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Epithelial ovarian cancer (EOC) is typically identified at advanced stage and usually incurable. This study analyzed 170 EOC tumors, searching for a possible link between patients’ gene profiles and survival. They were able to narrow in on KANSL1 as a master regulator of 3 key genes that monitor immune response. They found that KANSL1 alters expression of these genes through various DNA alterations, including KANSL1 amplifications, which were detected using our KANSL1 FISH probe.

Published: 02/01/2021

Related Probes: KANSL1 Fish Probe

This case study looked at a parotid gland carcinosarcoma in a 77 year old patient. Our PLAG1 and HMGA2 break apart probes were used to detect rearrangements of the genes in both the carcinomatous and sarcomatous components of his tumor, to determine whether they harbored different genetic lesions. Both components were positive for PLAG1 and negative for HMGA2 translocations.

Published: 08/20/2020

Related Probes: PLAG1 Break Apart Fish Probe

Nijmegen breakage syndrome (NBS) is a rare genetic disorder associated with an increased risk of developing lymphoproliferative malignancy. The lack of data around NBS genetics has led to limited biomarker validation and underdeveloped diagnostic protocols. This team followed a 4 year-old NBS patient, from initial diagnosis to eventual development to non-Hodgkin lymphoma, and tracked the genetic progression of his disease throughout. Our STIL break apart probe detected STIL duplication in the patient, one of the many lesions contributing to his complex karyotype.

Published: 08/20/2020

Related Probes: STIL Break Apart Fish Probe

JAK2 rearrangements are hallmarks of both Ph-Like B-cell ALL and myeloid/lymphoid neoplasms with eosinophilia and gene rearrangements (MLN-EGR). This study used our JAK2 break-apart probe to discover a new JAK2 fusion - ZBTB20/JAK2 - in a patient with B-ALL with eosinophilia. The team found that her disease originated with a JAK2-rearranged myeloid neoplasm that developed into B-ALL.

Published: 04/07/2020

Related Probes: JAK2 Break Apart Fish Probe

Cornelia de Lange syndrome (CdLS) is a disorder characterized by severe growth restriction, developmental delay, and various facial and limb structural abnormalities. In this study, an infant with CdLS was genetically analyzed using both whole-genome sequencing and FISH. Our RP11-244H11 FISH probe help detect a 1p31.2 amplification in the subject (later confirmed as inherited from her father), one of the many genetic alterations she was found to harbor.

Published: 03/03/2020

Related Probes: RP11-244H11 Fish Probe

This study investigated various components of the tumor microenvironment (TME) in medulloblastoma, one being astrocytic differentiation. Our PTCH1/Con9 probe was used to detect PTCH1 deletion in 6 cases of SHH-activated medulloblastoma, helping to confirm that astrocytes within the tumor masses shared a common lineage with tumor cells harboring the same genetic lesion.

Published: 02/06/2020

Related Probes: PTCH1 Fish Probe

PAX5 encodes a transcription factor that helps regulate B-cell development. Rearrangements of the gene have been found in several low-grade B-cell tumors, including diffuse large B-cell lymphoma (DLBCL), where it’s frequently found fused to IGH. This study examined PAX5 expression in 4 DLBCL patients harboring PAX5/IGH fusions. Our PAX5 break-apart probe was used to confirm these fusions.

Published: 01/28/2020

Related Probes: PAX5 Break Apart Fish Probe

This publication looked at 4 different ALCL subtypes to determine whether a correlation existed between several tumor microenvironment factors (PDL1 expression, FOXP3+ regulatory cell density, and CD8+ tumor-infiltrating lymphocyte density) and ALCL subtype. Our break apart probes for DUSP22/IRF4 and TP63 were used to determine which patients fell into 2 of the 4 ALCL subtypes under analysis: DUSP22/IRF-rearranged ALCL and TP63-rearranged-ALCL.

Published: 01/28/2020

Related Probes: DUSP22/IRF4 Break Apart Fish Probe

MRPS23 overexpression is linked to increased tumor cell proliferation in breast cancer. This study investigated the association between MRPS23 gene amplification and molecular subtype, tumor proliferation, and prognosis in breast cancer from two cohorts: one from the Cancer Registry of Norway, and one from the METABRIC database. Our MRPS23 FISH probe was used to detect MRPS23 amplification in the Norway cohort, which consisted of 144 BC cases. MRPS23 amplification was more prevalent in non-basal subtypes, and, as expected, correlated with tumor proliferation, but no association was found between MRPS23 amplification and prognosis.

Published: 01/16/2020

Related Probes: MRPS23 Fish Probe

This textbook – Modern Techniques in Cytopathology – references our PLAG1 break apart probe for detecting PLAG1 rearrangements in epithelial cells. The chapter focuses specifically on FISH, expanding on the different types of mutations that can be detected with FISH, including examples of several disease-specific mutations with accompanying probe recommendations.

Published: 01/13/2020

Related Probes: PLAG1 Break Apart Fish Probe

Although SIRPB1 amplification has been shown to correlate with increased aggressiveness in prostate cancer, the gene’s role in tumor development is still unclear. This study analyzed SIRPB1 amplification in 20 prostate adenocarcinomas using our SIRPB1 probe. The team also used several public prostate cancer data sets to compare SIRBP1 CNVs to clinical outcome in 5170 available samples. Results suggest that the gene plays an important growth-stimulatory role in prostate cancer progression.

Published: 01/06/2020

Related Probes: SIRPB1 Fish Probe

Ependymomas are rare and aggressive neuroepithelial tumors that are challenging to classify. Recent studies propose a multivariate classification system based on several factors including copy number variants (CNVs). Chr 22 loss and chr 5p15.31 gains are two common CNVs in ependymomas. Our C5orf49 probe and Chromsome 5 control probe were used to detect 5p15.31 amplification in 13 intracranial grade II and III ependymomas. Chr 15p15.31 gains were reported in 85% and chr 22 losses in 46% of patients.

Published: 01/01/2020

Related Probes: C5orf49 Fish Probe

Compared to adult renal cell carcinoma (RCC), pediatric and young adult RCC is fairly rare and poorly characterized. This team wanted to explore the genetic, molecular, and clinical spectrum of childhood and young adult RCC. They analyzed 68 RCC patients, all age 30 years or younger, using IHC and FISH. Our TFE3 and TFEB break apart FISH probes were used to detect rearrangements of the genes in cases that were morphologically suspicious for TFE3/TFEB translocations.

Published: 12/23/2019

Related Probes: TFEB Break Apart Fish Probe

This study examined the potential utility of the YE361 STAT6A monoclonal antibody for differentiating Hodgkin from non-Hodgkin lymphoma. The team assessed over 100 HL and non-HL biopsies using STAT6A immunohistostaining. Whole exome sequencing was performed on 2 STAT6A-positive cases to detect mutations in STAT6A pathway genes. Empire Genomics’ PD-L1 FISH probe was also used to determine the degree of PD-L1 amplification in one patient, who’d originally been diagnosed with classical HL but relapsed 4 years later with gray zone lymphoma. Interestingly, both the original and relapsed biopsy were negative for STAT6A, but PD-L1 amplification was found in both, suggesting that PD-L1 amplification occurs independently of upstream STAT6A activation.

Published: 12/10/2019

Related Probes: PD-L1 Fish Probe

Primary central nervous system diffuse large B cell lymphoma (PCNS-DLBCL) is a particularly aggressive DLBCL subtype, generally restricted to the brain, spinal cord, leptomeninges, or eyes. Its confinement to the CNS suggests that the tumor microenvironment (TME) might contribute to its aggressive behavior, and the PD-1/PD-L1 immune checkpoint could serve as a possible therapeutic target. This team investigated both the PD-1/PD-L1 checkpoint and the composition of the TME in 57 PCNS-DLBCs using IHC and FISH. Our PD-L1 break apart probe was used to detect PD-L1 rearrangements.

Published: 12/06/2019

Related Probes: PD-L1 Break Apart Fish Probe

This PhD thesis investigated ABCB6, a widely expressed transporter protein that’s been implicated in various cancers, where it’s associated with multidrug resistance. The student used Empire Genomics’ ABCB6 FISH probe to facilitate her research into the genetics of the ABCB6 gene, one of the many topics discussed in this paper.

Published: 12/01/2019

Related Probes: ABCB6 Fish Probe

Mutations in the LRKK2 gene are characteristic of autosomal dominant Parkinson's disease. In this study, a BAC-based homologous recombination system was used for gene therapy of LRKK2 GD2019S-mutant induced pluripotent stem cells. Our LRKK2 FISH probe was used to target mutant LRKK2 in the cell line.

Published: 12/01/2019

Related Probes: LRKK2 Fish Probe

Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is a rare cancer that’s challenging to distinguish from lupus panniculitis (LP). Few studies have been conducted on the genetic and molecular development of the disease. This team performed whole-exome sequencing on 4 SPTCLs and 1 systemic T-cell lymphoma, along with 2 cases of LP. They also used targeted sequencing to analyze 41 genes (with known implications across hematolyhpoid malignancies) on 5 additional SPTCL biopsies. Empire Genomics’ PDCD1 and PIK3CD FISH probes were used to detect copy number variants in the 2 genes, which are abnormalities associated with lymphoma but not LP.

Published: 12/01/2019

Related Probes: PDCD1 Fish Probe

This textbook provides a section on using FISH to detect gene fusions. It lists a protocol for our TMPRSS2-ETV1 fusion probe on tissue cells.

Published: 11/15/2019

Related Probes: TMPRSS2-ETV1 FUSION Fish Probe

Melanocytic tumors have been shown to harbor a diverse range of oncogenic kinase fusions, which tend to occur exclusively of one another. A novel MAP3K8 fusion was recently identified in a cohort of spitzoid tumors. This study expanded on the genetic and clinical profile of this new subtype via RNA sequencing, IHC, array CGH, and FISH analysis of 33 MAP3K8-fused spitzoid neoplasms. Our MAP3K8 break apart FISH probe was used to detect MAP3K8 rearrangements.

Published: 11/12/2019

Related Probes: MAP3K8 Break Apart Fish Probe

RICTOR amplification is common across many solid tumors, and recent studies point to the gene as a potential targetable alteration. This study used IHC to measure RICTOR protein expression and our RICTOR FISH probe to detect RICTOR amplification in 213 advanced solid tumors. RICTOR was found overexpressed in 47% of tumors, and IHC and FISH results were closely correlated, indicating that RICTOR overexpression is associated with tumor progression.

Published: 11/11/2019

Related Probes: RICTOR Fish Probe

This study investigated the effects of enhancers on chromatin remodeling and their cognate promoters during inflammation response. Of particular interest were two cytokine-induced factors on chromosome 4, IL-8 and IL-6. IL-8 controls secretion IL-8 and IL-6 factors, while also supporting sustained IL-1-alpha signaling to NF-kB and JNK/p38 MAP kinases. Our IL-8 and IL-6 probes, along with our chromosome 4 centromeric control probes, were used to detect extra copies of both genes in a tumor cell line.

Published: 11/08/2019

Related Probes: IL6 Fish Probe

A new DNAJB1-PRKACA fusion was recently discovered in fibrolamellar hepatocellular carcinoma (FHCC). This study sought to determine the specificity of this fusion for the disease through molecular and genetic analysis of six PRKACA-rearranged pancreatobiliary neoplasms. Empire Genomics’ PRKACA break apart FISH probe was used to detect PRKACA rearrangements in the tumors. Five cases were found to have DNAJB1-PRKACA fusions and one had ATP1B1-PRKACA fusion.

Published: 11/01/2019

Related Probes: PRKACA Break Apart Fish Probe

Detection of chromosomal translocations has proven crucial for diagnosis and management of acute myeloid leukemia (AML), a cancer known to harbor several distinct gene rearrangements that correlate with disease subtype. In this study, an AML patient was genetically profiled using both conventional karyotyping and next generation sequencing techniques. FISH was also used to detect NUP98 translocations using Empire Genomics’ NUP98 break-apart probe.

Published: 10/31/2019

Related Probes: NUP98 Break Apart Fish Probe

Renal oncocytoma (RO) is a benign epithelial neoplasm that makes up about 5 to 9% of all renal cell tumors. RO can be difficult to distinguish from a closely related but malignant counterpart, chromophobe renal cell carcinoma (ChrCC). This study used both IHC and FISH to detect the presence of RB1 and ERBB4, two genes that have been found deleted in ChrCC but not RO. A total of 28 ChrCCs and 25 RO cases were tested. Empire Genomics’ RB1 and ERBB4 FISH probes were used to detect deletions in these genes.

Published: 10/22/2019

Related Probes: RB1 Fish Probe

Lipoblastoma is a rare benign neoplasm that can be difficult to histologically distinguish from other lipomatous tumors. PLAG1 aberrations are recurrent in lipoblastoma. The subjects of this study were 3 pediatric lipoblastoma patients with varying types of PLAG1 aberrations (including deletions, amplifications, and rearrangements), all which resulted in different modes of PLAG1 upregulation. Our PLAG1 break apart probe was used to detect PLAG1 rearrangements in the tumors.

Published: 10/16/2019

Related Probes: PLAG1 Break Apart Fish Probe

While studies are plentiful on adult gliomas, infant cases are historically understudied. This team sought to account for that lack of data by analyzing glioma biopsies from 150 infants. As part of genetic profiling, our ALK break apart probe was used to detect ALK rearrangements. The team was able to divide the tumors into three genetic subtypes that were tightly tied to clinical outcome. They also found that many of the tumors harbored just a single oncogene, evidence that infant gliomas are usually single driver tumors.

Published: 09/25/2019

Related Probes: ALK Break Apart Fish Probe

Since the first report 2010, 22 cases of ALK-rearranged renal cell carcinoma (RCC) have been described. This study screened over 1000 Polish RCC patients for ALK translocations using IHC followed by FISH with our ALK break apart FISH probe. Only 31 cases were considered potentially positive or indeterminable by IHC; of these, none tested positive for ALK rearrangement with FISH. These results suggests that the mutation might be related to ethnicity, warranting further investigation into its prevalence in other ethnicities.

Published: 09/25/2019

Related Probes: ALK Break Apart Fish Probe

The TERT gene, which encodes a telomerase subunit, has long interested cancer researchers because it's required for cell proliferation and immortalization in 80-90% of human cancers. This study analyzed TERT expression across 10 human cancer lines using our TERT FISH probe. TERT expression was highly heterogeneous across different cancers, with variations in cellular location of the TERT protein, number of transcription sites, and ratio of transcription sites to gene copies.

Published: 09/10/2019

Related Probes: TERT Fish Probe

In BXSB murine lupus, extra copies of the X-linked TLR7 gene have been shown to aggravate autoimmunity in male mice. This team investigated the trend in human males with rheumatoid arthritis (RA). Our TLR7, Control X and Control Y probes were used to detect TLR7 copy number, and Chromosome X and Y aneuploidy, respectively. About a third of patients were found to have significantly higher copy numbers of TLR7, as well as substantial cellular mosaicism of female (46,XX) and/or Klinefelter (47,XXY) cells among male (46,XY) cells.

Published: 09/09/2019

Related Probes: TLR7 Fish Probe

Conjunctival squamous cell carcinoma (cSCC) and its precursors are some of the most common ocular surface neoplasms. ADAM3A amplification was recently identified in invasive cSCC. This study analyzed ADAM3A copy gains in cSCC and its precursors using Empire Genomics’ ADAM3A probe. A total of 54 cases of conjunctival squamous intraepithelial neoplasia (CIN), carcinoma in situ (CIS), and cSCC were studied. Nine (17%) of the tumors were found to harbor ADAM3A gains, and all ADAM3A alterations were restricted to high-grade lesions.

Published: 09/06/2019

Related Probes: ADAM3A Fish Probe

Plasma membrane remodeling is a mechanism employed by cancer cells to increase nutrient uptake and intercellular signaling. In this study, researchers identified the LPCAT1 gene as a driver of membrane remodeling, finding that growth factor receptor-driven cancers rely heavily on the gene to reshape cell membranes through enhanced saturated phosphatidylcholine content. Genomic analysis of publicly available cancer sequencing databases of clinical samples and the cancer cell line encyclopedia (CCLE) revealed LPCAT1 amplification in over 30% of pan-cancer patients. This discovery was made possible by Empire Genomics’ LPCAT1 FISH probe, which was used to detect amplification of the gene.

Published: 09/03/2019

Related Probes: LPCAT1 Fish Probe

Small cell lung carcinoma (SCLC) accounts for approximately 15% of all lung cancers and remains a challenging disease to treat, with no significant improvements in the development of targeted therapies. RICTOR is one of the most frequently amplified genes and a potential therapeutic target in SCLC. This study used IHC and Empire Genomics' RICTOR FISH probe to evaluate RICTOR overexpression and gene amplification in 100 SCLC tumors.

Published: 08/24/2019

Related Probes: RICTOR Fish Probe

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 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 IHC and FISH. Empire Genomics’ RP11-572M14 FISH probe was used to detect the 3p25 gene region. The team concluded that this rare tumor subtype has a predilection for oncocytoma and chromophobe RCC, and should be diagnosed as a collision of the two processes, not unclassified RCC.

Published: 08/23/2019

Related Probes: RP11- 572 M14 Fish Probe

Histiocytic sarcoma (HS) is a rare, aggressive cancer that can occur in the GI tract, skin and liver. This study analyzed 21 cases of HS using RNA sequencing, whole exome sequencing, and FISH. BAC FISH probes from Empire Genomics were used to detect NF1 (RP11-14206) and PTNP11 (RP11-748H13, RP11-9P8, RP11-90F3, RP11-660M3), while BRAF translocations were identified using our BRAF break-apart probe. The team found many 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).

Published: 08/21/2019

Related Probes: BRAF Break Apart Fish Probe

Renal cell carcinoma (RCC) can be subdivided into several categories based on morphology, histology, protein expression, and genetics. Although RCC can usually be classified using histological and immunohistochemical analysis, differential diagnosis can prove challenging in ambiguous cases. This study evaluated the efficacy of FISH in RCC classification via analysis of 539 RCC tumors. Empire Genomics’ TFEB break apart probes were used to detect TFEB translocations.

Published: 08/20/2019

Related Probes: TFEB Break Apart Fish Probe

T-cell acute lymphoblastic leukemia (T-ALL) is characterized by translocations of oncogenic transcription factor genes and T-cell receptor loci. This study reported the first case of T-ALL with 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. Our JAK2 break-apart probe was used to detect a novel JAK2 translocation, t(8;9)(p22;p24), in the subject under study. As the patient tested negative for JAK2 rearrangements at diagnosis, the translocation must have developed during disease progression.

Published: 08/19/2019

Related Probes: JAK2 Break Apart Fish Probe

CNTN4 copy number variations (CNVs) have been reported in children with autism spectrum disorder (ASD) and other neurodevelopmental conditions. In this study, three unrelated patients with CNTN4 CNVs were genetically and clinically characterized. Empire Genomics’ RP11-51F24 FISH probe helped to confirm CNTN4 loss in a patient with deletion of the gene. Results both point to CNTN4 as a potential regulator of language development, and call for further evaluation of affected individuals via comprehensive phenotyping to better understand the mechanisms of reduced penetrance and variable expressivity of CNTN4 CNVs.

Published: 08/15/2019

Related Probes: RP11-51F24 Fish 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 IHC, array CGH, whole RNA-sequencing, anchored multiplex PCR-based targeted NGS, and 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).

Published: 08/05/2019

Related Probes: TFCP2 Break Apart Fish Probe

Although survival rates have improved significantly in the past decade, multiple myeloma is still considered largely incurable. This patent aims to identify genetic biomarkers specific to MM that could serve as potential prognostic indicators. The authors propose 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.

Published: 08/01/2019

Related Probes: CD36 Fish Probe

This study investigated KDM1A and ZNF217 copy number variations (CNVs) in colorectal cancer (CRC). Empire Genomics’ RP11-152I19 FISH probe was used to detect KDM1A CNVs in tumor samples from 50 CRC patients. KDM1A was found deleted in 19 samples (38%), while ZNF217 was amplified in 11 samples (22%). The team found a significant association between KDM1A loss, lymph node metastasis, and advanced tumor stage.

Published: 08/01/2019

Related Probes: RP11-152I19 Fish Probe

Pleomorphic adenoma (PA), although considered benign, can undergo malignant transformation, and metastatic cases 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. PLAG1 rearrangements were detected in all four cases. Results demonstrated that MPA harbors the same disease-defining molecular hallmarks as their benign counterparts.

Published: 08/01/2019

Related Probes: PLAG1 Break Apart Fish Probe

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 her features were shared with both previously reported patients, 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.

Published: 07/25/2019

Related Probes: RP11-451A20 Fish Probe

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.

Published: 07/03/2019

Related Probes: RP11-450E20 Fish Probe

Invasive lobular carcinoma (ILC) is a type of breast cancer defined by functional loss of E-cadherin, which results in cellular adhesion defects. 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 FISH probes were used to detect amplification of the genes.

Published: 06/28/2019

Related Probes: FGFR1 Fish 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 IHC, 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).

Published: 06/25/2019

Related Probes: TRIM11 Break Apart Fish Probe

ERG rearrangement is recurrent in AML and Ewing’s sarcoma, but little research has been done on the effects of this translocation in lymphoma. In this study, diffuse large B-cell lymphoma (DLBCL) tumors were analyzed using IHC, miRNA expression profiling, RT-PCR, and whole exome sequencing. FISH was also used to detect ERG rearrangements, using RP-11 BAC FISH probes from Empire Genomics (RP11-476D17 and RP11-95121). FISH detected no ERG translocations in 10 randomly selected ERG+ DLBCL samples, but approximately 30% of tumors (37 of 118) were found to exhibit aberrant ERG.

Published: 06/24/2019

Related Probes: RP11-476D17 & RP11-95121 Fish Probe

BCR encodes a receptor expressed on both normal B-cells and their neoplastic counterparts. Studies have shown that BCR stabilizes and promotes MYC expression in diffuse large B-cell lymphoma (DLBCL). As MYC can directly bind the PD-L1 promoter, the team hypothesized that BCR drives PD-L1 expression through amplification of MYC. They investigated this relationship using qPCR, immunoblotting and flow cytometry in DLBCL cell lines. PD-L1 rearrangements were detected using Empire Genomics’ PD-L1 break-apart probe. Results supported their hypothesis, pointing to BCR as an upregulator of PD-L1 via amplified MYC.

Published: 06/13/2019

Related Probes: PD-L1 Break Apart Fish Probe

Unlike cutaneous melanoma, the genomics of mucosal melanoma (MM) remain poorly understood, which has hindered the development of targeted therapy for MM patients. In order to account for this gap in data, this team performed whole-genome sequencing on 65 MM samples to identify genomic alterations with prognostic and/or therapeutic implications. Our CDK4 and TERT probes were used to detect amplification of the genes.

Published: 06/01/2019

Related Probes: CDK4 Fish Probe

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.

Published: 05/29/2019

Related Probes: TFE3 Break Apart Fish Probe

The subject of this study was a two-and-a-half-year-old patient with an extensive list of developmental and physical abnormalities (e.g. trouble feeding, dysmorphic facial features, severe language delays). FISH analysis was performed on the patient to investigate potential genetic causes of her condition. Empire Genomics’ RP11-227H15 FISH probe was used to detect a de novo 10.2 MB deletion extending from 10q21.3-10q22.3, the second largest reported deletion in this region. Based on the patient’s unique clinical presentation, the team concluded that loss of the KAT6B was the likeliest cause of her condition.

Published: 05/17/2019

Related Probes: RP11-227H15 Fish Probe

Recently, researchers have found that certain small round cell bone tumors can be genetically classified based on the gene fusions they harbor. This study analyzed four of these tumors using Empire Genomics' BAC FISH probes (2L23 and 73P15) to detect aberrations in the NFATC2 gene. EWSR1-NFATc2 fusions were found in three cases, and FUS-NFATc2 fusion in one. The tumors were shown to have distinct clinical characteristics, morphology, and immunoprofiles that distinguish them from Ewing Sarcoma.

Published: 05/09/2019

Related Probes: RP11 2L23 Break Apart Fish Probe

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 9q21.33/q22.31 was studied. The deletion was confirmed using a BAC FISH probe (RP11-91M3) from Empire Genomics. 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.”

Published: 05/07/2019

Related Probes: RP-11 91M3 Fish Probe

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a particularly aggressive acute leukemia. BPDCN patients display significantly higher levels of RUNX2 compared to other leukemia patients, due to the RUNX2 super-enhancers harbored by BPDCN cells. Because MYC translocations are also recurrent abnormalities in BPDCN, the team wanted to determine whether RUNX2 super-enhancers also upregulate MYC expression in these tumors. Empire Genomics' RUNX2 probe was used to detect RUNX2 amplification in a series of BPDCNs. Results demonstrated that RUNX2 super-enhancers are in fact hijacked to activate MYC via t(6,8) in BPDCN.

Published: 04/10/2019

Related Probes: RUNX2 Fish Probe

The subject of this study was a 3 year-old male, born to nonconsanguineous healthy parents, who presented with various physical and developmental abnormalities. 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.

Published: 04/02/2019

Related Probes: RP11-462C5 Fish Probe

Systemic, primary cutaneous, and breast implant-associated ALK-negative anaplastic large cell lymphomas, although diverse in their clinical features, can be difficult to distinguish histopathologically. This study sought to cytogenetically discern between these 3 lymphoma subtypes using IHC and FISH. Twenty-two S-ALCLs, 13 PC-ALCLs, and 2 BI-ALCLs were analyzed. Empire Genomics' PD-L1 and TP63 break apart probes were used to detect PD-L1 and TP63 rearrangements.

Published: 04/01/2019

Related Probes: PD-L1 Break Apart Fish Probe

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 uncovered a novel FUS-TFCP2 fusion.

Published: 03/27/2019

Related Probes: TFCP2 Break Apart Fish Probe

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.

Published: 02/09/2019

Related Probes: USP6 Break Apart Fish Probe

NORAD is a powerful negative regulator of the PUMILIO family of proteins, which target mRNAs important to mitosis, DNA repair, and DNA replication. This study analyzed the effect of NORAD knockout on mice. Empire Genomics’ Mouse FISH Probes for Chromosomes 2 and 16 were used to detect aneuploidy, which was found to increase significantly in NORAD-negative mice. The team found that this genomic instability lead to premature aging in affected mice; their fur became thin and gray, and their brains developed age-related abnormalities much sooner than normal mice, evidence that NORAD prevents age-related problems from appearing in young animals.

Published: 02/09/2019

Related Probes: Mouse Chromosomes 2 & 16 Fish Probe

Plasmacytoid cells (PLCs) are frequently reported components of salivary pleomorphic adenoma (SPA), and regarded as modified myoepithelial cells. In rare cases where a SPA is composed mostly of PLCs, the neoplasm is referred to as plasmacytoid myoepithelioma (pMYO). A genetic hallmark of SPA is rearrangement of PLAG1. In this study, 3 pMYOS were analyzed for PLAG1 translocations using Empire Genomics’ PLAG1 break apart probe, to determine whether this aberration is shared by both tumor types. PLAG1 was found rearranged in 1 out of 3 pMYOs.

Published: 02/07/2019

Related Probes: PLAG1 Break Apart Fish Probe

CIC-fused sarcomas are round cell sarcomas first identified in 2006, characterized by recurrent CIC fusions with a variety of genes, including DUX4 and FOXO4. Recent studies have implicated NUTM1 as a potential new CIC fusion partner in these tumors. This team sought to determine the frequency of NUTM1 translocations in 6 cases of CIC-rearranged sarcoma. Empire Genomics’ CIC break apart probe was used to verify the presence of CIC translocations in the samples. All cases tested positive for NUTM1 rearrangement, suggesting CIC-NUTM1 fused cases represent a new subset of CIC-fused sarcomas.

Published: 01/31/2019

Related Probes: CIC Break Apart Fish Probe

The MYCN-IGH fusion has been described in blastic mantle cell lymphoma and follicular lymphoma, but, at the time of this study, still hadn’t been identified in marginal zone B-cell lymphoma (MZL). This study presented the first documented case of MYCN-IGH fusion in a MZL patient. Cytogenetic testing, including FISH, was performed to analyze the patient’s genome. Our CCND2 break apart probe and RP11-542H15 BAC FISH probe were used to detect CCND2 and MYCN rearrangements.

Published: 01/31/2019

Related Probes: CCND2 Break Apart Fish Probe

Anaplastic large cell lymphoma (ALCL) is a rare form of T-cell lymphoma that makes up about 3% of adult non-Hodgkin lymphoma. Recently, TP63 translocations have emerged as a new class of biomarkers in ALCL. This study examined two cases of TP63-rearranged ALCL, using Empire Genomics’ TP63 break apart probe to detect translocations of the gene. Although the effects of TP63 rearrangement still aren’t clear, results suggest that the N-terminal domain of the protein, which is truncated as a result of gene rearrangement, may act as a tumor suppressor.

Published: 01/31/2019

Related Probes: TP63 Break Apart Fish Probe

Hydropic leiomyoma (HLM) is an understudied subtype of uterine leiomyoma (ULM). Little is known about HLM's etiology, genetics, and clinical profile. To account for this lack of data, the team analyzed 24 HLM cases for histology, immunohistochemistry and molecular alterations. Empire Genomics’ HMGA2 break apart probe was used to detect rearrangements of HMGA2, an abnormality previously reported in ULM. The gene was found rearranged in 32% of cases.

Published: 01/31/2019

Related Probes: HMGA2 Break Apart Fish Probe

PTEN is a lipid phosphatase that antagonizes the PI3K/AKT pathway and is recognized as a major dose-dependent tumor suppressor. In this study, PTEN expression was evaluated across different mice and human tumor types using various techniques, including FISH. Empire Genomics’ PTEN FISH probe was used to detect amplification/deletion of the gene in 99 breast tumor and 86 prostate tumor samples, where the gene was found deleted in 16.5% and 14.7% of cases, respectively.

Published: 01/31/2019

Related Probes: PTEN/Con 10 Fish Probe

Autism is a common developmental disorder that has increased substantially in frequency since the 2000s. Studies have looked into various factors (vitamin deficiencies, viral infections, parental age) as potential causes of the condition, but no clear relationship has been found. In the last decade, studies have started to focus more on possible genetic causes. This study did just that, investigating a duplication on chromosome Xq13.1 in a patient with autism. Empire Genomics’ NLGN3 FISH probe helped to confirm the duplication.

Published: 01/31/2019

Related Probes: NLGN3 Fish Probe

Cutaneous melanocytic tumors can vary significantly in their morphology, especially in early stages. This study aimed to genetically and immunohistochemically distinguish between several cutaneous melanocytic tumor types - deep penetrating nevi (DPN), “blue” melanocytic tumors, Spitz tumors, nevoid and SSM melanomas, and pigmented epithelioid melanocytomas (PEM) – using IHC and FISH. Empire Genomics’ PRKCA break apart was used to detect PRKCA rearrangements in the samples, helping to confirm fusion of the gene in two PEM patients.

Published: 01/31/2019

Related Probes: PRKCA Break Apart Fish Probe

Hyalinizing trabecular tumor (HTT) is a rare, poorly understood thyroid neoplasm, with much mystery still surrounding its genetics, relationship to papillary thyroid carcinoma (PTC), and malignant potential. The goal of this study was to apply genome-wide sequencing analyses to elucidate the genetic mechanisms of HTT and its relationship to PTC. Empire Genomics’ PAX8, GLIS1, and GLIS3 probes were used to screen for PAX8-GLIS1 and PAX8-GLIS3 fusions in 17 HTTs and 220 PTCs. PAX8-GLIS3 fusions were identified in 93% and PAX8-GLIS1 in 7% of HTT samples, while both fusions were absent from all PTCs.

Published: 12/31/2018

Related Probes: PAX8-GLIS3 Fish Probe

DICER1 encodes an RNase II endonuclease protein that regulates the production of small non-coding RNAs. The majority of reported germline DICER1 mutations are truncating sequence-level alterations, suggesting that a loss-of-function type mechanism drives tumor formation in DICER1 syndrome. Empire Genomics’ BAC FISH probe, RP11-26J5, was used to detect DICER1 aberrations in two patients. One was found to have a 1.4 Mb deletion and the other a 5.0 Mb deletion in the 14q32 chromosomal region containing the gene.

Published: 12/31/2018

Related Probes: RP11-26J5 Fish Probe

ADGRB3 plays a key role in CNS regulation, directing axon guidance, myelination, and synapse formation and function. Copy number variations in the gene can lead to intellectual impairment and mood disorders. In this study, a family of four was genetically analyzed for ADGRB3 amplifications using two BAC FISH probes from Empire Genomics - RP11-980I14 for detecting ADGRB3 and RP11-661C14 as a control. The probes helped to confirm biallelic duplication of ADGRB3 in the two children, inherited from their heterozygous parents.

Published: 12/31/2018

Related Probes: RP11-980I14 Fish Probe

Renal cell carcinomas (RCCs) have historically been classified based on their morphology, anatomical location, or background renal disease. However, recurrent genetic abnormalities are being described more frequently in RCC, and have proven useful in the genetic classification of different RCC subsets. This study sought to clarify the underlying genetics of one such RCC subtype, TFEB-rearranged RCC. As part of genetic testing, Empire Genomics’ TFEB break apart probe was used to detect TFEB translocations in two RCC tumors, helping to verify the presence of a TFEB rearrangement in one case.

Published: 12/31/2018

Related Probes: TFEB Break Apart Fish Probe

Although several RUNX1-USP42 fusions have been described in acute myeloid leukemia (AML), the clinical effects of this abnormality remain poorly understood. The few reported cases have harbored additional genetic abnormalities, the most frequent being 5q deletions. This study reported on 3 cases of pediatric RUNX1-USP42-fused AML. Empire Genomics RUNX1 break apart probe and RUNX1-USP42 fusion probe were used to detect rearrangements of the genes. Co-occurring genetic aberrations included del(5q) and cnLOH of 11p. Results point to the fusion as a rare but recurrent mutation in pediatric AML, with distinct accompanying mutations.

Published: 12/31/2018

Related Probes: RUNX1-USP42 Break Apart Fish Probe

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.

Published: 12/31/2018

Related Probes: RP11-299D5 (SAMD4A) Fish Probe

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.

Published: 12/01/2018

Related Probes: SRC Fish Probe

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.

Published: 11/30/2018

Related Probes: ABL1/ETV6 Fish Probe

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.

Published: 11/30/2018

Related Probes: KRAS Fish 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.

Published: 11/30/2018

Related Probes: MYB Break Apart Fish Probe

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.

Published: 11/30/2018

Related Probes: CD274 (PD-L1) Fish Probe

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.

Published: 11/30/2018

Related Probes: Rat-specific X chromosome Fish Probe

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.

Published: 11/30/2018

Related Probes: RPCI11-98K7 Fish Probe

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.

Published: 11/30/2018

Related Probes: RP11-161B1 Fish Probe

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.

Published: 11/29/2018

Related Probes: RP11-264L1 Fish Probe

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.

Published: 11/22/2018

Related Probes: PLAG1 Break Apart Fish Probe

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.

Published: 11/01/2018

Related Probes: Con 1 Fish Probe

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.

Published: 10/31/2018

Related Probes: 21q21.1 Fish Probe

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.

Published: 10/31/2018

Related Probes: RPCL11-185E1 Fish Probe

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.

Published: 10/31/2018

Related Probes: Con 9 Fish Probe

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.

Published: 10/31/2018

Related Probes: PCM1/JAK2 Fish 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.

Published: 10/31/2018

Related Probes: PD-L1 Break Apart Fish Probe

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.

Published: 10/31/2018

Related Probes: RP11-383B16 Fish 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.

Published: 09/30/2018

Related Probes: RELA Break Apart Fish Probe

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.

Published: 09/30/2018

Related Probes: RP11-378O10 Fish Probe

Alveolar soft-part sarcoma (ASPS) is a rare malignant soft tissue tumor. The subject of this study was a 21 year old man who presented with ASPS of the prostate. Our ASPL and TFE3 break apart probes were used to confirm fusion of the two genes in the patient’s tumor, helping to elucidate the underlying genetic drivers of this extremely rare, aggressive neoplasm.

Published: 09/30/2018

Related Probes: ASPL Fish Probe

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.

Published: 09/30/2018

Related Probes: FGF4 Fish Probe

This study investigated a case of myeloid sarcoma (MS), a rare tumor often misdiagnosed as malignant lymphoma, that developed into acute myeloid leukemia (AML). Along with pathologic, morphologic, and immunophenotypic characterization, FISH was used to screen for cytogenetic abnormalities. Our MLLT10 helped detect a rare PICALM-MLLT10 fusion in the patient, an abnormality consistent with disease progression to AML.

Published: 09/30/2018

Related Probes: MLLT10 Break Apart Fish Probe

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.

Published: 09/30/2018

Related Probes: RP11 BAC Clone (not specified) Fish 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.

Published: 08/31/2018

Related Probes: ATF1 Break Apart Fish 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.

Published: 08/31/2018

Related Probes: MYBL1 Break Apart Fish Probe

Ependymoma is a tumor that arises from tissue of the nervous system. Rare cases involve a YAP1/MAMLD1 fusion that can occur in childhood. This study sought to expand on the unique clinical features of neoplasms harboring this fusion. Our YAP1 break apart probe was used to detect YAP1 gene rearrangements in several of the cases under study. It was determined that YAP1/MAMLD1 fusion ependymomas display characteristics that distinct from RELA fusion ependymomas.

Published: 08/31/2018

Related Probes: YAP1 Break Apart Fish Probe

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.

Published: 08/31/2018

Related Probes: RP11 BAC Clone (not specified) Fish Probe

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.

Published: 08/31/2018

Related Probes: PCGF2 Fish Probe

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.

Published: 08/31/2018

Related Probes: BRAF Fish Probe

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.

Published: 07/31/2018

Related Probes: RP11-450G24 Fish Probe

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.

Published: 07/31/2018

Related Probes: JAK2 Fish Probe

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.

Published: 07/31/2018

Related Probes: RP11-846M12 Fish Probe

Mutations in voltage-gated sodium channel (SCN) genes are thought to contribute to the development of certain psychiatric and neurological diseases. The subject of this study was a 28 year old male with autism and Tourette syndrome, who was found to have a heterozygous 718 kb deletion at 2q24.3, leading to loss of 2 SCN genes (SCN2A and SCN3A), as well as GRB14, COBBL1, and SCL38A11. Empire Genomics’ RP11-150F4 FISH probe confirmed deletion of SCN2A.

Published: 07/31/2018

Related Probes: RP11-150F4 Fish Probe

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.

Published: 07/31/2018

Related Probes: MERTK Fish Probe

Tumor cells sometimes display PD-L1 and PD-L2 to evade T-cell detection, allowing them to grow and proliferate without immune interference. In classical Hodgkin lymphoma, malignant cells have been found to upregulate PD-L1 expression via copy gains in the 9p24.1 region where PD-L1 and PD-L2 are found. This team wanted to find out whether the same mechanism is used by cancer cells in diffuse large B-cell lymphoma (DLCBCL). Empire Genomics’ PDL1 and PDL2 break-apart probes were used to detect aberrations in the genes in a series of DLBCL tumors. Of the 105 DLBCL cases analyzed, 27% were found to have PD-L1 alterations.

Published: 07/01/2018

Related Probes: PD-L1 Break Apart Fish Probe

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.

Published: 06/30/2018

Related Probes: MYB Fish 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.

Published: 06/30/2018

Related Probes: MYB Break Apart Fish Probe

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.

Published: 06/21/2018

Related Probes: RP11-117B23 Fish Probe

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.

Published: 06/20/2018

Related Probes: Con 21 Fish 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.

Published: 06/19/2018

Related Probes: MYBL1 Break Apart Fish Probe

Melanomas with ambiguous histology can be difficult to distinguish from benign nevi. Cytogenetic tests, therefore, have proven highly useful in differentiating melanomas from benign tumors. This study tested the efficacy of FISH at genetically characterizing 70 morphologically ambiguous melanocytic tumors. Our RREB1 probe was used to identify 6p25 amplifications in the samples. Compared to a gene expression test called myPath, FISH agreed better with histopathologic interpretations, had greater sensitivity, and correlated better with molecular diagnostics.

Published: 05/31/2018

Related Probes: RREB1 Fish Probe

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.

Published: 05/31/2018

Related Probes: Chromosome 17 Centromere Fish Probe

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.

Published: 05/20/2018

Related Probes: RP11-115B16 Fish Probe

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.

Published: 05/08/2018

Related Probes: Chromosome X Centromere Fish Probe

Our NTRK1 break apart probe was used to detect NTRK1 rearrangements in solid tumors from more than 1,000 patients. Over 14 different cancer types were analyzed, including lung, colorectal, and breast. NTRK1 translocations were identified in 5.9% of patients.

Published: 04/30/2018

Related Probes: NTRK1 Break Apart Fish Probe

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.

Published: 04/30/2018

Related Probes: DMRT1 Fish Probe

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.

Published: 03/31/2018

Related Probes: RP11-893E5 Fish 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.

Published: 03/31/2018

Related Probes: ETV6 Break Apart Fish 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.

Published: 03/31/2018

Related Probes: MYB Break Apart Fish Probe

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.

Published: 03/31/2018

Related Probes: FGFR1 Fish Probe

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.

Published: 03/09/2018

Related Probes: Chromosome 8 Centromere Fish 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.

Published: 03/01/2018

Related Probes: ROS1 Break Apart Fish Probe

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.

Published: 02/28/2018

Related Probes: Mouse Con X Fish Probe

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.

Published: 02/28/2018

Related Probes: RP11-1058B20 Fish Probe

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.

Published: 02/28/2018

Related Probes: Mouse Xqc3 Fish 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.

Published: 02/28/2018

Related Probes: TRIM11 Break Apart Fish 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.

Published: 01/31/2018

Related Probes: PLAG1 Break Apart Fish Probe

Prostate tumors have been shown to display marked genetic heterogeneity, which develops over the course of disease progression and contributes to treatment resistance. In this study, seven patients’ prostate tumors were genetically analyzed. Each patient contributed several biopsies, taken at different points during their clinical timeline. As part of genetic testing, our FKB4 FISH probes were used to detect FKB4 CNVs.

Published: 01/31/2018

Related Probes: FKBP4 Fish Probe

Acral melanomas vary considerably in their molecular, histological, and clinical presentation. In this study, acral melanomas from dorsal, volar, and subungual-interdigital body sites were assessed using several tests, including FISH. Our TERT, CCND1, CDK4, AURKA, CDKN2A, PAK1, PTEN, NF1, and GAB2 probes were used to detect copy number variations in these genes. Genetic profiles were found to be tightly tied to UV exposure.

Published: 01/31/2018

Related Probes: TERT Fish Probe

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.

Published: 01/01/2018

Related Probes: RP11-615F13 Fish Probe

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.

Published: 12/31/2017

Related Probes: NF 2 Fish 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.

Published: 12/31/2017

Related Probes: PLAG1 Break Apart Fish Probe

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.

Published: 12/31/2017

Related Probes: SEPT5 Fish Probe

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.

Published: 12/31/2017

Related Probes: KRT14-20 Fish Probe

This study investigated the foamy virus (FV) vector’s utility in gene therapy. The team found FV vectors to be significantly less genotoxic than y-retroviral (GV) and lentivirus (LV) vectors. They performed gene targeting of all three analogous proviral sequences into the same location of the LMO2 gene, which was detected using Empire Genomics’ RP11-1006P23 FISH probe.

Published: 12/14/2017

Related Probes: RP11-1006P23 Fish Probe

In previous studies, both on human cell lines and drosophila, mutations in the MAPT gene were shown to lead to frontotemporal lobar degeneration (FLTD). This study examined whether FLTD-causing mutations in human MAPT triggered aneuploidy and apoptosis in the mammalian brain. Empire Genomics’ mouse probe – RP24-288N19 – was used to detect chromosome 16 aneuploidy in MAPT-mutant mouse cells.

Published: 11/30/2017

Related Probes: RP24-288N19 Fish Probe

BRAF rearrangements are found in about 20% of acinar-type neoplasms, and may serve as a potential treatment target. This study examined the efficacy of FISH versus NGS for detecting BRAF translocations in 31 acinar-type neoplasms. As part of FISH analysis, our BRAF break apart probes were used to detect BRAF rearrangements. The team found that, compared to NGS, FISH was highly sensitive, specific, and time- and cost-effective.

Published: 08/31/2017

Related Probes: BRAF Break Apart Fish Probe

Renal cell carcinomas with MITF family abnormalities display diverse morphologies. In order to better understand the association between MITF alterations and clinicopathologic characteristics, this team performed FISH analysis on 85 renal tumors using our TFE3 and TFEB break apart probes.

Published: 07/31/2017

Related Probes: TFE3 Break Apart Fish Probe

Our NTRK1 break apart probe helped to detect a new NTRK1 fusion in a 61 year old patient with adenocarcinoma of the right colon and pancreas. The team was able to verify that this novel fusion – SCYL3-NTRK1 – was in fact an oncogenic driver by transfecting cells with a SCYL3-NTRK1 cDNA construct, which lead to IL3-independent proliferation.

Published: 07/24/2017

Related Probes: NTRK1 Break Apart Fish Probe

FGFR2 amplification occurs in about 5% of gastric cancers, but so far has only been reported in one colorectal cancer (CRC) cell line, where the cells were found to require FGFR2 amplification for survival. This was the first report of FGFR2 amplification in a CRC biopsy obtained directly from a patient’s primary tumor. Our FGFR2 FISH probe helped confirm FGFR2 amplification in the subject.

Published: 05/30/2017

Related Probes: FGFR2 Fish Probe

Our NTRK3 break apart probes were used to detect NTRK3 rearrangements in spitzoid neoplasms, a subtype of melanocytic tumors characterized by an absence of typical melanoma-associated mutations. Four of the patients tested positive for NTRK3 translocations, including a novel MYO5A-NTRK3 fusion.

Published: 05/01/2017

Related Probes: NTRK3 Break Apart Fish Probe

Atypical spitzoid neoplasms (APNs) are primarily pediatric lesions characterized by their intermediate features; clinically and histopathologically, they fall somewhere between benign spitz nevi and malignant melanoma. The genetics of these tumors are still poorly understood. In this study, 34 APNs were analyzed using FISH and IHC. Our ALK, BRAF, and NTRK1 break-apart FISH probes were used to detect rearrangements of the genes .

Published: 03/01/2017

Related Probes: ALK Break Apart Fish Probe

This study used CRISPR/Cas9 to eliminate extra copies of chromosome 21 in human cells, successfully generating disomic cells from trisomic cells. Normal cells harboring only 2 copies of chromosome 21 were induced by transfection of a Cre expression vector. This approach points to a potential therapeutic vulnerability for aneuploid disorders. Our chromosome 21 control probe was used to detect chromosome 21 copy counts in the cells.

Published: 02/28/2017

Related Probes: Con 21 Fish Probe

Our ETV6-NTRK3 fusion probe was used to detect fusion of the two genes in a 36 year old patient with a neck tumor originally diagnosed as papillary thyroid carcinoma. After thyroid-targeted treatment proved unsuccessful, further cytogenetic analysis revealed the presence of a NTRK3-ETV6 fusion consistent with MASC’s clinical profile.

Published: 04/13/2016

Related Probes: ETV6-NTRK3 Fish Probe