Detection of FOXO1 break-apart status by fluorescence in situ hybridization in atypical alveolar rhabdomyosarcoma

Fu, Libing; Jin, Yichen; Chen, Jia; Zhang, Jie; Tai, Jun; Li, Hongbin; Chen, Feng; Shi, Jin; Guo, Yongli; Ni, Xin; He, Lejian

doi:10.1007/s11427-017-9082-9

Cited by 6 publications

(2 citation statements)

References 24 publications

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“…CNVs are believed to originate via diverse mutational mechanisms such as errors in replication, meiotic recombination, and repair of double-strand breaks [2]. Evidence has mounted that CNVs make a significant contribution to rare variants involved in rare diseases [3][4][5][6] and more common diseases such as cancers [7,8] and neurodevelopmental disorders [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

X-CNV: genome-wide prediction of the pathogenicity of copy number variations

et al. 2021

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Background Gene copy number variations (CNVs) contribute to genetic diversity and disease prevalence across populations. Substantial efforts have been made to decipher the relationship between CNVs and pathogenesis but with limited success. Results We have developed a novel computational framework X-CNV (www.unimd.org/XCNV), to predict the pathogenicity of CNVs by integrating more than 30 informative features such as allele frequency (AF), CNV length, CNV type, and some deleterious scores. Notably, over 14 million CNVs across various ethnic groups, covering nearly 93% of the human genome, were unified to calculate the AF. X-CNV, which yielded area under curve (AUC) values of 0.96 and 0.94 in training and validation sets, was demonstrated to outperform other available tools in terms of CNV pathogenicity prediction. A meta-voting prediction (MVP) score was developed to quantitively measure the pathogenic effect, which is based on the probabilistic value generated from the XGBoost algorithm. The proposed MVP score demonstrated a high discriminative power in determining pathogenetic CNVs for inherited traits/diseases in different ethnic groups. Conclusions The ability of the X-CNV framework to quantitatively prioritize functional, deleterious, and disease-causing CNV on a genome-wide basis outperformed current CNV-annotation tools and will have broad utility in population genetics, disease-association studies, and diagnostic screening.

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Section: Introductionmentioning

confidence: 99%

X-CNV: genome-wide prediction of the pathogenicity of copy number variations

et al. 2021

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“…Frederic previously detected the fusion gene PAX3–FOXO1 in 78 cases of ARMS, and 43 cases were positive for PAX3–FOXO1, with a positive rate of 55%, which had a lower positive rate in their study ( Sorensen et al, 2002 ). We detected FOXO1 rearrangement by FISH in 14 cases of RMS samples, a typical positive signal (1F1R1G) was observed in 10 cases of ARMS ( Fu et al, 2017 ). The PAX3–FOXO1 fusion gene status was correlated with the TNM stage, lymph node metastasis, and distant metastasis.…”

Section: Discussionmentioning

confidence: 86%

Detection of various fusion genes by one-step RT-PCR and the association with clinicopathological features in 242 cases of soft tissue tumor

Song

Zhang

Wang

et al. 2023

Front. Cell Dev. Biol.

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Introduction: Over the past decades, an increasing number of chromosomal translocations have been found in different STSs, which not only has value for clinical diagnosis but also suggests the pathogenesis of STS. Fusion genes can be detected by FISH, RT-PCR, and next-generation sequencing. One-step RT-PCR is a convenient method to detect fusion genes with higher sensitivity and lower cost.Method: In this study, 242 cases of soft tissue tumors were included, which were detected by one-step RT-PCR in multicenter with seven types of tumors: rhabdomyosarcoma (RMS), peripheral primitive neuroectodermal tumor (pPNET), synovial sarcoma (SS), myxoid liposarcomas (MLPS), alveolar soft part sarcoma (ASPS), dermatofibrosarcoma protuberans (DFSP), and soft tissue angiofibroma (AFST). 18 cases detected by one-step RT-PCR were further tested by FISH. One case with novel fusion gene detected by RNA-sequencing was further validated by one-step RT-PCR.Results: The total positive rate of fusion genes was 60% (133/213) in the 242 samples detected by one-step RT-PCR, in which 29 samples could not be evaluated because of poor RNA quality. The positive rate of PAX3–FOXO1 was 88.6% (31/35) in alveolar rhabdomyosarcoma, EWSR1–FLI1 was 63% (17/27) in pPNET, SYT–SSX was 95.4% in SS (62/65), ASPSCR1–TFE3 was 100% in ASPS (10/10), FUS–DDIT3 was 80% in MLPS (4/5), and COL1A1–PDGFB was 66.7% in DFSP (8/12). For clinicopathological parameters, fusion gene status was correlated with age and location in 213 cases. The PAX3–FOXO1 fusion gene status was correlated with lymph node metastasis and distant metastasis in RMS. Furthermore, RMS patients with positive PAX3–FOXO1 fusion gene had a significantly shorter overall survival time than those patients with the negative fusion gene. Among them, the FISH result of 18 cases was concordant with one-step RT-PCR. As detected as the most common fusion types of AHRR–NCOA2 in one case of AFST were detected as negative by one-step RT-PCR. RNA-sequencing was used to determine the fusion genes, and a novel fusion gene PTCH1–PLAG1 was found. Moreover, the fusion gene was confirmed by one-step RT-PCR.Conclusion: Our study indicates that one-step RT-PCR displays a reliable tool to detect fusion genes with the advantage of high accuracy and low cost. Moreover, it is a great tool to identify novel fusion genes. Overall, it provides useful information for molecular pathological diagnosis and improves the diagnosis rate of STSs.

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The triphibious warfare against viruses

Liu

2017

Sci. China Life Sci.

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Detection of FOXO1 break-apart status by fluorescence in situ hybridization in atypical alveolar rhabdomyosarcoma

Cited by 6 publications

References 24 publications

X-CNV: genome-wide prediction of the pathogenicity of copy number variations

X-CNV: genome-wide prediction of the pathogenicity of copy number variations

Detection of various fusion genes by one-step RT-PCR and the association with clinicopathological features in 242 cases of soft tissue tumor

The triphibious warfare against viruses

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