in situ hybridization (FISH) allows for the observation of diverse and heterogeneous alterations, it is inherently time-consuming and challenging due to the limitations of the molecular method. Here, we report the development of 1p/19qNET, an advanced deep-learning network designed to predict fold change values of 1p and 19q chromosomes and classify isocitrate dehydrogenase (IDH)-mutant gliomas from whole-slide images. We trained 1p/19qNET on next-generation sequencing data from a discovery set (DS) of 288 patients and utilized a weakly-supervised approach with slide-level labels to reduce bias and workload. We then performed validation on an independent validation set (IVS) comprising 385 samples from The Cancer Genome Atlas, a comprehensive cancer genomics resource. 1p/19qNET outperformed traditional FISH, achieving R2 values of 0.589 and 0.547 for the 1p and 19q arms, respectively. As an IDH-mutant glioma classifier, 1p/19qNET attained AUCs of 0.930 and 0.837 in the DS and IVS, respectively. The weakly-supervised nature of 1p/19qNET provides explainable heatmaps for the results. This study demonstrates the successful use of deep learning for precise determination of 1p/19q codeletion status and classification of IDH-mutant gliomas as astrocytoma or oligodendroglioma. 1p/19qNET offers comparable results to FISH and provides informative spatial information. This approach has broader applications in tumor classification.

Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants.

Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies.

Advanced Risk Stratification in Multiple Myeloma Beyond Traditional FISH: The First Prospective Real-World Evidence for SKY92 Gene Expression Profiling

Background The prognosis of multiple myeloma (MM) has been significantly improved in the last decades. However, high-risk (HR) MM still suffers from early disease progression. Therefore, identifying HR MM patients may be a crucial step to improve the prognosis of this patient group. To date, fluorescence in situ hybridization (FISH) is the most commonly used method for risk stratification in MM. In recent years, gene expression profiling (GEP) approaches, e.g. SKY92, have been developed for detection of HR MM patients. Currently, real-world data of MM risk stratification applying SKY92 alone or in addition to traditional FISH are still missing. In this study, we provide the first prospective real-world evidence of the prognostic value of the combined SKY92 and FISH risk stratification in newly diagnosed (ND) and relapsed/refractory (RR) MM. Methods We prospectively collected bone marrow (BM) samples and clinical data of 147 MM patients. Cytogenetics were analyzed on purified CD138 positive MM cells by FISH, and HR cytogenetics was defined applying the Revised International Staging System (del(17p), t(4;14), and t(14;16)) (Palumbo et al, J Clin Oncol. 2015). SKY92 risk classification was determined with MMprofiler gene expression assay (Kuiper et al, Leukemia 2012). In addition, whole genome sequencing (WGS) was performed, and 150 bp paired-end sequences were generated on the NovaSeq6000 sequencing instruments (Illumina) with 100x coverage. Structural variations (SV) were called using Manta, and copy number variations (CNV) calling was performed with GATK4. Strelka2 variant caller was used for single nucleotide variations (SNV). Variants with global population frequencies >1% were excluded. Results We included 147 patients in our study (NDMM: n=51, RRMM: n=96). SKY92 classification was available for 121 (82.3%) patients. The median follow-up time was 344 days. HR SKY92 was significantly enriched in RRMM (40/76) compared with NDMM (6/45) (P<0.0001). RRMM patients with HR SKY92 showed significantly shorter progression free survival (PFS) (P<0.0001) and overall survival (OS) (P=0.0004) than standard-risk (SR). In NDMM, HR SKY92 also indicated a significantly inferior PFS (P=0.001) in comparison with SR. Of note, samples of 26 (17.7%) patients did not meet the SKY92 quality control criteria due to low BM infiltration (median BM infiltration: 25% vs 55% in other patients, P=0.038). We then combined the SKY92 classification with cytogenetic analyses by FISH, which were performed in 99 patients (NDMM: n=33; RRMM: n=66). We noticed a discrepancy between both risk stratification systems, with 44 (44.4%) and 42 (42.4%) patients being classified as HR by SKY92 and FISH, respectively. In total, 24 (36.3%) RRMM patients and 6 (18.2%) NDMM patients displayed HR in both SKY92 and FISH (double-HR) (Figure). Regarding survival outcome in RRMM, double-HR patients showed the worst PFS (P<0.0001) and OS (P<0.0001) when compared to the other patients (Figure). Noteworthy, RRMM patients with only HR SKY92 demonstrated significantly worse PFS than those with only HR FISH (P=0.007). In addition, double-HR presented a negative prognostic factor for PFS in NDMM (P=0.01). To further elucidate the discrepancy between FISH and SKY92 classifications, we performed WGS in 12 patients who exhibited either HR SKY92 only (n=9) or HR FISH only (n=3). Interestingly, 1 patient with bi-allelic TP53 inactivation (deletion + mutation) and 2 patients harbouring t(4;14) or t(14;16) were determined as SR by SKY92 but as HR by FISH; all the 3 patients were still in remission at the time point of data cut-off (July 2022). Moreover, we found abnormalities at chromosome 1 in 7 out of the 9 patients with HR on SKY92 only (gain1q21: n=6; del1p32: n=2) and, notably, gain1q21 and del1p32 were detected only by WGS in 3 and 2 patients, respectively. The remaining 2 patients did not show any known HR SV/CNV/SNVs, suggesting that HR MM may be associated with some other mechanisms, e.g. epigenetic modifications. Conclusion Altogether, risk classification using SKY92 performed well for detecting HR MM in the clinical routine. Here, we provide the first prospective real-world evidence that advanced risk stratification combining SKY92 and FISH may help to identify the "highest-risk" MM, which requires intensive anti-MM therapy and close monitoring in the course of the disease. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Ré-utilisation de lames d’immunohistochimie pour la réalisation de FISH : une solution pertinente d’épargne tissulaire

Diagnostic updates, an increased precision of tumor sub-type classification and the development of new diagnostic biomarkers (immunohistochemistry (IHC), Fluorescence in situ hybridization (FISH) and other molecular pathology techniques), have a significant impact on pathologists' management of tissue samples. The objective of this work was to test and validate the FISH technique on detached IHC slides. An IHC technique was first performed on 30 tissue samples. After detachment of the lamella, a FISH technique was then performed according to the usual protocol with a centromeric probe. A validation cohort (n=10) with duplicate testing using a traditional FISH technique and an IHC slide with a detached lamella was then carried out. Finally, a cohort of 20 "old" cases (IHC carried out over 2years ago) was also tested. Different types of probes (specific locus, break apart) have been used. All the slides were interpreted by a technician and a pathologist. Evaluation criteria were: the general interpretability of the slide; the percentage of labeled nuclei; intensity of the signal and the presence or absence of autofluorescence. FISH was interpretable in 100% of recently treated cases and 90% of "old" cases with a satisfactory intensity and a high percentage of labeled nuclei, without autofluorescence. The results of our study show that the reuse of IHC slides for performing FISH is a powerful means of economizing tissue samples, especially for small samples and in the absence of archived representative material.

Superresolution Microscopy for Visualization of Physical Contacts Between Chromosomes at Nanoscale Resolution.

This protocol describes the fluorescence in situ hybridization (FISH) of DNA probes on mitotic chromosome spreads optimized for two super-resolution microscopy approaches-structured illumination microscopy (SIM) and stimulated emission depletion (STED). It is based on traditional DNA FISH methods that can be combined with immunofluorescence labeling (Immuno-FISH). This technique previously allowed us to visualize ribosomal DNA linkages between human acrocentric chromosomes and provided information about the activity status of linked rDNA loci. Compared to the conventional wide-field and confocal microscopy, the quality of SIM and STED data depends a lot more on the optimal specimen preparation, choice of fluorophores, and quality of the fluorescent labeling. This protocol highlights details that make specimens suitable for super-resolution microscopy and tips for good imaging practices.

Prenatal diagnosis from fetal urine in bladder outlet obstruction: Success rates for traditional cytogenetic evaluation and interphase fluorescence in situ hybridization

Purpose: To determine the optimal approach to the prenatal chromosome analysis of fetal urine from fetuses with bladder outlet obstruction.Methods: Retrospective evaluation of traditional cytogenetic and interphase fluorescence in situ hybridization (FISH) analysis on fetal urine specimens from fetuses with bladder outlet obstruction.Results: Traditional cytogenetic analysis was successful on 71 (95%) of 75 samples, and FISH was informative on 20 (65%) of 31 specimens. The combination of traditional cytogenetic analysis and FISH yielded a 96% diagnostic success rate. The mean turnaround time was 8 days (range 5–14) for traditional cytogenetic analysis and 1.6 days (range 1.0–4.0) for FISH. Chromosome abnormalities were detected in 6 (7.9%) of 76 pregnancies.Conclusion: Traditional cytogenetic analysis achieves a high success rate (95%) and is superior to FISH for chromosome evaluation of fetal urine. However, FISH, when informative, can complement traditional cytogenetics as it will expeditiously rule out common trisomies in fetuses with bladder outlet obstruction.

Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol for detection of microbes in sediments

Fluorescence in situ hybridization (FISH) is a canonical tool commonly used in environmental microbiology research to visualize targeted cells. However, the problems of low signal intensity and false-positive signals impede its widespread application. Alternatively, the signal intensity can be amplified by incorporating Hybridization Chain Reaction (HCR) with FISH, while the specificity can be improved through protocol modification and proper counterstaining. Here we optimized the HCR-FISH protocol for studying microbes in environmental samples, particularly marine sediments. Firstly, five sets of HCR initiator/amplifier pairs were tested on the laboratory-cultured bacterium Escherichia coli and the archaeon Methanococcoides methylutens, and two sets displayed high hybridization efficiency and specificity. Secondly, we tried to find the best combination of sample pretreatment methods and HCR-FISH protocol for environmental sample analysis with the aim of producing less false positive signals. Various detachment methods, extraction methods and formulas of hybridization buffer were tested using sediment samples. Thirdly, an image processing method was developed to enhance the DAPI signal of microbial cells against that of abiotic particles, providing a reliable reference for FISH imaging. In summary, our optimized HCR-FISH protocol showed promise to serve as an addendum to traditional FISH for research on environmental microbes.

FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas.

BackgroundMolecular profiling of gliomas is vital to ensure diagnostic accuracy, inform prognosis, and identify clinical trial options for primary and recurrent tumors. This study aimed to determine the accuracy of reporting the whole arm 1p19q codeletion status from the FoundationOne platform.MethodsTesting was performed on glioma samples as part of clinical care and analyzed up to 395 cancer-associated genes (including IDH1/2). The whole arm 1p19q codeletion status was predicted from the same assay using a custom research-use only algorithm, which was validated using 463 glioma samples with available fluorescence in-situ hybridization (FISH) data. For 519 patients with available outcomes data, progression-free and overall survival were assessed based on whole arm 1p19q codeletion status derived from sequencing data.ResultsConcordance between 1p19q status based on FISH and our algorithm was 96.7% (449/463) with a positive predictive value (PPV) of 100% and a positive percent agreement (PPA) of 91.0%. All discordant samples were positive for codeletion by FISH and harbored genomic alterations inconsistent with oligodendrogliomas. Median overall survival was 168 months for the IDH1/2 mutant, codeleted group, and 122 months for IDH1/2 mutant-only (hazard ratio (HR): 0.42; P < .05).Conclusions1p19q codeletion status derived from FoundationOne testing is highly concordant with FISH results. Genomic profiling may be a reliable substitute for traditional FISH testing while also providing IDH1/2 status.

Pitfalls in RET Fusion Detection Using Break-Apart FISH Probes in Papillary Thyroid Carcinoma

A standardized procedure of fused REarranged during Transfection (RET) gene detection using fluorescence in situ hybridization (FISH) remains to be established in papillary thyroid carcinoma (PTC). Our purpose was to investigate false-negative and false-positive events and their FISH signal characteristics. A total of 111 PTC cases were analyzed using break-apart FISH probes for RET status evaluation. All FISH results were validated using fusion-induced asymmetric transcription assay (FIATA)-based reverse transcription droplet digital PCR (RT-ddPCR). Then, suspected RET-positive cases were tested using quantitative reverse transcription-PCR (RT-qPCR), followed by next-generation sequencing (NGS) for recognizing fusion variants. Thirty RET+ cases were revealed, including 20 CCDC6 (exon 1)-RET (exon 12), 6 NCOA4 (exon 8)-RET (exon 12), 1 NCOA4 (exon 7)-RET (exon 12), 1 CCDC186 (exon 7)-RET (exon 12), 1 ERC1 (exon 12)-RET (exon 12) and 1 SPECC1L (exon 9)-RET (exon 12) tumors. All RET fusion cases occurred in the BRAF- population, with a prevalence of 41.7% (30/72). Four cases of 8% to 13% (cutoff was 7.6%) dominant isolated 3' green (IG) FISH signals were RET-. One FISH- case with isolated 5' red (IR) signals with 94% abnormal tumor cells was demonstrated to be positive, harboring the NCOA4 (exon 7)-RET (exon 12) variant. Compared with RET fusions characterized by dominant break-apart signals with 29% to 100% aberrant cells, RET + with dominant IG-signal patterns all showed more frequent FISH+ cells (84%-92%). RET+ PTC with a break-apart signal pattern was more frequently found in unifocal lesions than in multifocal/bilateral tumors (P = 0.049). A false-positive or false-negative event may exist for RET status detection in PTCs using the traditional FISH scoring method with break-apart probes.

PF518 SOMATIC COPY NUMBER GAINS IN MYC, BCL2, OR BCL6, IN ADDITION TO TRANSLOCATIONS, IDENTIFIES A SUBSET OF AGGRESSIVE ALTERNATIVE‐DH/TH DLBCL PATIENTS

Background:Diffuse Large B Cell Lymphoma (DLBCL) is characterized by both biologic and genetic heterogeneity. While significant therapeutic advances have been made, nearly 30% of cases fail frontline treatment. Recent data suggest that 5–10% of DLBCL can be categorized as double/triple hit lymphoma (DH/TH), defined as having concurrent MYC, BCL2 and/or BCL6 gene rearrangements, identified by fluorescence in‐situ hybridization (FISH) probes. According to the 2017 revision of the World Health Organization classification of lymphoid neoplasms, DH/TH DLBCL is now considered a high grade B‐cell lymphoma (HGBL). While gene rearrangements represent significant genetic events in cancer, copy number alterations (CNAs) also play an important role, often through genomic amplification of oncogenes or loss of tumor suppressors. Despite their similarities, the contributions of CNAs in MYC, BCL2, and BCL6, alone, or in combination with gene rearrangements, are largely unknown in DLBCL and could identify a group of previously uncharacterized patients that may have high expression of MYC, BCL2 and/or BCL6 driven by alternative mechanisms.Aims:The goal of the study is to define the landscape and prognostic significance of gene rearrangements and copy gains in MYC, BCL2, and BCL6 in a cohort of newly diagnosed DLBCL.Methods:A total of 176 cases of DLBCL with both FISH and CNA data were available for the study. FISH was performed on formalin‐fixed paraffin‐embedded sections using break‐apart probes to MYC, BCL2, and BCL6 in the Mayo Clinic Department of Lab Medicine and Pathology. Somatic copy number alterations were identified using whole exome sequencing and the Affymetrix OncoScan® FFPE assay on patient tumor FFPE tissue, and were interrogated using Nexus Copy Number 9.0 software. All patients were treated with immunochemotherapy and prospectively followed for event‐free and overall survival.Results:FISH identified 3 groups of previously described patients, DH/TH or HGBL (n = 11), translocation positive (single MYC, BCL2, BLC6, or double BCL2/BLC6, n = 86), and translocation negative (n = 79). Expanding upon the translocation positive subgroup, copy number analysis identified patients (19 of 86, 22%) with copy number gains in a second or third gene resulting in genomic hits at both MYC and BCL2/6; we classified these as alternative‐double/triple‐hit (A‐DH/TH). An example of this would be a MYC translocation plus a BCL2 and/or BCL6 gain (n = 5), or a BCL2 and/or BCL6 translocation plus a copy gain in MYC (n = 14). Similar interrogation of a publically available dataset (n = 250), revealed similar proportions of these patient groups in an independent cohort of DLBCL, validating our findings. Cell of origin classification of the A‐DH/TH cases revealed that they were 53% GCB. A‐DH/TH patients, in comparison to the translocation‐positive/copy‐gain‐negative cases, were at greater risk of an event (Cox HR = 1.5, 95% CI = 0.71–3.0) and the cases trended towards a worse overall survival (log‐rank P = 0.065; Cox HR = 2.0, 95% CI = 0.94–4.3). Patients with copy‐gains alone had similar outcomes as those with no copy‐gain or translocations, suggesting a central role for at least one translocation event in predicting outcome.Summary/Conclusion:Our data suggest that use of CNA data in combination with traditional FISH can identify a unique subset of DLBCL, A‐DH/TH, that are missed by standard clinical practice. More importantly, we find that these patients do poorly and may benefit from more aggressive treatment, although we do acknowledge that our population size was small and further validation is needed.image

Intrinsic molecular subtypes of breast cancers categorized as HER2-positive using an alternative chromosome 17 probe assay

The 2013 update of the American Society of Clinical Oncology-College of American Pathologists (ASCO-CAP) human epidermal growth factor receptor 2 (HER2) testing guidelines recommend using an alternative chromosome 17 probe assay to resolve HER2 results determined to be equivocal by immunohistochemistry (IHC) or fluorescence in-situ hybridization (FISH). However, it is unclear if cases considered HER2-positive (HER2+) by the alternative probe method are similar to those classified as HER2+ by traditional IHC and FISH criteria and benefit the same from HER2-targeted therapies. We studied the clinical and pathologic features of all 31 breast cancers classified as HER2+ by the alternative probe method at our institution since 2013 and determined their PAM50 intrinsic molecular subtypes. For comparison, we analyzed 19 consecutive cases that were classified as HER2+ by traditional FISH criteria during the same time period. Thirty (97%) cancers in the alternative probe cohort were estrogen receptor (ER)-positive (ER+), while only 9/19 (47%) of traditional HER2 controls were ER+ (p = 0.0002). Sufficient tissue for intrinsic subtype analysis was available for 20/31 cancers in the alternative probe cohort and 9/19 in the traditional HER2+ group. None (0%) of the 20 alternative probe-positive cases were of the HER2-enriched intrinsic subtype, while 8/9 (89%) of those HER2+ by traditional FISH criteria were HER2-enriched (p = 0.0001). These findings suggest that breast cancers classified as HER2+ only by the alternative probe method are biologically distinct from those classified as HER2+ by traditional criteria, and raises questions as to whether or not they derive the same benefit from HER2-targeted therapies.

Abstract P2-09-25: Clinical and pathologic characteristics of breast cancers determined to be HER2-positive by fluorescence in-situ hybridization (FISH) using alternative chromosome 17 probes

Abstract Background: Based on updated 2013 ASCO/CAP guideline for HER2 testing, cases with a HER2/CEP17 ratio &amp;lt; 2.0 but with an average HER2 copy number &amp;gt; 4.0 and &amp;lt;6.0 signals/cell are considered equivocal. In such cases, HER2 testing using alternative chromosome 17 probes was proposed as one way to resolve the equivocal FISH results. Using the alternative probe method increases the number of cancers categorized as HER2 positive but brings to question if these cancers truly represent HER2 amplified breast cancers and derive the same benefit from anti-HER2 therapies. Methods: Since 2013, all breast cancers at our institution that were HER2 equivocal by traditional FISH but classified as HER2 positive using the alternative probe method were assessed for clinical and pathologic features including histologic type and grade, TNM stage, HER2: alternative probe ratio, treatment, and clinical outcome. Results: We identified 24 invasive breast cancers considered HER2 positive by the alternative probe method: 23 (96%) were estrogen receptor-positive (ER+) and 20 (83%) were progesterone receptor- positive. Histologically, only 2 were invasive lobular carcinomas; all others were ductal or had ductal and lobular features. Most cancers (63%) had low or intermediate histologic grade: Grade 1 (n=3); Grade 2 (n=12); Grade 3 (n=9). Clinical information was available for 18 patients: 2 had metastatic disease, 1 had a local recurrence after mastectomy and 15 patients had early stage disease; 9 with node negative disease and 6 with nodal involvement. HER2 IHC was equivocal (2+) in 16 (66.7%) cases, positive (3+) in 4 (16.7%) cases, and negative (0 or 1+) in 4 (16.7%) cases. The average HER2 copy number was 4.77, the average HER22:p53 ratio was 2.61. Repeat HER2 testing on a 2nd tumor sample was performed in 8 cases: HER2-positivity was confirmed in only 2 (25%) cases and by the alternative probe only. Treatment information was available for 17 patients: 1 had T1aN0M0 lesion and did not get chemotherapy, 16 received chemotherapy and 13 received trastuzumab-based chemotherapy. Eleven patients with early stage disease received chemotherapy and trastuzumab. Of these patients, 10/11 were ER+, 7/11 were node negative and 5/11 had grade 2 tumors, yet only one tumor was assessed by oncotype recurrence score ( RS = 29). Three patients received chemotherapy and trastuzumab in the neoadjuvant setting: 1 had a complete pathologic response, 1 a partial response, and 1 has not yet gone to surgery. One additional patient received neoadjuvant chemo alone and achieved a partial response. Conclusions: Breast cancers considered HER2+ by the alternative probe method but not by traditional FISH are almost always ER-positive and most have low or intermediate histologic grade. Repeat HER2 testing on a subsequent tumor sample did not confirm HER2-positivity in 75% of cases. Almost all patients with early stage disease received chemotherapy and trastuzumab based on the alternative probe results without molecular assessment to predict chemotherapy response. Intrinsic molecular subtyping using PAM50 analysis on these cancers is underway to determine how many are HER2-enriched by molecular assessment. Citation Format: Desai NV, Torous V, Cruz C, Schnitt SJ, Tung N. Clinical and pathologic characteristics of breast cancers determined to be HER2-positive by fluorescence in-situ hybridization (FISH) using alternative chromosome 17 probes [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-25.

Evaluation of multiprobe fluoresence in-situ hybridization panel in the detection of common chromosomal abnormalities of acute myeloid leukemia

Background Numerous recurrent chromosomal aberrations have been identified in acute myeloid leukemia (AML), and their detection has become essential for accurate diagnosis, classification, and prognosis of the disease. Fluorescence in-situ hybridization (FISH) provides a powerful technique complementary and even alternative to chromosome banding studies for the identification of selected chromosome aberrations. Aim Evaluation of the multiprobe FISH panel in the detection of common cytogenetic abnormalities in AML and to investigate their association with clinical diagnosis, chemotherapy, and prognosis. Patients and methods This study was conducted on 20 newly diagnosed AML patients. All patients were subjected to full history taking, clinical examination, laboratory investigations including complete blood count, bone marrow aspiration, immunophenotyping, and interphase FISH using cytocell multiprobe AML/myelodysplastic syndrome panel designed to detect AML/Eight-twenty-one (ETO), Promyelocytic leukaemia- Retinoic acid receptor alpha (PML-RARA), and core-binding factor beta/Myosin, heavy chain 11, smooth muscle (CBFβ/MYH11) translocations, mixed-lineage leukaemia (MLL) break apart, P53, 5q, 7q, and 20q deletions. Results Interphase FISH analysis showed 5q deletion in 8/20 (40%) cases, positive PML/RARA in 3/20 (15%) cases p53 deletion in 15/20 (75%) cases, positive AML1/ETO in 1/20 (5%) cases, no MLL break apart cases (0%), 7q deletion in 4/20 (20%) cases, positive CBFβ/MYH11 fusion gene in 4/20 (20%) cases, 20q deletion in 9/20 (45%) cases, and trisomy 8 in 7/20 (35%) cases. There was a statistically significant relationship between 5q deletion and prognosis (P=0.028). Conclusion Multiprobe FISH is more cost effective and time effective compared with traditional FISH. It is an efficient technique for the detection of cytogenetic aberrations AML, providing critical information for diagnosis and prognosis, and for monitoring the course of the disease.

FISHing in the dark: How the combination of FISH and conventional karyotyping improves the diagnostic yield in CpG-stimulated chronic lymphocytic leukemia.

Despite significant advances in molecular genetic approaches, fluorescence in situ hybridization (FISH) remains the gold standard for the diagnostic evaluation of genomic aberrations in patients with chronic lymphocytic leukemia (CLL). Efforts to improve the diagnostic utility of molecular cytogenetic testing have led to the expansion of the traditional 4-probe CLL FISH panel. Not only do these efforts increase the cost of testing, they remain hindered by the inherent limitations of FISH studies - namely the inability to evaluate genomic changes outside of the targeted loci. While array-based profiling and next generation sequencing (NGS) have critically expanded our understanding of the molecular pathogenesis of CLL, these methodologies are not routinely used by diagnostic laboratories to evaluate copy number changes or the mutational profile of this disease. Mitogenic stimulation of CLL specimens with CpG-oligonucleotide (CpG-ODN) has been identified as a reliable and reproducible means of obtaining a karyotype, facilitating a low-resolution genome-wide analysis. Across a cohort of 1255 CpG-ODN-stimulated CLL specimens, we describe the clinical utility associated with the combinatorial use of FISH and karyotyping. Our testing algorithm achieves a higher diagnostic yield (∼10%) through the detection of complex karyotypes, well-characterized chromosomal aberrations not covered by the traditional CLL FISH panel and through the detection of concurrent secondary malignancies. Moreover, the single cell nature of this approach permits the evaluation of emerging new clinical concepts including clonal dynamics and clonal evolution. This approach can be broadly applied by diagnostic laboratories to improve the utility of traditional and molecular cytogenetic studies of CLL. Am. J. Hematol. 91:978-983, 2016. © 2016 Wiley Periodicals, Inc.

A 24-chromosome FISH technique in preimplantation genetic diagnosis: validation of the method

Embryo screening for aneuploidy (AS) is part of preimplantation genetic diagnostics (PGD) and is aimed at improving the efficiency of assisted reproduction. Currently, several technologies, including the well-established fluorescence in situ hybridization (FISH) technique, cover the screening of all chromosomes in a single cell. This study evaluates a novel 24-chromosome FISH technique protocol (FISH-24). A total of 337 embryos were analyzed using the traditional 9-chromosome FISH technique (FISH-9) while 251 embryos were evaluated using the new FISH-24 technique. Embryos deemed nontransferable on Day 3 were cultured in vitro to Day 5 of development, then fixed and reanalyzed according to the technique allocated to each treatment cycle (107 embryos analyzed by FISH-9 and 111 by FISH-24). The global error rate (discrepancy between Day 3 and Day 5 results for a single embryo) was 2.8% after FISH-9 and 3.6% after FISH-24, with a p value of 0.95. Thus, we have established and validated a 24-chromosome FISH-based single cell aneuploidy screening technique, showing that the error rate obtained for FISH-24 is independent of the number of chromosomes analyzed and equivalent to the error rate observed for FISH-9, as a useful tool for chromosome segregation studies and clinical use.

Is It Necessary to Evaluate Nuclei in HER2 FISH Evaluation?

A new method that simplifies the evaluation of the traditional HER2 fluorescence in situ hybridization (FISH) evaluation in breast cancer was proposed. HER2 status was evaluated in digital images (DIs) captured from 423 invasive breast cancer stained sections. All centromeric/CEP17 and HER2 gene signals obtained from separated stacked DIs were manually counted on the screen. The global ratios were compared with the traditional FISH evaluation and the immunohistochemical status. The 2 FISH scores were convergent in 96.93% of cases, showing an "almost perfect" agreement with a weighted k of 0.956 (95% confidence interval, 0.928-0.985). The new method evaluates at least 3 times more nuclei than traditional methods and also has an almost perfect agreement with the immunohistochemical scores. The proposed enhanced method substantially improves HER2 FISH assessment in breast cancer biopsy specimens because the evaluation of HER2/CEP17 copy numbers is more representative, easier, and faster than the conventional method.

Array-based comparative genomic hybridization is more informative than conventional karyotyping and fluorescence in situ hybridization in the analysis of first-trimester spontaneous abortion

BackgroundArray-based comparative genomic hybridization (aCGH) is a new technique for detecting submicroscopic deletions and duplications, and can overcome many of the limitations associated with classic cytogenetic analysis. However, its clinical use in spontaneous abortion needs comprehensive evaluation. We used aCGH to investigate chromosomal imbalances in 100 spontaneous abortions and compared the results with G-banding karyotyping and fluorescence in situ hybridization (FISH). Inconsistent results were verified by quantitative fluorescence PCR.ResultsAbnormalities were detected in 61 cases. aCGH achieved the highest detection rate (93.4%, 57/61) compared with traditional karyotyping (77%, 47/61) and FISH analysis (68.9%, 42/61). aCGH identified all chromosome abnormalities reported by traditional karyotyping and interphase FISH analysis, with the exception of four triploids. It also detected three additional aneuploidy cases in 37 specimens with ‘normal’ karyotypes, one mosaicism and 10 abnormalities in 14 specimens that failed to grow in vitro.ConclusionsaCGH analysis circumvents many limitations in traditional karyotyping or FISH. The accuracy and efficiency of aCGH in spontaneous abortions highlights its clinical usefulness for the future. As aborted tissues have the potential to be contaminated with maternal cells, the threshold value of detection in aCGH should be lowered to avoid false negatives.

P3.05 A New Non-Toxic Hybridization Buffer Reduces the Fish Assay Time From 16-20 Hours to 3½ Hours Without Compromising the Quality

ABSTRACT Fluorescence in-situ hybridization (FISH) is a powerful technique for direct visualization and quantitative determination of gene amplifications, deletions and translocations in human cancer cells. It is recognized as a reliable and reproducible method, and FISH assays are often referred to as 'Gold Standard' for determining the patient status with predictive tests for HER2 and ALK. But FISH is also known to have characteristics which limit a more widespread use, including the long assay time (staining and scoring), requirement for a fluorescence microscope and complexity involved in handling small volumes and toxic reagents. Dako has addressed the toxicity and long hybridization time by introducing a new hybridization buffer. The new non-toxic hybridization buffer (IQFISH buffer), which allows for significant reduction in hybridization time, brings the total assay time for a FISH assay down from 16-20 hours to just 3½ hours without compromising the quality. The new Dako HER2 IQFISH pharmDx™ (assay time 3½ hours) has been compared with the traditional Dako HER2 FISH pharmDx™ Kit (assay time 16-20 hours) in a comparative study on 78 breast tissue specimens of human breast carcinoma ( Fig 1 ). Cross tabulation of HER2 status obtained by the two assays gave an overall agreement of 98.7% (95% CI: 94.2%-99.9%). Disagreement between the two assays was observed for one specimen that most likely was a heterogeneous tissue with a very small area of amplification. A similar comparative study on 79 gastric adenocarcinoma specimens showed an overall agreement of 98.7% (95% CI: 94.2%-99.9%). The disconcordant sample was a heterogeneous tissue with a very small area of amplification. A third concordance study on 80 breast cancer tissues compared TOP2A IQFISH pharmDx™ with the traditional TOP2A FISH pharmDx™ Kit ( Fig 2 ). A 100% overall agreement (95% CI: 96.9%-100%) was found. Conclusion: We have developed new non-toxic hybridization buffer that by reduction of the hybridization time from 16 to 2 hours allows for a ½ day FISH protocol. The IQFISH buffer has been validated for HER2 on breast and gastric cancer and for TOP2A on breast cancer. Both assays showed a very high agreement with the traditional 2 day FISH procedure. Download : Download full-size image Fig. 1 . Agreement between the new Dako HER2 IQFISH pharmDx™ and the traditional Dako HER2 FISH pharmDx™ Kit. Download : Download full-size image Fig. 2 . Agreement between the new Dako TOP2A IQFISH pharmDx™ and the traditional Dako TOP2A FISH pharmDx™ Kit.

Differentiation of melanoma and benign nevi by fluorescence in-situ hybridization

Malignant melanoma is sometimes difficult to distinguish from benign nevus, and ancillary confirmatory studies would be of value in selected cases. To accurately differentiate melanoma from benign nevus, we investigated the utility of chromosomal anomalies in skin biopsy specimens using multitargeted fluorescence in-situ hybridization (FISH). Skin biopsy specimens were retrospectively collected from 63 patients diagnosed with benign compound nevus (n=32) or malignant melanoma (n=31); each diagnosis was independently confirmed before study by a second dermatopathologist. Unstained tissue sections were hybridized for 30 min using fluorescence-labeled oligo-DNA probes for chromosomes 6, 7, 11, and 20. Fluorescent signals for each chromosome were enumerated in 30 cells per case. Numeric chromosomal anomalies were found in 0% (0 of 32) of normal epidermis, 6% (two of 32) of compound nevi, and 94% (29 of 31) of melanomas (nevus vs. melanoma, P<0.0001). The mean number of cells with chromosomal changes was 23 in melanoma specimens, significantly higher than that in compound nevi (P<0.0001). The most frequent chromosomal anomaly in melanoma was gain of chromosome 11, followed consecutively by gains of chromosomes 7, 20, and 6. Chromosomal anomalies detected by FISH had an overall sensitivity of 94% and specificity of 94% in the separation of nevus and melanoma. With the use of oligo-DNA probes, multitargeted FISH directed against chromosomes 6, 7, 11, and 20 is highly sensitive and specific for separation of nevus and melanoma. Unlike other traditional FISH probes, oligo-DNA probes required shorter hybridization time, allowing faster diagnostic evaluation.

Multicolor FISH analysis of rDNA and telomere on spinach

In this study, multicolor fluorescence in situ hybridization (FISH) analysis on metaphase chromosomes of spinach with biotin-labeled 25S rDNA, DIG-labeled telomere sequences and biotin-labeled and DIG-labeled 5S rDNA was performed. There were six 25S rDNA loci located on the satellites of the third, the fifth and the sixth chromosomes, and four 5S rDNA loci located on the long arms of the third and the fifth chromosomes. The telomere loci were located on the end of the sixth chromosome and also on both the end and centromeric regions of other chromosomes. This study is an important complement to both traditional karyotype analysis and FISH karyotype analysis in spinach.