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A Clinicopathologic and Molecular Analysis of 34 Mediastinal Germ Cell Tumors Suggesting Different Modes of Teratoma Development
KRAS FISH Probes
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.
https://www.ingentaconnect.com/content/wk/ajsp/2018/00000042/00000012/art00010
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.
https://www.nature.com/articles/modpathol2017106
A Hemizygous 370 Kilobase Microduplication at Xq13.1 in a Three-Year-Old Boy With Autism and Speech Delay
NLGN3 FISH Probes
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.
https://www.tandfonline.com/doi/abs/10.1080/15513815.2019.1571132?journalCode=ipdp20
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.
https://molecularcytogenetics.biomedcentral.com/articles/10.1186/s13039-019-0419-3
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.
https://link.springer.com/article/10.1007/s00401-018-1833-z
Acute myeloid leukemia with KMT2A-SEPT5 translocation: A case report and review of the literature
SEPT5 FISH Probes
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.
https://journals.sagepub.com/doi/abs/10.1177/2050313X17750334
Alternative lengthening of telomeres, ATRX loss and H3_K27M mutations in histologically defined pilocytic astrocytoma with anaplasia
BRAF FISH Probes
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.
https://onlinelibrary.wiley.com/doi/full/10.1111/bpa.12646
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.
https://onlinelibrary.wiley.com/doi/abs/10.1111/pin.12758
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.
https://jcp.bmj.com/content/early/2019/02/08/jclinpath-2018-205561.info
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.
https://www.nature.com/articles/s41431-018-0321-1
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.
https://onlinelibrary.wiley.com/doi/full/10.1002/ana.25207
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.
https://www.sciencedirect.com/science/article/pii/S193131281830430X
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.
https://onlinelibrary.wiley.com/doi/full/10.1111/bpa.12659
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.
http://www.neurologyindia.com/article.asp?issn=0028-3886;year=2018;volume=66;issue=1;spage=156;epage=160;aulast=Sugur
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.
https://journals.lww.com/ajsp/Abstract/2019/02000/Clinicopathologic_Features_of_CIC_NUTM1_Sarcomas,.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.
https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-018-1689-y
Comparison of melanoma gene expression score with histopathology, fluorescence in situ hybridization, and SNP array for the classification of melanocytic neoplasms
RREB1 FISH Probes
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.
https://www.nature.com/articles/s41379-018-0087-6
Consistent LEF-1 and MYB Immunohistochemical Expression in Human Papillomavirus-Related Multiphenotypic Sinonasal Carcinoma: A Potential Diagnostic Pitfall
MYB FISH Probes
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.
https://link.springer.com/article/10.1007/s12105-018-0951-1
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.
https://www.ingentaconnect.com/content/wk/ajsp/2018/00000042/00000003/art00015
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.
https://www.sciencedirect.com/science/article/abs/pii/S2210776218301601
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.
https://journals.sagepub.com/doi/abs/10.1177/0883073818811454
Delineation of human prostate cancer evolution identifies chromothripsis as a polyclonal event and FKBP4 as a potential driver of castration resistance
FKBP4 FISH Probes
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_na?ve (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.
https://onlinelibrary.wiley.com/doi/full/10.1002/path.5052
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.
https://diagnosticpathology.biomedcentral.com/articles/10.1186/s13000-018-0752-6
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.
https://onlinelibrary.wiley.com/doi/full/10.1111/bpa.12664
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.
https://www.ingentaconnect.com/content/wk/ajsp/2018/00000042/00000001/art00004
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.
http://dmm.biologists.org/content/11/1/dmm031716
FGFR1 and HER1 or HER2 co_amplification in breast cancer indicate poor prognosis
FGFR1 FISH Probes
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.
https://www.spandidos-publications.com/10.3892/ol.2018.8423?text=abstract
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.
http://cancerres.aacrjournals.org/content/early/2018/11/28/0008-5472.CAN-17-3864
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 (_-SNCA). Induced pluripotenet stem cells (iPSCs) were used to generate _-SNCA with an A53T mutation. One of our BAC clones containing the _-SNCA gene was modified with recombineering. The BAC containing the normal _-SNCA successfully corrected the iPSC?s _-SNCA mutation. The iPSC following the correction was found to have normal karyotype and pluripotency.
https://www.sciencedirect.com/science/article/pii/S1873506118301508
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5929417/
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.
https://www.sciencedirect.com/science/article/pii/S0022202X18319882
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.
https://www.nature.com/articles/s41467-018-07578-z
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.
https://www.sciencedirect.com/science/article/pii/S0169500218305968
Genomic Fusions in Pigmented Spindle Cell Nevus of Reed
MERTK FISH Probes
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.
https://www.ingentaconnect.com/content/wk/ajsp/2018/00000042/00000008/art00006
GLIS Rearrangement is a Genomic Hallmark of Hyalinizing Trabecular Tumor of the Thyroid Gland
PAX8-GLIS3 FISH Probes
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.
https://www.liebertpub.com/doi/abs/10.1089/thy.2018.0791
Hematopoietic neoplasms with 9p24/JAK2 rearrangement: a multicenter study
PCM1/JAK2 FISH Probes
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.
https://www.nature.com/articles/s41379-018-0165-9
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.
https://bmcpsychiatry.biomedcentral.com/articles/10.1186/s12888-018-1822-8
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.
https://link.springer.com/article/10.1007/s00428-019-02526-8
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.
https://link.springer.com/article/10.1007/s12105-018-0895-5
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.
https://www.sciencedirect.com/science/article/pii/S0046817718303769
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.
https://www.sciencedirect.com/science/article/pii/S1769721217308418
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.
https://www.sciencedirect.com/science/article/pii/S0046817718302570
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.
https://www.sciencedirect.com/science/article/pii/S1769721218304816
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.
https://onlinelibrary.wiley.com/doi/full/10.1111/bjh.15538
Loss of DMRT1 gene in a Mos 45,XY,-9[8]/46,XY,r(9)[29]/47,XY,+idic r(9)__2[1]/46,XY,idic r(9)[1]/46,XY[1] female presenting with short stature
DMRT1 FISH Probes
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.
https://molecularcytogenetics.biomedcentral.com/articles/10.1186/s13039-018-0379-z
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.
https://link.springer.com/article/10.1007/s00428-018-2423-0
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.
https://onlinelibrary.wiley.com/doi/abs/10.1111/his.13708
Myeloproliferative neoplasm with ABL1/ETV6 rearrangement mimics chronic myeloid leukemia and responds to tyrosine kinase inhibitors
ABL1/ETV6 FISH Probes
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.
https://www.sciencedirect.com/science/article/abs/pii/S2210776218302837
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.
https://www.sciencedirect.com/science/article/pii/S0002944017308817
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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186884/
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.
https://onlinelibrary.wiley.com/doi/abs/10.1002/gcc.22740
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.
https://www.sciencedirect.com/science/article/pii/S2212440319301099
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.
https://www.sciencedirect.com/science/article/pii/S0046817718302193
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.
https://www.sciencedirect.com/science/article/pii/S0046817717303969
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.
https://www.sciencedirect.com/science/article/pii/S1525505017306996
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.
https://www.nature.com/articles/s41467-019-08481-x
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.
https://molecularcytogenetics.biomedcentral.com/articles/10.1186/s13039-018-0405-1
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.
https://onlinelibrary.wiley.com/doi/abs/10.1111/aos.13667
Role of MEL-18 Amplification in Anti-HER2 Therapy of Breast Cancer
PCGF2 FISH Probes
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.
https://academic.oup.com/jnci/advance-article-abstract/doi/10.1093/jnci/djy151/5103386
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.
http://www.freepatentsonline.com/10167466.html
Targeting p38_ 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 p38_ 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 p38_ 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 p38_.
https://www.sciencedirect.com/science/article/pii/S1535610818301818
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.
https://www.karger.com/Article/Abstract/494645
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.
https://www.liebertpub.com/doi/abs/10.1089/scd.2018.0010
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.
https://jcp.bmj.com/content/71/10/926
_-Catenin nuclear expression discriminates deep penetrating nevi from other cutaneous melanocytic tumors
PRKCA Break Apart Probe
Nuclear _-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 _-catenin IHC expression is useful in differentiating DPN tumors from blue or Spitz melanocytic tumors and PEM.
https://link.springer.com/article/10.1007/s00428-019-02533-9