12q13 abnormality in rhabdomyosarcoma

Roberts, Paul; Browne, Charmaine; Lewis, Ian; Bailey, Chris; Spicer, R. D.; Williams, Jeffrey; Batcup, G.

doi:10.1016/0165-4608(92)90005-s

Cited by 42 publications

(19 citation statements)

References 20 publications

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“…The authors mentioned that a similar translocation had also been reported as part of complex karyotype in an embryonal rhabdomyosarcoma (RMS) cell line [2] and as part of a three-way translocation t(4;19;12)(q35;q13.1;q13) in an undifferentiated/embryonal RMS [3] and suggested that it might be a recurrent chromosomal aberration in malignant primitive mesenchymal stem cells [1]. Sommers et al [4] described a subcutaneous primitive neuroectodermal tumor/Ewing sarcoma without EWSR1 rearrangement but with a complex karyotype containing a t(4;19)(q33∼35;q13).…”

Section: Introductionmentioning

confidence: 89%

The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

et al. 2014

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Whole transcriptome sequencing was used to study a small round cell tumor in which a t(4;19)(q35;q13) was part of the complex karyotype but where the initial reverse transcriptase PCR (RT-PCR) examination did not detect a CIC-DUX4 fusion transcript previously described as the crucial gene-level outcome of this specific translocation. The RNA sequencing data were analysed using the FusionMap, FusionFinder, and ChimeraScan programs which are specifically designed to identify fusion genes. FusionMap, FusionFinder, and ChimeraScan identified 1017, 102, and 101 fusion transcripts, respectively, but CIC-DUX4 was not among them. Since the RNA sequencing data are in the fastq text-based format, we searched the files using the “grep” command-line utility. The “grep” command searches the text for specific expressions and displays, by default, the lines where matches occur. The “specific expression” was a sequence of 20 nucleotides from the coding part of the last exon 20 of CIC (Reference Sequence: NM_015125.3) chosen since all the so far reported CIC breakpoints have occurred here. Fifteen chimeric CIC-DUX4 cDNA sequences were captured and the fusion between the CIC and DUX4 genes was mapped precisely. New primer combinations were constructed based on these findings and were used together with a polymerase suitable for amplification of GC-rich DNA templates to amplify CIC-DUX4 cDNA fragments which had the same fusion point found with “grep”. In conclusion, FusionMap, FusionFinder, and ChimeraScan generated a plethora of fusion transcripts but did not detect the biologically important CIC-DUX4 chimeric transcript; they are generally useful but evidently suffer from imperfect both sensitivity and specificity. The “grep” command is an excellent tool to capture chimeric transcripts from RNA sequencing data when the pathological and/or cytogenetic information strongly indicates the presence of a specific fusion gene.

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Section: Introductionmentioning

confidence: 89%

The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

et al. 2014

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“…Mitoses and apoptoses were abundant (Figs. [3][4][5]. A periodic acid-Schiff stain with and without diastase treatment demonstrated abundant glycogen in the cytoplasm of the tumor cells.…”

Section: Pathologic Findingsmentioning

confidence: 98%

Translocation (4;19)(q35;q13.1)–Associated Primitive round Cell Sarcoma: Report of a Case and Review of the Literature

et al. 2008

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We report the 4th case of a primitive round cell sarcoma with the translocation (4;19)(q35;q13.1) as the primary cytogenetic abnormality. This undifferentiated sarcoma shows some features of Ewing sarcoma/primitive neuroectodermal tumor (ES/PNET), including a diffuse reactivity for FLI1, but it shows only focal and weak reactivity for CD99 and is negative for a rearrangement of EWS, the molecular signature of ES/PNET. Recognition of the histopathologic and cytogenetic features of this entity is necessary to avoid its misdiagnosis as ES/PNET, especially in small biopsy samples.

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“…[12][13][14] 12q13 are frequently observed in a variety of solid tumors including myxoid liposarcoma, chondrosarcoma, clear cell sarThis chromosomal abnormality was also identified in ovarian carcinoma, Wilms' tumor, peripheral neuroectodermal tumor, coma and rhabdomyosarcoma. [15][16][17][18] Various chromosomes can act as translocation partners in these tumors. Chromosome astrocytoma and retinoblastoma.…”

Section: Molecular Analysis For T(16;21)(p11;q22) Translocationmentioning

confidence: 99%

Establishment of a novel human acute myeloblastic leukemia cell line (YNH-1) with t(16;21), t(1;16) and 12q13 translocations

et al. 1997

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The t(16;21)(p11;q22) translocation is a non-random chromothe fused FUS/ERG protein is shown to function as a transcripsomal aberration observed in several types of human acute tional regulator. 8,11 myeloblastic leukemia (AML), whereas the der(16)t(1;16) and On the other hand, the der (16) A 46-year-old male engineer was admitted to our hospital because of fever in June 1994. Peripheral blood examination Introduction showed white blood cells 120 × 10 9 /l with 91% myeloblasts, hemoglobin 8.3 g/dl and platelets 104 × 10 9 /l. Bone marrow Chromosomal translocations in specific subtypes of leukemia examination revealed 91% myeloblasts that were positive for are recognized to play an important role in the process of myeloperoxidase (MPO) but negative for ␣-naphthyl butylate leukemogenesis by synthesis of chimeric proteins. 1,2 The esterase (␣-NBE) and chloroacetate esterase (CAE) stainings. t(16;21)(p11;q22) translocation is one of the non-random There was no abnormal feature in the eosinophils or monochromosomal aberrations observed in human acute myelocytes. In surface marker analysis the blasts from bone marrow blastic leukemia (AML), blastic crisis of chronic myelogenous were positive for CD13 (79.5%), CD33 (93.3%) and CD34 leukemia (CML) and myelodysplastic syndrome (MDS) that (64.5%). Chromosome analysis of bone marrow cells showed progressed to AML. 3-10 AML with t(16;21) has been classified 46,XY, der(16)t(16;21)(p11;q22)t(1;16)(q12;q13), der (21) An induction therapy was started with enocitabine, daunoruberythrophagocytosis. 3,4 Clinical prognosis of AML with icin, 6-mercaptopurine and prednisolone and complete t(16;21) seems to be poor. Recently, molecular characterizremission (CR) was achieved with normal karyotype. Despite ation of this translocation has revealed that the FUS gene (also two courses of consolidation therapy, the patient relapsed called TLS) encoding an RNA-binding protein on chromosome after 3 months from remission. The second CR was obtained 16 is fused with the ERG gene, a member of the ets gene by low-dose etoposide and aclarubicin treatment in March superfamily, on chromosome 21 to produce the FUS/ERG 1995. However, the second relapse occurred after 1 month chimeric transcript. [7][8][9][10][11] As a result, the RNA-binding domain with blastoma in the colon. The patient died of progressive of FUS is replaced with the DNA-binding domain of ERG and disease and pneumonia in May 1995. CytokinesCorrespondence: H Hamaguchi, Department of Hematology, Musashino Red Cross Hospital, 1-26-1 Kyonan-cho, Musashino-shi, TokyoAll cytokines used in this study, ie recombinant human gra-180, Japan

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12q13 abnormality in rhabdomyosarcoma

Cited by 42 publications

References 20 publications

The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC-DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

Translocation (4;19)(q35;q13.1)–Associated Primitive round Cell Sarcoma: Report of a Case and Review of the Literature

Establishment of a novel human acute myeloblastic leukemia cell line (YNH-1) with t(16;21), t(1;16) and 12q13 translocations

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