Product Citations

β-Catenin nuclear expression discriminates deep penetrating nevi from other cutaneous melanocytic tumors from other cutaneous melanocytic tumors
PRKCA Break Apart Probe
Nuclear β-catenin expression was analyzed in several types of cutaneous melanocytic tumors, including deep penetrating nevi (DPN), “blue” melanocytic tumors, Spitz tumors, nevoid and SSM melanomas, and pigmented epithelioid melanocytomas (PEM). In addition to IHC, RNA-sequencing, and other tests, FISH analysis was performed with our PRKCA break apart probe. It was found that 2/6 cases of PEM had a PRKCA rearrangement. The study concluded that nuclear β-catenin IHC expression is useful in differentiating DPN tumors from blue or Spitz melanocytic tumors and PEM.
A Clinicopathologic and Molecular Analysis of 34 Mediastinal Germ Cell Tumors Suggesting Different Modes of Teratoma Development
Mediastinal teratomas can be both malignant and benign. Increased 12p copy numbers are uniform in malignant testicular germ cell tumors (GCT), so the 12p copy numbers were analyzed in mediastinal GCTs to see if this is indicative of malignancy. FISH analysis was used with our KRAS and chromosome 12 centromere probes to look for 12p copy number increases. The sensitivity for increased 12p copies for malignant GCT was 69%. This is less than reports for other tumors, and a negative test for increased 12p copies should not necessarily rule out malignancy.
A FISH assay efficiently screens for BRAF gene rearrangements in pancreatic acinar-type neoplasms
BRAF Break Apart Probe
In acinar cell carcinomas, it is possible to have rearrangement in the BRAF gene. This is present in about 20% of acinar neoplasms, and provides a possible target for treatment. FISH analysis was used with our BRAF break apart probe. The experiment showed that FISH is a cost effective, sensitive, and specific way to identify the BRAF gene aberration.
A Hemizygous 370 Kilobase Microduplication at Xq13.1 in a Three-Year-Old Boy With Autism and Speech Delay
The genetic background of autism spectrum disorders continues to be under study. Some studies look at the link between the disorder and the X chromosome because autism is more commonly diagnosed in men. Alterations of NLGN3 on Xq13 have been reported. This case study focused on a three-year-old boy. FISH analysis was done with our NLGN3 probe to confirm duplication of Xq13.1. It was concluded that duplications observed in the Xq13.1 region may be a risk site for autism.
A patient with a diagnosis of nodal marginal zone B-cell lymphoma and a t(2;14)(p24;q32) involving MYCN and IGH
CCND2 Break Apart Probe
This study investigated a case of nodal marginal zone B-cell lymphoma to better understand the cytogenics of the disease. A t(2;14)(p24;q32) translocation affecting the MYCN and IGH genes had been reported in two other types of lymphoma, but not nodal marginal zone B-cell lymphoma. FISH analysis was performed with our break apart CCND2 probe and RP11-542H15. The case of marginal B-cell lymphoma was found to have the t(2;14)(p24;q32) translocation, possibly demonstrating that this deviation is not unique to the other two types of lymphoma where it occurs.
A subset of epithelioid and spindle cell rhabdomyosarcomas is associated with TFCP2 fusions and common ALK upregulation
TFCP2 Break Apart Probe
Rhabdomyosarcomas with TFCP2 fusions is an emerging family of tumors, characterized by a predilection for female patients, spindle cell morphology, and ALK overexpression. The subset also occurs most frequently in the bones, especially the craniofacial skeleton, which is very uncommon for rhabdomyosarcomas. In this study, the clinicopathological, transcriptional, and genomic features of 14 rhabdomyosarcomasa cases were evaluated. Patients were analyzed using immunohistochemistry, array-comparative genomic hybridization, whole RNA-sequencing, anchored multiplex PCR-based targeted NGS, and fluorescent in situ hybridization (FISH). TFCP2 translocations were detected using Empire Genomics’ TFCP2 break-apart FISH probe. TFCP2 rearrangements were found in all tested cases, fused with either EWSR1 (n = 6) or FUS (n = 8). FET-TFCP2 rhabdomyosarcomas clustered together and distinctly from other rhabdomyosarcomas subgroups. Taken together, the findings expand on the unique clinical characteristics of this new subgroup of FET-TFCP2 rhabdomyosarcomas. Their association with ALK overexpression could serve as a potential therapeutic vulnerability.
Aberrant cerebellar Purkinje cell function repaired in vivo by fusion with infiltrating bone marrow-derived cells
Mouse Con X FISH Probes
Bone marrow cells have been known to fuse with cerebellar Purkinje cells, neurons in the brain. It has been suggested that this fusion could preserve and restore the neurons. Mice were subjected to bone marrow transplants to observe the effects. FISH analysis was performed with our mouse control X and Y probes. The FISH results allowed for the visualization of chromosomal content in Purkinje cells. The experiment was successful in the formation of a spontaneously firing neuron from the bone marrow/Purkinje fusion. There was also evidence that the fusion mitigated effects of cell injury on electrical activity.
Aberrant ERG expression associates with downregulation of miR-4638-5p and selected genomic alterations in a subset of diffuse large B-cell lymphoma
RP11-476D17 & RP11-95121 FISH Probes
ERG is an oncogene associated with poor prognosis in AML and Ewing’s sarcoma, but little research has been done on ERG’s effects in lymphoma. In this study, diffuse large B-cell lymphoma (DLBCL) tumors were analyzed using immunohistochemistry, miRNA expression profiling, RT-PCR, and whole exome sequencing. FISH was also used to detect ERG rearrangements, using RP-11 BAC clones from Empire Genomics (RP11-476D17 and RP11-95121). FISH detected no ERG translocations in 10 randomly selected ERG+ DLBCL samples. Approximately 30% of tumors (37 of 118) were found to exhibit aberrant ERG. Expression of the gene was found to be associated with downregulation of miR-4638-5p, but not cell-of-origin classification, patient age, sex, nodal/extranodal disease status, or tumor expression of p53 or p63.
Acute myeloid leukemia with KMT2A-SEPT5 translocation: A case report and review of the literature
Acute myeloid leukemia (AML) is commonly characterized by a chromosomal rearrangement of KMT2A. Up to 94 translocation partner genes have been identified thus far. This case study focuses on a rare gene translocation of KMT2A with SEPT5. FISH analysis was performed with two probes including our SEPT5 probe. FISH confirmed rearrangement of the KMT2A and SEPT5 genes. The study concluded that they had a new case of AML KMT2A-SEPT5 fusion, making it one of nine reported cases.
ADAM3A copy number gains occur in a subset of conjunctival squamous cell carcinoma and its high grade precursor
Conjunctival squamous cell carcinoma (cSCC) and its precursors are some of the most common ocular surface neoplasms. Recently, ADAM3A gene amplification was identified in invasive cSCC, via copy number gains of the 8p11.22 locus harboring ADAM3A.This team sought to analyze ADAM3A amplification in cSCC and its precursors using FISH. They used Empire Genomics’ ADAM3A probe, along with our CON 8 centromeric control probe, to detect ADAM3A gains. A total of 54 cases of conjunctival squamous intraepithelial neoplasia (CIN), carcinoma in situ (CIS), or cSCC were studied. Nine (17%) cases harbored ADAM3A or chr 8 gains, with one of these cases demonstrating high level amplification. All ADAM3A alterations were restricted to high-grade lesions. The team concluded that ADAM3A gains occur in a subset of cSCC and its precursors, specifically in high-grade lesions. This finding warrants further investigation into amplified ADAM3A as a biomarker for ocular SCC.
Alterations in Cell Motility, Proliferation, and Metabolism in Novel Models of Acquired Temozolomide Resistant Glioblastoma
Chromosome X Centromere FISH Probes
Glioblastoma (GBM) is an aggressive tumor treated with temozolomide (TMZ). TMZ only extends the survival of patients another few months due to the development of resistance to TMZ. The mechanism for TMZ resistance is not fully understood. GBM cell lines were characterized to better understand the resistance development. Part of this characterization included FISH analysis, which was used with our centromeric X-chromosome probe in order to understand the changes in chromosomal copy number. It was found that TMZ resistant germlines displayed increases in proliferation, migration, chromosomal aberrations, and secretion of cytosolic lipids.
Altered development of dopaminergic neurons differentiated from stem cells from human exfoliated deciduous teeth of a patient with Down syndrome
Con 21 FISH Probes
Down-syndrome (DS) is a developmental disorder that occurs from an additional copy of chromosome 21. One symptom of DS is associated with dopamine signaling. Stem cells from human exfoliated deciduous teeth (SHED) in people with DS (DS-SHED) were examined at the cellular level to better understand this dopamine signaling. FISH analysis was performed with our chromosome 21 control probe to identify the number of chromosome 21 copies present in the DS-SHED nuclei. The results concluded that the sample under study had a malfunction in the dopaminergic neurons, and that SHED may be useful in studying DS pathology due to its non-invasive nature.
Alternative lengthening of telomeres, ATRX loss and H3_K27M mutations in histologically defined pilocytic astrocytoma with anaplasia
Pilocytic astrocytoma (PA) is a type of brain tumor. Certain molecular abnormalities can be indicative of PA such as alternative lengthening of telomeres or loss of ATRX. In many cases of PA, there is a duplication in the kinase domain of the BRAF gene called KIAA1549_BRAF. Red and green FISH probes were used to identify this BRAF gene duplication. The duplication was found to be present in 31% of the PA patients.
Anaplastic large cell lymphoma with TP63 rearrangement: A dismal prognosis
TP63 Break Apart Probe
Anaplastic large cell lymphoma (ALCL) is a rare form of T-cell lymphoma. Cases of ALCL with rearrangements in the TP63 gene have been shown to have the most dismal prognosis. Our TP63 break apart probe was used to test for this rearrrangement. The samples under study did in fact display the TP63 rearrangment, suggesting that more needs to be done in creating treatment options.
Atypical Spitzoid Neoplasms in Childhood: A Molecular and Outcome Study
Atypical spitzoid neoplasms are primarily pediatric lesions characterized by their intermediate features; clinically and histopathologically, they fall somewhere between benign spitz nevi and malignant melanoma. The condition’s cytogenetic characteristics have yet to be defined. Researchers sought to better characterize the condition by identifying the prevalence of certain genetic abnormalities in a cohort of 34 affected patients. Empire Genomics’ break-apart FISH probes were used to test for translocations of the ALK, BRAF and NTRK1 genes. Of the patients assessed, 30.9% tested positive for fusions in one or more of the aforementioned genes.
Benign spindle cell lesions of the breast: a diagnostic approach to solitary fibrous tumour, nodular pseudoangiomatous stromal hyperplasia and nodular fasciitis
USP6 FISH Probes
Benign spindle cell lesions of the breast are a rare and varied subset of lesions that can be difficult to distinguish from other tumor types. This study presented three different cases of benign spindle cell lesions - solitary fibrous tumor (SFT), nodular pseudoangiomatous stromal hyperplasia (PASH) and nodular fasciitis (NF) - and highlighted the different histological and cytogenetic techniques that could be used to identify them. Empire Genomics’ USP6 break-apart probe was used to test breast tissue biopsies for rearrangements in the USP6 gene, which has been found to occur in more than 90% of NF cases. Researchers recommended using FISH to help diagnose future cases where NF is suspected but can’t be solely determined through morphological or immunohistochemical means.
Biallelic intragenic duplication in ADGRB3 (BAI3) gene associated with intellectual disability, cerebellar atrophy, and behavioral disorder
RP11-980I14 FISH Probes
Abnormalities in the ADGRB3 gene have been found to be associated with psychological disorders. The study looked for intrachromosomal duplication of ADGRB3 in all members of a single family. FISH was performed on the chromosome using RP11-980I14, with RP11-661C14 serving as the control clone. The FISH analysis confirmed intrachromosomal duplication.
BLM prevents instability of structure-forming DNA sequences at common fragile sites
RP11-264L1 FISH Probes
Common fragile sites (CFSs) on the chromosome are more prone to cancer-associated rearrangements. The role of BLM in protecting these CFSs was under analysis. FISH analysis was used to show that inactivation of BLM resulted in increased FRA16D expression after Ras expression. FISH was performed with the use of one our BAC clone probe RP11-264L1. It was concluded that BLM is important in protecting AT-rich sequences at CFSs.
Bone marrow transplantation stimulates neural repair in Friedreich's ataxia mice
Mouse Xqc3 FISH Probes
Friedreich's ataxia is a neurological disease caused by a deficiency in frataxin. The neuroreparative effects of a bone marrow transplant were analyzed in mice. FISH analysis was performed with our mouse chromosome X (Xqc3) and Y (control) probes. The FISH results showed that the male donor Y chromosome was present in both Purkinje cells and DRG neurons. The transplantation resulted in several improvements in the mice, and it was concluded that gene replacement therapy for Friedreich's ataxia could be possible through allogeneic bone marrow transplantation.
Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration
RP11 BAC Clone (not specified) FISH Probes
By eliminating the interaction between cofactor CPSF6 and HIV-1, the nuclear localization of HIV-1 can be greatly altered. Recurrent integration genes in the nuclei were mapped using FISH to peripheral and mid-nuclear areas. This was done using our BAC probe. The data showed that HIV-1 does not preferentially target the nuclear periphery under baseline infection conditions.
Childhood supratentorial ependymomas with YAP1_MAMLD1 fusion: an entity with characteristic clinical, radiological, cytogenetic and histopathological features
YAP1 Break Apart Probe
Ependymoma is a tumor that arises from tissue of the nervous system, particularly the brain as described in this experiment. A rare case of this tumor involves a YAP1_MAMLD1 fusion that can occur in childhood. This study sought to more holistically characterize neoplasms with this fusion, including their histopathology, immunophenotype, cytogenetic features, etc. FISH analysis was used with our YAP1 break apart probe. FISH demonstrated rearrangements of the YAP1 gene in several of the cases under study. It was determined that YAP1_MAMLD1 fusion ependymomas have unique characteristics that require a diagnosis separate from that of RELA fusion ependymomas.
Chromosomal aberrations in chordoid meningioma—An analysis
NF 2 FISH Probes
Chordoid meningiomas are rare tumors that have been found to have deletions such as 22q, 18p, 14q, and 1p. Although the deletions are known, their correlation to their clinical findings is not as established. FISH analysis was used with a variety of our probes to see which deletion(s) each case under study had. It was found that any recurrence of chordoid meningioma had all four chromosome loci deleted.;year=2018;volume=66;issue=1;spage=156;epage=160;aulast=Sugur
Chromosome 3p Inverted Duplication with Terminal Deletion: Second Postnatal Case Report with Additional Clinical Features
RP11-451A20 FISH Probes
Distal deletions and duplications of 3p are individually well-characterized chromosome aberrations. The subject of this study was a 17 month old girl who had prenatal intrauterine growth restriction and cardiac defects. She was found to have inverted duplication of 3p with an adjacent terminal 3p deletion, revealed by microarray analysis and FISH. Empire Genomics’ RP11-451A20 FISH probe was used to confirm duplication and rearrangement of 3p. Only one postnatal patient and one second trimester pregnancy have been reported with this finding. Many of the patient’s features have been found previously in both 3p deletion and 3p duplication syndromes, including congenital heart disease, growth restriction, microcephaly, hypotonia, and developmental delay. However, the subject also had additional features not reported in cases of 3p deletion or duplication, such as aortic dilation, hemangiomas, and neutropenia. The study helps to further cytogenetically and clinically characterize this rare concurrent deletion and inverted duplication of 3p. This report may assist clinicians working with patients who have constellations of similar features or genetic abnormalities.
Clinical and molecular cytogenetic characterization of a novel 10q interstitial deletion: a case report and review of the literature
RP11-227H15 FISH Probes
The subject of this study was a two-and-a-half-year-old patient with a de novo 10.2-Mb deletion extending from 10q21.3 to 10q22.3, the second largest reported interstitial deletion (out of 10) involving this region. The patient presented with an extensive list of developmental and physical abnormalities (e.g. trouble feeding, dysmorphic facial features, severe language delays). FISH analysis was performed using Empire Genomics’ RP11-227H15 clone to detect aberrations in chromosome 10, and a deletion was identified at 10q22. Based on the patient’s unique clinical presentation, researchers concluded that loss of the KAT6B gene within the deleted region is the likeliest cause of her condition.
Clinicopathologic Features of CIC-NUTM1 Sarcomas, a New Molecular Variant of the Family of CIC-Fused Sarcomas
CIC Break Apart Probe
CIC-fused sarcomas are aggressive tumors that can grow throughout the body, including the central nervous system and lungs. CIC sarcomas fuse to a variety of genes such as DUX4, FOXO4, and NUTM1, with NUTM1 fusion being the basis of the study. CIC-NUTM1 has been identified as a new variant in CIC-fused sarcomas. FISH analysis was performed on FFPE tissue using break apart probes including our CIC probe. FISH analysis coupled with RNA sequencing were done to better understand the genomic makeup of CIC-NUTM1.,.15.aspx
Clinicopathologic implication of PD-L1 and phosphorylated STAT3 expression in diffuse large B cell lymphoma
PD-L1 Break Apart Probe
The antitumor immune response of PD-L1 has clinical value in EBV-negative diffuse large B cell lymphoma (DLBCL). The association between PD-L1 and pSTAT3 expression/gene alteration wih EBV-negative DLBCL was under analysis. FISH analysis was used with our PD-L1 break apart and PD-L1/chromosome 9 probes. It was found that gene alteration and protein expression of PD-L1 and pSTAT3 expression were closely related in DLBCL.
Comparison of melanoma gene expression score with histopathology, fluorescence in situ hybridization, and SNP array for the classification of melanocytic neoplasms
Some melanocytic tumors have less understood histology that can lead to difficulty in diagnosing. Molecular assays such as FISH have been proposed to lead to more certainty in diagnoses. FISH analysis was used to detect several genes, including our RREB1 probe that targets chromosome 6p25. It was found that compared to a gene expression test called myPath, FISH agrees better with histopathologic interpretations, has greater sensitivity, and correlates better with molecular diagnostics.
Comprehensive Genomic Profiling of Malignant Effusions in Patients with Metastatic Lung Adenocarcinoma
ROS1 Break Apart Probe
In this study, the utility of performing targeted next-generation sequencing (NGS) on malignant effusions from patients with metastatic lung adenocarcinoma was investigated. NGS is a high throughput technology, which utilizes a small sample input, but the suitability of NGS analysis for tissue-free cytology samples such as malignant body fluids is not well understood. In order to investigate the adequacy of NGS on liquid biopsies of MLA, targeted NGS was performed using custom target panels consisting of many oncogenes. Additional non-NGS molecular tests were performed on the effusion samples, including fluorescence in situ hybridization (FISH) analysis for the oncogene ROS1, using a break-apart FISH probe manufactured by Empire Genomics.
Congenital hypoplastic bone marrow failure associated with a de novo partial deletion of the MECOM gene at 3q26.2
RP11-115B16 FISH Probes
Congenital hypoplastic bone marrow failure is a rare condition in newborns with largely unknown genetics and mechanisms. A newborn patient with congenital thrombocytopenia and anemia was characterized at the cellular level. Along with other testing, FISH analysis was performed with various probes including our RP11-115B16 BAC clone. Our probe confirmed a 3q26.2 deletion that was detected with array-CGH analysis. It was concluded that this deletion is a very rare recurrent abnormality in congenital thrombocytopenia, and that the locus could be an important target for diagnosing.
Consistent LEF-1 and MYB Immunohistochemical Expression in Human Papillomavirus-Related Multiphenotypic Sinonasal Carcinoma: A Potential Diagnostic Pitfall
HPV-related multiphenotypic sinonasal carcinoma (HMSC) is a sinonasal tract neoplasm with a salivary gland tumor-like appearance. The morphologic profile of HMSC is still not fully understood and is under study. One aspect of this morphologic study included FISH analysis with our MYB break apart probes. No rearrangements in MYB were detected by FISH in the cases under study. It was concluded that MYB protein cannot be used to separate adenoid cystic carcinoma from HMSC.
Correlation between immunohistochemistry and RICTOR FISH amplification in small cell lung carcinoma
Small cell lung carcinoma (SCLC) accounts for approximately 15% of all lung cancers and remains a challenging disease, with no significant improvement in the development of targeted therapies. The RICTOR gene, which encodes a key structural protein of mTOR complex 2 (mTORC2), has recently been identified as one of the most frequently amplified genes and a potential therapeutic target in SCLC. The aim of this study was to compare immunohistochemical (IHC) expression of Rictor and phospho-Akt (a downstream target of mTORC2) with RICTOR amplification as detected by FISH in SCLC. FISH and IHC were performed on 100 SCLC tumors. Empire Genomics’ RICTOR FISH probe was used, accompanied by our Con5 control probe, to detect RICTOR copy number variations. RICTOR amplification was detected in 15% of sample using FISH, while IHC positivity for Rictor and phospho-Akt was observed in 37% and 42% of samples, respectively. Rictor expression was higher in distant metastases than in primary tumor samples and lymph node metastases. There was no association between RICTOR amplification and clinical outcome. However, high expression of either Rictor or phosphor-Akt was associated with significantly decreased overall survival.
CRTC1-TRIM11 Fusion Defined Melanocytic Tumors: A Series of Four Cases
TRIM11 Break Apart Probe
Recently, a new entity of cutaneous melanocytic tumor morphologically resembling clear cell sarcoma was identified in 5 adult patients, characterized by CRTC1-TRIM11 gene fusion. In this study, 4 new cases of this malignancy were analyzed using immunohistochemistry, RNA sequencing, and FISH. TRIM11 rearrangement was verified using Empire Genomics’ break-apart TRIM11 FISH probe. Tumors were all positive for SOX10 and MiTF, mostly positive for S100 protein, and only focally expressed other melanocytic biomarkers (Melan-A and HMB45). The team suggested changing the name of this new tumor to cutaneous melanocytic tumor with CRTC1-TRIM11 fusion, as it may display more aggressive behavior than conventional melanocytoma.
Cutaneous Melanocytoma With CRTC1-TRIM11 Fusion
TRIM11 Break Apart Probe
Primary intradermal nodular unpigmented tumors in several patients were analyzed for genetic similarities. It was thought that the CRTC1-TRIM11 fusion would be a novel genetic marker for the tumor. FISH analysis was used with our TRIM11 break apart probe to confirm the presence of the gene fusion. Other FISH analysis was done before TRIM11 as "diagnostic molecular testing". Of the five tumors under analysis, each of them did contain the CRTC1-TRIM11 fusion, which was concluded to be specific to the type of nodular tumor being studied.
De Novo Interstitial Deletion of 9q in a Pediatric Patient With Global Developmental Delay
RP-11 91M3 FISH Probes
Interstitial deletions of chromosome 9q, although rare, are characteristic of many congenital abnormalities, including dysmorphic features, developmental delay, and intellectual disability. A child with global developmental delay (GDD) and a de novo interstitial 7.0 Mb deletion of 9q21.33q22.31 was studied. The deletion was confirmed by FISH analysis using a bacterial artificial chromosome (BAC) probe targeted to the 9q21.33 region (RP11- 91M3) from Empire Genomics’ BAC clone library. The patient was unique in that her condition was less severe than the majority of 9q deletion cases, suggesting that her “…clinical synopsis is not predicted simply by the roles of each of the genes involved in this novel interstitial deletion.”
Deletion of the 3' MEIS2 (15q14) gene in two siblings with mild phenotypes and parental mosaicism
RP11-450G24 FISH Probes
MEIS2 is a gene that codes for three amino acid loop extension proteins. Deletions and mutations in this gene can cause developmental issues. These deletions can be confirmed using FISH analysis. This analysis was performed using the RP11-450G24 probe.
Delineating the Clinical Spectrum Associated With Xq25q26.2 Duplications: Report of 2 Families and Review of the Literature
RP11-383B16 FISH Probes
Duplications of Xq25q26.2 have been shown to cause developmental delay, learning disabilities, and microcephaly, among other harmful cognitive effects. FISH probes were used in order to confirm duplication in the patients. FISH probes also aided in determining that the duplication is maternally inherited.
Delineation of human prostate cancer evolution identifies chromothripsis as a polyclonal event and FKBP4 as a potential driver of castration resistance
Castration–resistant (CR) prostate cancer (PC) was delineated by the genomic profiling of patients progressing to castration resistance. A patient showing amplification of FKBP4 raised interest of the gene's role in the development of the cancer. FISH analysis was performed with our FKBP4 custom FISH probe from BAC clone RP11_958H19. The results of the FISH analysis in CRPC and hormone–naïve (HN) PC tissues indicated that FKBP4 gene amplification from chromothripsis could be the cause of high protein expression. In conclusion, amplification and overexpression of FKBP4 could be a selective advantage in tumor evolution and the development of CRPC.
Detection of specific gene rearrangements by fluorescence in situ hybridization in 16 cases of clear cell sarcoma of soft tissue and 6 cases of clear cell sarcoma-like gastrointestinal tumor
ATF1 Break Apart Probe
Clear cell sarcoma can be identified by the fusion of EWSR1 to CREB genes like ATF1 and CREB1. FISH was used to analyze the arrangements of the genes. FISH analysis was performed with our dual-color break apart probes for ATF1, CREB1, and CREM. It was determined that EWSR1-ATF1 fusion was primarily found in clear cell sarcoma in soft tissue, while EWSR1-CREB1 fusion was found in clear cell sarcoma-like gastrointestinal tumors.
Diagnosis of uncommon renal epithelial neoplasms: performances of fluorescence in situ hybridization
TFEB Break Apart Probe
Renal cell carcinoma (RCC) can be subdivided into several categories based on morphology, histology, protein expression, and genetic profiling. The main subtypes include clear cell, papillary, chromophobe, oncocytoma, and TFE3 and TFEB-rearranged RCC. Although RCC can usually be easily classified using histological and immunohistochemical analysis, differential diagnosis can prove challenging in certain cases. Therefore, accompanying diagnostic techniques, like FISH, are sometimes required to verify subtype identification. This study evaluated the efficacy of FISH in complementary classification of RCCs via the cytogenetic analysis of 539 RCC tumor samples. For tumors with TFEB-rearranged RCC histological features, Empire Genomics’ TFEB Break Apart probe was used to detect TFEB translocations. FISH was found to contribute to diagnosis in 73% of cases. Considering the variety of RCC subtypes, the team found that FISH was highly efficient to confirm the histological diagnosis of CCRCC, PRCC, and TFE3/TFEB-rearranged RCC.
Diagnostics of pediatric supratentorial RELA ependymomas: integration of information from histopathology, genetics, DNA methylation and imaging
RELA Break Apart Probe
Ependymoma is a tumor of the central nervous system that can exhibit fusion of the RELA gene. Diagnosing these accurately is important, and can be done with FISH, IHC, or DNA methylation. FISH analysis was performed with RELA break apart probes (RP11_58D3 and RP11_436C17/RP11_1104L6). An MN1 and YAP1 break apart probe were also used in conjunction with the DNA methylation.
Distinct Patterns of Acral Melanoma Based on Site and Relative Sun Exposure
Acral melanomas have been found to have considerable variation. Clinical, histologic, and molecular features were characterized in samples of acral melanoma that occurred throughout different body areas such as the dorsal and volar. Part of this characterization included FISH analysis, which was performed using various FISH probes that target loci associated with aberrancy in acral melanoma. Different locations of acral melanoma were found to have variation in gene mutations and aberrations, with the results suggesting these differences may be due to UV exposure.
Epithelial-Myoepithelial Carcinoma Frequent Morphologic and Molecular Evidence of Preexisting Pleomorphic Adenoma, Common HRAS Mutations in PLAG1-intact and HMGA2-intact Cases, and Occasional TP53, FBXW7, and SMARCB1 Alterations in High-grade Cases
PLAG1 Break Apart Probe
There is though to be a relationship between genetic aberrations, preexisting pleomorphic adenoma (PA), and the structural abnormality of epithelial-myoepithelial carcinomas (EMCAs). EMCAs were analyzed on a molecular level for PA by using FISH. FISH analysis was used with our break apart probes to detect PLAG1 and HMGA2 rearrangements. It was found that a relationship was present, as 80% of EMCA arise from PA, and EMCA genetics can vary with the status of PLAG1 and HMGA2.
EWSR1/FUS - NFATc2 rearranged round cell sarcoma: Clinicopathological series of four cases and literature review
RP11 2L23 FISH Probes
Recently, researchers have found that different subsets of bone tumors composed of small round cells can be categorized based on characteristic gene fusions. These biomarkers can help determine diagnosis, prognosis, and treatment. For this study on four patients with small round cell tumor of the bone (all with NFATC2 translocations involving either the EWSR1 or FUS genes), Empire Genomics' RP11 probes (2L23 and 73P15) were used to detect aberrations in the NFATC2 region. EWSR1-NFATC2 fusions were found in three cases, and FUS-NFATC2 fusions in one case. It was concluded that the tumors have distinct clinical implications, morphology, and immunoprofiles that differ from that of Ewing Sarcoma, and also do not respond to Ewing sarcoma chemotherapy regimens.
Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing
KRT14-20 FISH Probes
Due to limited case numbers, the availability of cell models can slow investigation of salivary gland neoplasms. Conditionally reprogrammed cell (CRC) technology was investigated to see if primary cell cultures from the neoplasms provide sufficient material for gene sequencing and analyzing chemosensitivity. In addition to other testing, FISH analysis was performed on both the cultured and original cancer cells to see if the probes would colocalize to the same chromosome due to a KRT14-KRT5 fusion. FISH was performed with our KRT14-20-RE and KRT5-20-GR probes which cover the entirety of the KRT14 and KRT5 genes respectively. The FISH analysis did not provide definitive evidence for fusion in the cultured cells. The experiment concluded that CRCs are a cost-effective and fast way to analyze salivary gland neoplasms for genetic and chemosensitivity studies.
Familial 3-Way Balanced Translocation Causes 1q43>qter Loss and 10q25.2>qter Gain in a Severely Affected Male Toddler
RP11-462C5 FISH Probes
The subject of this study was a 3 year-old male, born to nonconsanguineous healthy parents, who presented with various physical and developmental abnormalities, including microcephalia, premature closure of the fontanelles, midfacial hypoplasia, developmental delay, and a heart murmur. The toddler was found to have the first reported balanced chromosomal complex rearrangement involving chromosomes 1, 9 and 10, inherited from his partially affected mother. FISH probes from Empire Genomics verified the 1qter and 10qter rearrangement after microarray analysis.
FGFR1 and HER1 or HER2 co-amplification in breast cancer indicate poor prognosis
HER1, HER2, and FGFR1 are important in the progression of breast cancer. The copy number variation of HER1/2 and FGFR1 in invasive ductal breast cancer (IDC) were under study. Various FISH tests were performed including one with our FGFR1 probe. It was concluded that those with co-amplification of FGFR1 and HER1/2 faced a less favorable prognosis than those with single or no amplification of these genes.
First Case of Double T-Cell Receptor Alpha/Delta Rearrangements of t(11;14) and inv(14) and Subsequent JAK2 Rearrangement in a Patient with T-Cell Acute Lymphoblastic Leukemia
JAK2 Break Apart Probe
T-cell acute lymphoblastic leukemia (T-ALL) is characterized by translocations of oncogenic transcription factor genes and T-cell receptor loci. These rearrangements are generally mutually exclusive, and found only in certain genetic subtypes of the disease. This study reported the first case of T-ALL with distinct and rare abnormalities of sequential TCR alpha/delta (TRA/D) locus rearrangements associated with t(11;14)(p13;q11.2), inv(14)(q11.2q32), and clonal evolution of JAK2 rearrangement. Empire Genomics’ JAK2 break-apart probe was used to detect JAK2 translocations, revealing a t(8;9)(p22;p24) rearrangement. As the patient tested negative for JAK2 rearrangements at diagnosis, the translocation must have developed with disease progression. The researchers recommend follow-up cytogenetic evaluations and supporting tests, specifically FISH, to monitor cytogenetic clonal evolution in cancer patients.
Functional analysis and fine mapping of the 9p22.2 ovarian cancer susceptibility locus
RPCL11-185E1 FISH Probes
This experiment assesses the biological mechanisms at a specific chromosome locus (9p22.2) relating to the risk associated with ovarian cancer. Part of this analysis included our BAC clones which were used as a template in PCR in addition to being digested by EcoR1. The experiment concluded that the 9p22.2 locus is susceptible for ovarian cancer mechanisms and can likely be mediated by changing parts of the transcriptional regulatory network.
Gastric Perivascular Epithelioid Cell Tumor (PEComa): A Morphologic, Immunohistochemical, and Molecular Study Cell Tumor (PEComa)
TFE3 FISH Probes
Gastric Perivascular epithelioid cell tumor (PEComa) is an extremely rare tumor type - at the time of the study, only 7 cases had been reported so far. In this study, 2 new cases of PEComa were histologically and cytogenetically analyzed. In light of a recent study on a case of PEComa that harbored TFE3 fusion (and also exhibited unique features not typical of conventional PEComa), the tumors were screened for TFE3 rearrangements using Empire Genomics' TFE3 break-apart probe. Neither of the tumors were found to display TFE3 translocations.
Generation of gene-corrected iPSC line from Parkinson's disease patient iPSC line with alpha-SNCA A53T mutation
RP11-458H10 FISH Probes
Parkinson's Disease is one of the most common age-related neurodegenerative disorders, with one cause identified as a mutation in alpha-synuclein (α-SNCA). Induced pluripotenet stem cells (iPSCs) were used to generate α-SNCA with an A53T mutation. One of our BAC clones containing the α-SNCA gene was modified with recombineering. The BAC containing the normal α-SNCA successfully corrected the iPSC's α-SNCA mutation. The iPSC following the correction was found to have normal karyotype and pluripotency.
Genetic rearrangements, hotspot mutations, and microRNA expression in the progression of metastatic adenoid cystic carcinoma of the salivary gland
MYB Break Apart Probe
Adenoid cystic carcinoma (ACC) is a common salivary gland malignancy. The malignancy is associated with gene fusions between MYB, MYBL1, and NFIB. FISH analysis was used to evaluate any rearrangements in these genes with the use of our break apart probes. It was found through FISH that MYB aberrations were preserved between primary tumors and metastases. Additionally, MYB and NFIB aberrations are preserved in ACC metastatic lesions.
Genomic Analyses Identify Recurrent Alterations in Immune Evasion Genes in Diffuse Large B-Cell Lymphoma, Leg Type
Con 9 FISH Probes
Diffuse large B-cell lymphoma (DLBCL) is a form of lymphoma with a poor prognosis. The genetics of DLBCL were under analysis. One focus of the experiment was the presence of a PD-L1/PD-L2 aberration. FISH analysis was used with our PD-L1 and PD-L2 probes to look for translocations of these genes. This translocation was present in 40% of DLBCL-LT (leg type) samples. The presence of this translocation as well as associated over expression in some of the samples suggest novel therapeutic approaches for DLBCL-LT.
Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma
RPCI11-98K7 FISH Probes
Olfactory neuroblastoma (ONB) is a rare malignant tumor that forms in the nasal cavity. ONB was subjected to genome sequencing in order to better understand its genomic landscape. FISH analysis was used with our probe from BAC clone RPCI11-98K7 for the DMD gene. It was found that deletions involving DMD were present in 86% of tumors.
Genomic changes of chromosomes 8p23.1 and 1q21: Novel mutations in malignant mesothelioma
RP11-161B1 FISH Probes
Genomic hybridization was done on a series of cases of peritoneal mesothelioma, an aggressive malignancy that can be lethal. To study the genome, array-comparative genomic hybridization (a-CGH) was done as well as FISH analysis. Two of our BAC clones were used in FISH to identify the 8p23.1 and 1q21 genes. The study concluded that proteins coded by these genes lose function, which could contribute to the progression of mesothelioma.
Genomic Fusions in Pigmented Spindle Cell Nevus of Reed
Pigmented spindle cell nevus (PSCN) of Reed is a type of Spitz nevus that can be difficult to diagnose. It is thought that gene fusions could be the basis of PSCN. The molecular characteristics of PSCN was under study with the use of RNA-sequencing and FISH. FISH analysis was performed with our MERTK and PITX3 fusion probes among other FISH tests. It was found that the majority of PSCN of Reed cases are the result of gene fusions, with the most frequent fusion involving NTRK3.
Genomic Profiling of Primary Histiocytic Sarcoma Reveals Two Molecular Subgroups
BRAF Break Apart Probe
Histiocytic sarcoma (HS) is a rare and aggressive malignant neoplasm, occurring predominantly in adulthood. Sites of involvement may be nodal or extranodal, and include the gastrointestinal (GI) tract, skin and liver. In. this study, 21 cases of HS were analyzed using RNA sequencing, whole exome sequencing, and FISH. RP11 BAC clones from Empire Genomics were used to detect NF1 (RP11-142O6) and PTNP11 (RP11-748H13, RP11-9P8, RP11-90F3, RP11-660M3). Additionally, BRAF translocations were identified using our BRAF break-apart probe, and our Con 9 and Con 12 control probes were used to verify the location of CDKN2A and PTNP11, respectively. The team found a high number of abnormalities within the RAS-RAF-MAPK pathway in all 21 cases, with aberrations in NF1 (6/21), MAP2K1 (5/21), PTPN11 (4/21), BRAF (4/21), KRAS (4/21), NRAS (1/21) and LZTR1 (1/21), including single cases with homozygous deletion of NF1, high-level amplification of PTPN11 and a novel TTYH3- BRAF fusion.
GLIS Rearrangement is a Genomic Hallmark of Hyalinizing Trabecular Tumor of the Thyroid Gland
The thyroid hyalinizing trabecular tumor (HTT) was analyzed by sequencing its genome in order to better understand its genetic effects. The study found that PAX8 and GLIS3 genes fused together in the tumors, and some PAX8 and GLIS1 fusion also occurred. This fusion was identified using FISH probes. HTT differs from papillary thyroid carcinoma in that the latter does not show the same gene fusion.
Hematopoietic neoplasms with 9p24/JAK2 rearrangement: a multicenter study
Hematopoietic neoplasms and genetic aberrations related to the JAK2 gene were under study, with one purpose of the study being to look for any PCM1-JAK2 fusions. FISH analysis was done including the use of our PCM1-JAK2 fusion fish probe. The two cases under study with this probe both had the fusion present. In concurrence with other experimental results, it is suggested that cases with t(8;9)(p22;p24) could be assumed to have JAK2 rearrangement, most likely with PCM1.
Heterozygous deletion of SCN2A and SCN3A in a patient with autism spectrum disorder and Tourette syndrome: a case report
RP11-150F4 FISH Probes
There is a potential susceptibility for autism spectrum disorders at the chromosomal locus 2q, which encompasses SCN1A, SCN2A and SCN3A genes. A case study was looked at of a patient with both autism and Tourette syndrome. FISH analysis was used with our RP11-150F4 probe to confirm deletion at 2q24.3. It was concluded that there is an association of SCN2A, SCN3A, GRB14, COBLL1 and SCL38A11 deletions with autism spectrum disorders and Tourette syndrome, with possible implication for treatment.
Histological and molecular characterization of TFEB-rearranged renal cell carcinomas
TFEB Break Apart Probe
Renal cell carcinomas (RCC) have different effects and can be distinguished based on their genes. The focus of this investigation was the TFEB gene. TFEB-rearranged RCC's tend to be less aggressive than TFEB-amplified RCC's, so it's important to differentiate the two. TFEB split or amplification was analysed using our TFEB break apart probe. FISH analysis remains the most effective way to detect TFEB rearrangements.
Human Papillomavirus-Related Multiphenotypic Sinonasal Carcinoma: A Case Report Documenting the Potential for Very Late Tumor Recurrence
MYB Break Apart Probe
Human papillomavirus (HPV)-related multiphenotypic sinonasal carcinoma (HMSC) is a tumor of the sinonasal tract with a wide morphologic spectrum. A case study of HMSC was under analysis to contribute more information about it to the literature. In addition to other analyses, FISH was done with our MYB break apart probe. It was concluded that HMSC tumors can have a long-term recurrence as well as indolent behavior.
Hydropic leiomyoma: a distinct variant of leiomyoma closely related to HMGA2 overexpression
HMGA2 Break Apart Probe
Hydropic leiomyoma (HLM) is a type of uterine leiomyoma characterized by nodule or cord-like tumors among other features like increased vascularity. Not much is known about HLM, making diagnosis more difficult. Cyto-histologic, immunohistochemical profile, and molecular alterations in the HMGA2 gene were under study in order to better understand HLM. FISH analysis was used with our HMGA2 break apart probe to assess any possible gene rearrangements and copy numbers. It was concluded with the help of FISH that HMGA2 overexpression is a likely indicator of HLM.
Hydroxysteroid 11-Beta Dehydrogenase 1 Overexpression with Copy-Number Gain and Missense Mutations in Primary Gastrointestinal Stromal Tumors
Con 1 FISH Probes
Progression in gastrointestinal stromal tumors (GISTs) is associated with upregulation of the HSD11B1 gene. Various forms of analysis were used to correlate the characteristics of HSD11B1 in GISTs with clinical findings. One test included FISH analysis, which was performed to understand the copy numbers present. FISH analysis was performed with various probes, including our chromosome 1 control probe. It was concluded that HSD11B1 has oncogenic potential, with aberrations in the gene possibly causing more aggressive behavior in GISTs.
Identification of two 14q32 deletions involving DICER1 associated with the development of DICER1-related tumors
RP11-26J5 FISH Probes
Mutations in DICER1 can increase predisposition to certain cancers. Clinical findings were analyzed in patients with 14q32 deletions that encompass the DICER1 locus. Metaphase FISH probes were used to identify the 14q32 band. Presence of the deletion was correlated with increased risk for developing DICER1 tumors.
Immune checkpoint blockade as a potential therapeutic strategy for undifferentiated malignancies
CD274 (PD-L1) FISH Probes
Undifferentiated malignancies (UMs) are a set of aggressive tumors that pose a challenge both diagnostically and clinically due to poor cell lineage differentiation. It is thought that UMs are likely to be affected by checkpoint inhibitors. To predict the responsiveness of checkpoint inhibitors, aberrations in PD-L1 and chromosomal 9p24.1/PD-L1/PD-L2 can be analyzed. FISH analysis was performed with our PD-L1, PD-L2 and chromosome 9 centromere probes. The results showed that many UMs express PD-L1 aberration. Additionally, UMs may be sensitive to checkpoint inhibitors which suggests treatment options.
Intragenic CNTN4 copy number variants associated with a spectrum of neurobehavioral phenotypes
RP11-51F24 FISH Probes
CNTN4 gene deletions and duplications have been reported in children with autism spectrum disorder (ASD) and other neurodevelopmental conditions. In this study, three unrelated patients with CNTN4 copy number variations were genetically and clinically characterized. Empire Genomics’ RP11-51F24 FISH probe was used to confirm deletion of CNTN4 in the single patient bearing loss of the gene. Patients exhibited cognitive delay (3/3), growth restriction (3/3), motor delay (2/3), speech delay, and febrile seizure/epilepsy (2/3), but none were diagnosed with ASD. Parental screening indicates a pattern of inheritance originating with unaffected fathers. Results both point to CNTN4 as a potential regulator of language development and call for further evaluation of affected individuals via comprehensive phenotyping and molecular characterization in order to achieve a better understanding of the underlying mechanisms of reduced penetrance and variable expressivity of CNTN4 CNVs.
Intragenic duplication of KCNQ5 gene results in aberrant splicing leading to a premature termination codon in a patient with intellectual disability
RP11 BAC Clone (not specified) FISH Probes
Mutations in the KCNQ2 and KCNQ3 genes have been shown to cause harmful neurological effects on humans. Therefore, it is thought that KCNQ5 mutations could also cause harmful effects. FISH anaysis was used with one of our BAC clones in addition to molecular karyotyping. It was concluded that a new case of intellectual disability and absence epilepsy was determined from duplication of the KCNQ5 gene.
JAK2 double minutes with resultant simultaneous amplification of JAK2 and CD274 in a therapy-related myelodysplastic syndrome evolving into an acute myeloid leukaemia
JAK2 FISH Probes
Amplification with double minutes (DM) of the JAK2 gene could potentially accelerate the progression of leukemia. FISH analysis was used in conjunction with SNP microarray to observe the effects of the amplification. FISH was performed using our JAK2 probe, showing multiple copies of JAK2 residing on the DMs. It was concluded that amplification of JAK2 could indeed contribute to progression of the disease.
Lineage-specific RUNX2 super-enhancer activates MYC and promotes the development of blastic plasmacytoid dendritic cell neoplasm
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a particularly aggressive type of acute leukemia thought to originate in plasmocytoid dendritic cells (pDCs). BPDCN patients display significantly higher levels of RUNX2 compared to patients with other types of leukemia. BPDCN cells have been found to harbor super-enhancers of RUNX2, which contribute majorly to the development of pDCs. Because MYC translocations are also a recurrent feature of BPDCN, researchers wanted to determine whether the RUNX2 super-enhancer promoted abnormal MYC expression. Empire Genomics' RUNX2 probe was used to verify the presence of the gene. Results indicated that the RUNX2 super-enhancer does in fact upregulate MYC and RUNX2 expression, via MYC translocations, thereby promoting the development of BPDCN.
LobSig is a multigene predictor of outcome in invasive lobular carcinoma
Invasive lobular carcinoma (ILC) is the most common special type of breast cancer. It’s defined by functional loss of E-cadherin, which results in cellular adhesion defects. ILC’s clinical presentation is generally estrogen receptor positive, grade 2 breast cancer, with a promising short-term prognosis. This study sought to further characterize ILC’s genetic profile via analysis of 196 tumors. Using in silico integrative analyses, a 194-gene set – named ‘LobSig’ by the team – was identified, made up of genes frequently mutated in the tumor samples. LobSig was tested against the Nottingham Prognostic Index, PAM50 risk-of-recurrence (Prosigna), OncotypeDx, and Genomic Grade Index (MapQuantDx) for a 10-year follow-up period, and outperformed them all. As part of genetic profiling, Empire Genomics’ FGFR1 And CCND1 genes were used to detect amplifications. All tumors were found to display multiple signals for the genes, verifying their identity as biomarkers for ILC.
Loss of DMRT1 gene in a Mos 45,XY,-9[8]/46,XY,r(9)[29]/47,XY,+idic r(9)x2[1]/46,XY,idic r(9)[1]/46,XY[1] female presenting with short stature
A 46,XY sex reversal syndrome is characterized genetically by aberrations in chromosome 9pter due to involvement of the DMRT1 gene. A case study was under analysis to better understand the syndrome. FISH analysis was used with our DMRT1 gene probe. It was found that sex reversal can be due to haploinsufficiency of the DMRT1 gene in ring chromosome 9, although it is rare. This finding highlights the importance of the DMRT1 gene in sex determination.
Metastasizing Pleomorphic Adenoma: Recurrent PLAG1/HMGA2 Rearrangements and Identification of a Novel HMGA2-TMTC2 Fusion
PLAG1 Break Apart Probe
Pleomorphic adenoma, the most common salivary gland neoplasm, is considered a benign tumor. However, PA can undergo malignant transformation, and cases of metastasis to lymph nodes and distant body sites are well documented. There is a lack of research on genetic characterization of metastasizing versus benign PA. In this study, four cases of metastasizing PAs were cytogenetically profiled using both RNA sequencing and FISH. PLAG1 and HMGA2 break-apart probes from Empire Genomics were used to confirm rearrangements of the genes, including a novel HMGA2-TMTC2 translocation in one patient. PLAG1 rearrangements were detected in all four cases. Results demonstrated that MPA harbors the same disease-defining molecular hallmarks as their benign counterparts.
Method for the Prognosis of Multiple Myeloma
CD36 FISH Probes
Multiple myeloma is the second most common hematological malignancy, characterized by uncontrolled clonal proliferation of B-lymphocytes in the bone marrow. The disease is still considered, for the most part, incurable, although survival rates have improved significantly in the past decade. Standard treatment for MM is currently chemotherapy accompanied by autologous stem cell transplantation (ASCT). This patent aims to identify genetic biomarkers specific to MM that could serve as potential prognostic indicators. Currently, the expression of some CD markers have already been shown to have prognostic value in MM, leading to the development of anti-CD monoclonal antibodies for treatment of the disease. These drugs have demonstrated anti-tumor activity in clinical trials. This patent proposes using gene expression values of four CD markers - CD24, CD27, CD36 and CD302 – to predict clinical outcome in MM. The team suggests Empire Genomics’ CD36 and CD302 FISH probes for detection of these genes.
Methods of cell renewal
RP11-117B23 FISH Probes
A patent was proposed for a method of cell renewal in which cells are rejuvenated by improving their replication and differentiation capacity. Several of our BAC clones were used to span gene regions critical to developing the technology.
MicroRNA dysregulation in adenoid cystic carcinoma of the salivary gland in relation to prognosis and gene fusion status: a cohort study
MYBL1 Break Apart Probe
Adenoid cystic carcinoma (ACC) is a frequent malignancy of the salivary gland that is challenging due to an unpredictable clinical course. In hopes of improving this predictability, the association of microRNA with prognostic value in ACC is under study. Along with microRNA tests, FISH analysis was performed with various break apart probes, including our MYLB1 and NFIB probes, to look for any fusion or rearrangement. It was found that several microRNAs were associated with the outcome of ACC and that the most unifying feature of ACC is still involvement of the MYB gene.
Molecular Diagnostics in Pediatric Cytopathology
Compared to adult neoplasms, only a small portion of pediatric tumors display large epithelioid morphology, including certain salivary gland, thyroid, hepatic, and head and neck tumors. FISH testing can be used to elucidate the identity of these cancers in pediatric and adolescent patients, as many of these tumor types harbor characteristic translocations. One of the cases in this book involved FISH analysis of an 18-year-old boy’s parotid gland lesion. Empire Genomics’ PLAG1 dual-color break-apart probe was used to test for PLAG1 gene rearrangements. Results were positive, clarifying the tumor’s identity as pleomorphic adenoma or benign mixed tumor.
Molecular features of adenoid cystic carcinoma with an emphasis on microRNA expression
MYBL1 Break Apart Probe
Adenoid cystic carcinoma (ACC) is a subtype of salivary gland tumor that can have a poor prognosis. ACC can also be present in lacrimal glands and the breasts with the tumors appearing to be seemingly identical to one another. The phenotypes, genetics, and microRNA expression of ACC in the salivary glands, lacrimal glands, and breasts was characterized in order to better understand the differences between them. Among other characterization tools, FISH analysis was performed with several break apart probes, including our MYBL1 and NFIB probes. The results seemed to indicate that microRNA has value in distinguishing between the tumors.
Mosaicism of XX and XXY cells accounts for high copy number of Toll like Receptor 7 and 8 genes in peripheral blood of men with Rheumatoid Arthritis
TLR7 FISH Probes
In BXSB murine lupus, extra copies of the X-linked TLR7 gene have been shown to aggravate autoimmunity in male mice. Researchers sought to investigate this trend in human males with rheumatoid arthritis (RA), finding that patients had significantly higher copy numbers of TLR7. Empire Genomics’ TLR7, Control X and Control Y probes were used to detect TLR7 copy number, and Chromosome X and Y aneuploidy, respectively. Patients were also found to have substantial cellular mosaicism of female (46,XX) and/or Klinefelter (47,XXY) cells among male (46,XY) cells, reaching up to 1.4% in peripheral blood. Results present a potential new trigger for RA in men and open a new field of investigation into gender-biased autoimmune diseases.
Mutational and copy number asset of primary sporadic neuroendocrine tumors of the small intestine
Small intestine neuroendocrine tumors (SI-NETs) are a common type of small-intestine neoplasm. The SRC gene was under analysis to determine a link between aberrations in the gene and SI-NET prognosis. Copy number variations were analyzed with FISH testing. FISH analysis was performed with our SRC gene specific probe along with a chromosome 20 control probe. It was found that gains in SRC gene copy number were associated with a poorer prognosis.
MYB rearrangement and immunohistochemical expression in adenomyoepithelioma of the breast: a comparison with adenoid cystic carcinoma
MYB Break Apart Probe
Adenomyoepithelioma (AME) and adenoid cystic carcinoma (ACC) often occur simultaneously, suggesting that AME may be a related or precursor lesion to ACC. MYB gene rearrangements are frequently reported with ACC. Therefore, the rates of MYB rearrangement were compared between AME and ACC. Translocation of the MYB gene was detected by using FISH analysis with our MYB break apart probe. It was concluded that AMEs do not have MYB gene rearrangement.
MYC amplification in subtypes of breast cancers in African American women
Chromosome 8 Centromere FISH Probes
Overexpression of the MYC gene can have a poor prognosis in breast tumors. This MYC overexpression was characterized in African American women to determine any relations to clinico-pathological characteristics. As part of understanding the MYC amplification, FISH analysis was performed with our centromere 8 probe. This FISH test helped to determine how many MYC signals occurred per chromosome 8 signal. A relationship was found between HER2 and MYC amplification, the ratios suggesting that MYC drives HER2 amplification.
Myeloproliferative neoplasm with ABL1/ETV6 rearrangement mimics chronic myeloid leukemia and responds to tyrosine kinase inhibitors
Myeloproliferative neoplasms (MPN) are a type of cancer in the blood. One specific kind of the cancer involves a fusion of ABL1-ETV6 genes, which is very rare and has not yet been closely characterized cytogenetically. FISH analysis was done on bone marrow cultures, including one test with our ABL1-ETV6 fusion probe. This helped in identifying that the culture had the ABL1-ETV6 fusion and was the correct type of MPN cancer for analysis. It was concluded that subjects with the ABL1-ETV6 fusion of MPN could be more sensitive to tyrosine kinase inhibitor (TKI) therapy.
Next-Generation Sequencing to Detect Deletion of RB1 and ERBB4 Genes in Chromophobe Renal Cell Carcinoma: A Potential Role in Distinguishing Chromophobe Renal Cell Carcinoma from Renal Oncocytoma
RP11-893E5 FISH Probes
Chromophobe renal cell carcinoma (ChRCC) and renal oncocytoma (RO) are two tumors that are difficult to distinguish from one another. It is important to distinguish them because ChRCC is a malignant tumor whereas RO is a benign tumor. Deletion of the RB1 and ERBB4 genes are indicative of ChRCC because these are tumor-suppressant genes. FISH analysis was used to identify these deletions. Our dual color probes were used that targeted RB1-Orange (MAC clone RP11-893E5) and 13q11-Green (RP11-408E5). A green ERBB4 probe was also used.
Novel 1.3 Mb germline duplication in chromosome 8q21.11 by microarray comparative genomic hybridization?plus single nucleotide polymorphism analysis in an adult patient with pancytopenia and urinary bladder complications
RP11-846M12 FISH Probes
A case of a 30-year-old woman was assessed. She has had a history of medical problems relating to perinatal complications, pancytopenia, and bladder/urinary diseases throughout her life. Cytogenetic analysis was done on a sample of her bone marrow to try and better understand her complications. One of our BAC probes was used for FISH analysis to confirm the results of microarray comparative genomic hybridization (aCGH). The aCGH and FISH confirmed a novel duplication at chromosome 8q21.11 encompassing the CASC9 and HNF4G genes.
Oncogene Amplification in Growth Factor Signaling Pathways Renders Cancers Dependent on Membrane Lipid Remodeling
Plasma membrane remodeling is a mechanism that cancer cells have been shown to employ in order to increase nutrient uptake and oncogenic signaling of cancerous cells. This propels tumorigenesis via heightened intercellular communication and quickened cell growth. In this study, researchers identified the LPCAT1 gene as a driver of plasma membrane rearrangement, finding that growth factor receptor-driven cancers rely heavily on the gene to reshape cell membranes through enhanced saturated phosphatidylcholine content, which is required for oncogenic signal transduction. Genomic analysis of publicly available cancer sequencing databases of clinical samples and the cancer cell line encyclopedia (CCLE) revealed that LPCAT1 copy number was increased in over 30% of pan-cancer patients and some of the most aggressive cancers, including lung adenocarcinoma and squamous carcinoma, ovarian cancers, bladder cancers, and invasive breast cancers. This discovery was made possible by Empire Genomics’ LPCAT1 FISH probe, which was used to detect amplification of the gene.
PD-L1 gene alterations identify a subset of diffuse large B-cell lymphoma harboring a T cell-inflamed phenotype
PD-L1 FISH Probes
Tumor cells frequently display programmed death ligand 1 (PD-L1) and 2 (PD-L2) to trick T-cells into ignoring them, thereby evading detection and destruction. In classical Hodgkin lymphoma, malignant cells have been found to upregulate PD-L1 expression via copy gains in the 9p24.1 chromosomal region that house the PD-1 gene, which codes for the PD-L1 and PD-L2 ligands. Researchers sought to determine whether this same mechanism is used by cancer cells in diffuse large B-cell lymphoma (DLCBCL), and to what extend PD-L1 is overexpressed in the malignancy. Empire Genomics’ PDL1 and PDL2 break-apart probes were used to test for aberrations in the gene. Of the 105 DLBCL cases analyzed, 27% were found to have PD-L1 alterations. Patients with abnormal PD-L1 expression were also found to have poorer progression-free survival time.
PD-L1 over-expression is driven by B-cell receptor signaling in diffuse large B-cell lymphoma
PD-L1 FISH Probes
PD-L1 has been found to be expressed in a subset of diffuse large B-cell lymphoma (DLBCL) cases, mainly activated B-cell-like (ABC) and non-germinal center B-cell-like (non-GCB). B-cell receptor (BCR), a receptor protein found on the outer surface of B-cells, is expressed on normal mature B-cells and their neoplastic counterparts. Studies have shown that BCR stabilizes and promotes MYC expression in DLBCL. As MYC can directly bind the PD-L1 promoter, the team hypothesized that PD-L1 expression is regulated by BCR via amplified MYC expression. The team investigated this potential relationship using qPCR, immunoblotting and flow cytometry in DLBCL cell lines. PD-L1 amplification was detected using FISH, including Empire Genomics’ PD-L1 break-apart probe. Based on these analyses, it was found that BCR signaling does in fact regulate PD-L1 via increasing MYC expression.
Pediatric acute myeloid leukemia with t(7;21)(p22;q22)
RUNX1-USP42 Break Apart Probe
RUNX1-USP42 gene fusion has been present in cases of both acute myeloid leukemia and myelodysplastic syndromes. The clinical features of RUNX1-USP42 are not as well understood as the fusion of RUNX1 with other genes. FISH analysis was used with the RUNX1 break apart and RUNX1-USP42 translocation probe. It was concluded that RUNX1-USP42 fusion is a rare occurence in acute myeloid leukemia and can result in unusual expression of CD56 and CD7.
Plasmacytoid cells in salivary pleomorphic adenoma. An alternative interpretation of their immunohistochemical characteristics highlights function and capability for epithelial-mesenchymal transition
PLAG1 Break Apart Probe
Salivary pleomporphic adenoma (SPA) is a rare benign tumor of the palate that makes up about 1% of salivary gland tumors. SPA masses are composed of plasymocytoid cells (PLC’s). These cells can be difficult to identify because they fail to display distinct immunohistochemical or structural characteristics, which makes diagnosing SPA tricky. This study sought to analyze PLC’s by testing for both epithelial-mesenchymal transition (whereby stationary epithelial cells transform into migrating mesenchymal cells that can potentially contribute to tumorigenesis) and rearrangements of the PLAG1 gene, which are found in about 39% of pleomorphic adenomas. Empire Genomics’ break-apart PLAG1 FISH probe was used to test for PLAG1 translocations. Of the three tumors tested, one contained a PLAG1 translocation. Researchers concluded that PLC’s generally don’t express myoepethelial markers but are neoplastic cells with distinct adaptive capabilities related to abnormal cell growth and differentiation.
Poor prognostic impact of FGF4 amplification in patients with esophageal squamous cell carcinoma
FGF4 FISH Probes
Esophageal squamous cell carcinoma (ESCC) is one of the most common types of esophageal cancer and has a poor prognosis. The FGF4 gene was analyzed to determine the prognostic impact and clinicopathological features associated with amplification. FISH analysis was used with our FGF4 probe to detect the amplification status of the gene. It was found that those with the FGF4 amplification showed a significantly shorter disease-free and overall survival compared to those without the amplification. Therefore, the presence or absence of FGF4 amplification can be used to give patients a predictor for how much longer they can expect to live.
Primary mammary analogue secretory carcinoma of the lung: a case report
ETV6 Break Apart Probe
Mammary analogue secretory carcinoma (MASC) is a type of salivary gland tumor. A rearrangement in the ETV6 gene can be characteristic of MASC, particularly fusion of ETV6-NTRK3. Our dual-color break apart probe was used to detect ETV6 translocation and aid in the diagnosis of MASC for the patient?s tumor.
Prospective longitudinal overnight video-EEG evaluation in Phelan–McDermid Syndrome
RP11-1058B20 FISH Probes
Phelan–McDermid Syndrome (PMS) is a rare condition associated with intellectual disability, autism spectrum disorder, and seizures. It can be identified by deletions in the 22q13 chromosome region. The focus of this study was the analysis of electroencephalograms (EEG) during sleep to identify abnormalities. Additionally, FISH analysis was performed with our RP11-1058B20 probe that targets the 22q11.21 chromosome region. The results from FISH confirmed that the patients under study had the deletion associated with PMS. The study concluded that EEG improved the identification of epileptiform abnormalities in the PMS patients, and that EEG should continue to be used on PMS patients.
PTEN self-regulates through USP11 via the PI3K-FOXO pathway to stabilize tumor suppression
PTEN/Con 10 FISH Probes
PTEN is a liquid phosphate that can act as a dose-dependent tumor suppressor. Its stability and regulation were under study. FISH analysis was done with our PTEN/Con 10 probe. It was found with FISH that over 80% of patients had two copies of PTEN. The experiment concluded that PTEN-PI3K-FOXO-USP11 make up a regulatory loop that assists with the stability and tumor-suppressant ability of PTEN.
PUMILIO hyperactivity drives premature aging of Norad-deficient mice
Mouse Chromosomes 2 & 16 FISH Probes
The conserved long noncoding RNA (IncRNA) Norad is a powerful negative regulator of the PUMILIO family of proteins, which are known to target mRNAs important to mitosis, DNA repair, and DNA replication. Therefore, loss of Norad results in extreme genomic instability. While previous studies on cell lines showed that NORAD loss or PUMILIO upregulation generates genomic breakdown, the consequences of mammalian PUMILIO hyperactivity in vivo hadn’t yet been evaluated. In this study, the physiological function of Norad was analyzed in vivo in mice. Absence of Norad was found to repress key genes required for mitosis and mitochondrial function. Empire Genomics’ Mouse Idetect FISH Probes for Chromosomes 2 and 16 were used to detect aneuploidy in order to determine whether loss of Norad would result in abnormal chromosome number in lymphocytes, splenocytes, and primary MEFs. Aneuploidy rates were found to significantly increase in all 3 cell types for Norad-negative mice, a primary indicator of genomic instability.
Rare gene fusion rearrangement SPTNB1-PDGFRB in an atypical myeloproliferative neoplasm
RP11-378O10 FISH Probes
Myeloid neoplasms and acute leukemia can take on different forms based on their specific gene rearrangement. A rare case was under study having a PDGFRB rearrangement with SPTNB1. Only one previous report had determined a SPTNB1/PDGFRB fusion. FISH analysis was used with two of our BAC probes that span a region containing the SPTBN1 gene to see if there is any sign of fusion. The FISH analysis did show a rearrangement of SPTNB1/PDGFRB, making it the second documented report of this type of cancer.
Recurrent rearrangements of the PLAG1 and HMGA2 genes in lacrimal gland pleomorphic adenoma and carcinoma ex pleomorphic adenoma
PLAG1 Break Apart Probe
Lacrimal gland tumors are histologically similar to salivary gland tumors. In the salivary glands, pleomorphic adenoma (PA) and carcinoma ex pleomorphic adenoma (ca_ex_PA) are both characterized by PLAG1 and HMGA2 gene rearrangements. However, it is not known if these rearrangements are present in lacrimal gland PA and ca_ex_PA. FISH analysis was done with our PLAG1, HMGA2, and NFIB break apart probes. It was found that rearrangements were frequent in the tested lacrimal glands and that testing for the rearrangement can help in distinguishing lacrimal gland PA and ca_ex_PA from de novo carcinomas.
Renal cell tumors with an entrapped papillary component: a collision with predilection for oncocytic tumors
RP11- 572 M14 FISH Probes
Renal cell tumors with mixed morphology resembling multiple renal cell carcinoma (RCC) subtypes have historically been categorized as unclassified RCC. Sometimes, however, papillary adenoma or RCC appears admixed with a larger, different tumor histology. In this study, 17 renal tumors bearing a papillary adenoma or papillary RCC component admixed with another tumor histology were analyzed using immunohistochemistry and FISH. Empire Genomics’ RP11-572M14 FISH probe was used to detect the 3p25 gene region, as part of an effort to genetically characterize these rare admixed tumors. Eight of 15 (53%) collision tumors had differing FISH results in the two components. The team concluded that this type of tumor, with papillary renal cell proliferation within a different tumor, is a rare phenomenon with a predilection for oncocytoma and chromophobe RCC, and should be diagnosed as a collision of the two processes, not unclassified RCC.
Role of MEL-18 Amplification in Anti-HER2 Therapy of Breast Cancer
HER2 is a receptor that can trigger oncogenic signals, which can be amplified in breast cancer. Under study was the connection between amplification of the MEL-18 gene and HER2-positive breast cancer. FISH analysis was used to verify the amplification of MEL-18. Our PCGF2 FISH probe was used to monitor the number of gene copies. It was determined that amplification of MEL-18 is a unique biomarker for HER2-positive breast cancer.
Single-cell imaging reveals unexpected heterogeneity of telomerase reverse transcriptase expression across human cancer cell lines.
Telomerase, which extends DNA at chromosome ends, is composed of an RNA template and a catalytic protein subunit, telomerase reverse transcriptase (TERT). TERT gene expression has been of great interest because it's needed for cell proliferation and immortalization in 80-90% of human cancers, but expression studies have been limited due to low endogenous mRNA levels. This study addressed that lack of data by analyzing TERT expression across 10 human cancer lines using Empire Genomics’ TERT FISH probe. TERT expression was highly heterogeneous across human cancer cells, with significant differences in cellular location of the TERT protein, as well as substantial cell-to-cell variation in number of transcription sites and ratio of transcription sites to gene copies, revealing surprising complexity in TERT expression among human cancers.
Site-specific nuclease single-cell assay targeting gene regulatory elements to silence gene expression
RP11-299D5 (SAMD4A) FISH Probes
This patent is for an invention that determines the effect of chromosomal contact on transcriptional activity of genes and methods of silencing gene expression in cells by disrupting regulatory genes. Several of our DNA probes were modified with aminoallyl-dUTP and dye-labeling for FISH analysis.
Somatic deletion of KDM1A/LSD1 gene is associated to advanced colorectal cancer stages
RP11-152I19 FISH Probes
While ZNF217 amplification is well documented in colorectal cancer (CRC), the amplification status of KDM1A/LSD1 in any cancer type is, so far, unknown. The aim of this study was to evaluate gene copy number variation in KDM1A/LSD1 and ZNF217 and its association with clinicopathological features in CRC. Empire Genomics’ RP11-152I19 BAC clone was used to detect the KDM1A/LSD1 gene in tumor samples from 50 CRC patients. KDM1A/LSD1 deletion was present in in 19 samples (38%), and ZNF217 amplification in 11 samples (22%). The team also found a significant association between lymph node metastasis or advanced tumor stage and KDM1A/LSD1 gene deletion, concluding that loss of KDM1A/LSD1 could serve as a novel prognostic biomarker of late-stage CRC.
Spindle cell rhabdomyosarcoma in a lumbar vertebra with FUS-TFCP2 fusion
A 70 year old woman who presented with intense buttock pain that developed into a walking impairment was found to have an osteoloytic lesion in her spine, along with severe osteosclerosis. Histological and immunoreactivity analysis was performed first. Empire Genomics TFCP2 break-apart FISH probe was then used to test for TFCP2 fusions, and revealed a 64% frequency of split signals. This result prompted researchers to further analyze the tumor using reverse transcription PCR, which showed FUS-TFCP2 fusion. The patient’s final diagnosis was spindle cell rhabdomyosarcoma with FUS-TFCP2 fusion, an extremely rare tumor-fusion pairing. Researchers recommend further study in order to better characterize this poorly understood subtype of rhabdomyosarcoma.
Superresolution microscopy reveals linkages between ribosomal DNA on heterologous chromosomes
RP11-450E20 FISH Probes
In this study, superresolution microscopy was utilized to determine the degree of ribosomal DNA (rDNA) linkage with chromosomes, in an effort to better understand the complex spatial organization of the genome. Linkages were observed in many different human cell types during interphase, and were found to occur frequently between transcriptionally active loci. Human and mouse BAC clones (RP11-450E20 and RP23-225M6) from Empire Genomics were used to detect rDNA. The team concluded that linkages are topological intertwines that occur often between transcriptionally active rDNA in the same nucleolar compartments, suggesting that these interchromosomal connections are an important and ubiquitous aspect of genome organization.
Systemic, primary cutaneous, and breast implant-associated ALK-negative anaplastic large-cell lymphomas present similar biologic features despite distinct clinical behavior
PD-L1 FISH Probes
Systemic, primary cutaneous, and breast implant-associated ALK-negative anaplastic large cell lymphomas, although varied in their clinical traits and prognosis, display marked similarities in their histopathological presentation, like cells with horseshoe-shaped nuclei and CD30 protein expression. This study sought to cytogenetically distinguish between the conditions using immunohistochemistry and FISH to highlight each condition’s respective biomarkers, hopefully shedding light on the way said biomarkers contribute to pathogenesis. Twenty-two S-ALCL, 13 PC-ALCL, and 2 BI-ALCL were tested for genetic aberrations, including PD-L1 and TP63 translocations that were screened for using Empire Genomics’ PD-L1 and TP63 break-apart probes. PDL1 amplification was found to be the most common alteration present in the three entities.
Targeting p38α Increases DNA Damage, Chromosome Instability, and the Anti-tumoral Response to Taxanes in Breast Cancer Cells
Chromosome 17 Centromere FISH Probes
The role of protein kinase p38α in causing cancer cell death and regressing tumor growth was explored, specifically in breast cancer. FISH analysis was used in conjunction with other testing such as patient derived xenografts and immunoblotting. FISH was used with our probe to detect the chromosome 17 centromere. This led to a conclusion that p38α limits DNA replication stress and improves taxanes ability to kill breast cancer cells. There was also a correlation found between the aneuploidy in tumor cells with how well they would respond to therapy involving p38α.
The contribution of 7q33 copy number variations for intellectual disability
RP11-615F13 FISH Probes
Copy number variations in the 7q33 region have been associated with intellectual disability in patients. FISH analysis was performed with our RP11-615F13 BAC clone to help in identifying any copy number variations on chromosome 7. The results from the analysis showed that one patient had gene duplication present on chromosome 7. With the aid of other analytical methods, the duplication found with FISH was able to be confirmed.
Thrombocytopenia and Predisposition to Acute Myeloid Leukemia due to Mosaic Ring 21 with Loss of RUNX1: Cytogenetic and Molecular Characterization
21q21.1 FISH Probes
Aberrations in the RUNX1 gene have been associated with familial platelet disorder and leave the patient predisposed to acute myeloid leukemia. By analyzing the genetics of abnormal chromosomes 21, the genetic aberrations of RUNX1 can be detected. Among other forms of analysis, our 21q21.1 FISH probe was used to show that a regular chromosome 21 had one band, whereas a circular chromosome 21 had two copies of the band.
Transplanted Human Pluripotent Stem Cell-Derived Mesenchymal Stem Cells Support Liver Regeneration in Gunn Rats
Rat-specific X chromosome FISH Probes
Crigler-Najjar syndrome, a disorder of the liver, is analogous to a mutation in the Ugt1a1 gene in Gunn rats. This makes Gunn rats a good model organism in looking at Crigler Najjar synrome. FISH analysis was used with our rat-specific X chromosome probe along with a different human-specific Y chromosome probe. The FISH analysis indicated that after a liver transplant, fusion was present between the rat and human cells. It was concluded that induced mesenchymal stem cells can help contribute to liver regeneration.
TRKA expression and NTRK1 gene copy number across solid tumours
RP11-349I17 Break Apart Probe
The NTRK1 gene codes for the protein TRKA. Deregulated activity in TRKA has been shown to have oncogenic effects. The NTRK1 gene was analyzed with FISH analysis and our break apart probe. The BAC probes RP11-349I17 in orange and RP11-1038N13 in green were used.