A case report of malignant neuroectodermal tumor of the gastrointestinal tract without common gene fusion in a soft tissue tumor
Case Report

A case report of malignant neuroectodermal tumor of the gastrointestinal tract without common gene fusion in a soft tissue tumor

Zi-Lin Liu1^, Bin Zhou2^, Yi-Jun Zhao1^, Miao-Qing Yu3^, Jie Liang1^, Yong Li1^

1Zhuhai Interventional Medical Center, Zhuhai Hospital Affiliated with Jinan University, Jinan University (Zhuhai People’s Hospital), Zhuhai, China; 2Department of Pathology, Zhuhai Hospital Affiliated with Jinan University, Jinan University (Zhuhai People’s Hospital), Zhuhai, China; 3Department of Radiology, Zhuhai Hospital Affiliated with Jinan University, Jinan University (Zhuhai People’s Hospital), Zhuhai, China

^ORCID: Zi-Lin Liu, 0000-0002-0653-1369; Bin Zhou, 0000-0001-6248-5769; Yi-Jun Zhao, 0000-0002-0616-0414; Miao-Qing Yu, 0000-0001-9582-8254; Jie Liang, 0000-0002-5613-5794; Yong Li, 0000-0001-6568-6857.

Correspondence to: Professor Yong Li, MD. Zhuhai Interventional Medical Center, Zhuhai Hospital Affiliated with Jinan University, Jinan University (Zhuhai People’s Hospital), Zhuhai, China. Email: lorry5160@163.com.

Background: Malignant gastrointestinal neuroectodermal tumor (GNET) is extremely rare in soft tissue sarcoma and occurs mainly in the small intestine of young adults, without sex predilection. Local recurrence and metastasis are common in GNET, resulting in a poor prognosis. GNETs are histologically and immunohistochemically similar to many sarcomas, especially clear cell sarcoma (CCS), making their identification difficult. The majority of GNET cases have EWSR1 gene rearrangements, which can be characterized at the genetic level and provide important clues for diagnosis of GNETs. However, very few studies have been conducted on GNET cases without common gene fusion in soft tissue tumors.

Case Description: A 48-year-old woman was admitted due to melena and worsening fatigue and dizziness. An abdominal computed tomography scan revealed a mass arising from the stomach with hepatic metastases. Based on the evidence of histology and immunohistochemistry, the final diagnosis was GNET. Then we performed a gene analysis of the tumor using fluorescence in situ hybridization and next-generation sequencing, including whole-exome sequencing and multiplex polymerase chain reaction. We did not detect any common gene fusion in the soft tissue tumors, such as EWSR1. The results of the whole-exome sequencing revealed 11 genes involved in the occurrence and development of soft tissue sarcomas. Six months after surgery, the patient's abdominal computed tomography (CT) showed new metastases in the liver. Hence, we used targeted therapy and immunotherapy to treat her and liver metastases were reduced.

Conclusions: Genetic diagnosis is one of the important evidences for the diagnosis of GNET. However, the cases of GNET with negative EWSR1 expression are rare, which makes clinical diagnosis difficult. Our findings may extend genetic understandings of GNET and provide more help for clinical diagnosis of GNET.

Keywords: Malignant gastrointestinal neuroectodermal tumor (GNET); gene fusion; next-generation sequencing; whole-exome sequencing; case report

Submitted Mar 28, 2022. Accepted for publication Jun 09, 2022.

doi: 10.21037/jgo-22-387


Malignant gastrointestinal neuroectodermal tumor (GNET), which is also known as clear cell sarcoma (CCS)-like tumor of the gastrointestinal tract (CCSLTGT), is a rare type of malignant soft tissue sarcoma that mainly occurs in the wall of the gastrointestinal tract (1). To date, <50 articles on CCSLTGTs have been published. This type of tumor mainly affects young people, and it has a poor prognosis and a controversial origin. Because of its similarity to CCS in terms of its histology, immunohistochemistry, and gene fusion (2), GNET is histologically and immunohistochemically similar to many sarcomas, especially clear cell sarcoma (CCS). (3). And more and more evidence supports that GNET and CCS were different kind of tumors (4). To the best of our knowledge, CCSLTGT GNET has only seldomly been diagnosed in the absence of EWSR1-CREB1 or EWSR1-ATF1 gene fusions (3,4). Here, we presented a case of hepatic metastases from GNETs negative for common gene fusion in a soft tissue tumor. This case will provide more evidence for the diagnosis of EWSR1 fusion-negative GNET in clinic. We present the following case in accordance with the CARE reporting checklist (available at https://jgo.amegroups.com/article/view/10.21037/jgo-22-387/rc).

Case presentation

Ethical statement

All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee(s) and with the Declaration of Helsinki (as revised in 2013). Written informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal.

Clinical history

A 48-year-old woman experienced melena accompanied by dizziness and fatigue for >15 days. A gastroscopic examination at another hospital revealed a mass in the gastric antrum with bleeding at the center. The patient initially refused surgery and received only symptomatic treatment, including the maintenance of hemostasis and the administration of gastrointestinal medications and infusions. A few days after discharge, the patient’s symptoms of melena, dizziness, and fatigue worsened. On admission to our hospital, her blood pressure was 92/56 mmHg. Routine blood tests revealed a low hemoglobin level (6.4 gm/dL); however, her tumor index was normal.

Gastroscopy was performed again after admission (see Figure 1A). An abdominal computed tomography (CT) scan showed a mass arising from the stomach with hepatic metastasis. Chest CT showed local rib metastasis. After admission, the patient's hemoglobin level reduced from 6.4 to 5.5 gm/dL, and symptoms of anemia were observed. We administered 200 mL of a red-blood cell suspension to the patient 4 times, and her anemia symptoms improved. Radical gastrectomy with resection of the liver metastasis was performed 5 days later. The gross operative findings included the stomach and segment VI of the liver. The gastric tumor was located in the posterior wall of the gastric antrum, approximately 1.5 cm from the pylorus. The excised tumor had a round shape and measured approximately 5 cm in diameter. There was a 5-cm diameter mass in segment VI of the liver. No mass or fluid accumulation was observed in other organs in the abdominal cavity. There were no family members with a disease similar to the patient’s disease.

Figure 1 Gastroscopic, histological images of the tumor, and the timeline of the patient. (A) On gastroscopy, 2 masses were observed in the antrum of the stomach, with ulcer bleeding at the center; (B,C) the tumor cells were arranged in the nest, and the nucleus was oval with small nucleoli surrounded by medium amounts of eosinophilic cytoplasm (magnifications: 20× and 40×, hematoxylin-eosin stain); (D) the timeline of the patient’s diagnosis, treatment and progression. GNET, gastrointestinal neuroectodermal tumor.


The surgical specimens were fixed with 10% neutral buffered formalin, 40 g/L of formaldehyde buffer, and embedded in paraffin, as per the routine process. At the microscopic level, the tumor, in which a local ulcer had formed, was observed in the submucosa and muscularis propria of the stomach wall. The tumor had medium epithelioid cells, and exhibited a nested growth pattern. Most of the tumor cells had round or oval nuclei with small nucleoli surrounded by moderate amounts of eosinophilic cytoplasm. Additionally, multinucleated osteoclast-like giant cells were found in the tumor (see Figure 1B,1C). However, there was no tumor invasion at the surgical margin and hepatic serosa, and there were no tumor cells in the lymph nodes. Further, the tumor cells in the liver were similar to those in the stomach. The timeline of the patient’s diagnosis, treatment and progression was showed in Figure 1D.

Immunohistochemical studies were performed on representative paraffin specimens. The following commercial immunohistochemical antibodies were listed: CK-pan, CgA, SYN, desmin, MyOD1, TTF-1, napsin-A, DOG1, CDX2, AFP, hepatocyte, Arginase-1, Cam5.2, HMB45, MelanA, vimentin, SMA, and SOX10 were obtained from Guangzhou Lbp Medicine Science & Technology Company Limited. CD99 and CD117 were obtained from Fuzhou Maixin Biotechnology Development Company Limited. CK7, CK20, and Ki-67 were obtained from Roche Life Science Company. Among them, SYN, CD34, vimentin, S-100, SOX10, CD56, TTF-1, CgA, CDX2 and desmin were analyzed on the Dako-link 48 platform. CD99, Napsin, SMA, Melan-A, HMB-45, AFP, Arginase-1, and hepatocyte were analyzed on the Dako-omnis platform. Ki-67 and Cam5.2 were analyzed on the Roche-XT platform. Immunohistochemical staining showed that the tumor cells were positive for S100 protein, Ki-67 (the positive rate of Ki-67 is 40%), CD56, and vimentin, focally positive for CD34 and SMA, and negative for CD117, CK-pan, CK7, CK20, chromogranin A, synaptophysin, desmin, MyOD1, TTF-1, napsin-A, DOG1, CDX2, AFP, hepatocyte, Arginase-1, Cam5.2, CD99, HMB-45, Melan-A, and SOX-10 (see Figure 2A-2F). Based on the histological and immunohistochemical findings, GNET was diagnosed.

Figure 2 The immunohistochemistry results of the tumor. (A,B) The biopsy tissue, which was examined immunohistochemically, was positive for S100 (magnifications: 20× and 40×); (C,D) the tumor cells were negative for HMB-45 (diaminobenzidine stain, magnifications: 20× and 40×); (E,F) the tumor cells were negative for Melan-A (diaminobenzidine stain, magnifications: 20× and 40×). The red boxes represent the position of the high magnification observation.

EWSR1 gene fusion is common in GNET. To confirm the GNET diagnosis in our case, we analyzed 200 interphase tumor cells in at least 2 fields by fluorescence in situ hybridization using the EWSR1 gene probe (obtained from Guangzhou Lbp Medicine Science and Technology Company Limited). No rearrangements in EWSR1 were detected (see Figure 3A). Next, we detected 64 pairs of common soft tissue tumor fusion genes using next-generation sequencing, including multiplex polymerase chain reaction. The detected gene panels are listed in Table 1. We extracted total ribonucleic acid (RNA) from paraffin tissue using the magnetic bead method, amplified soft tissue tumor-related fusion genes using an Ampliseq RNA SARC fusion panel, and performed amplicon library construction and sequencing experiments (using the Ion PGM™ system kit). We further tested for other mutations, including single nucleotide polymorphisms (SNPs), insertions and deletions, base deletions of <50 bp, somatic mutations, predisposing genes, and driver mutations, in the tumor genes using whole-exome sequencing more comprehensively. We compared these results with those obtained from a series of databases (see Figure 3B).

Figure 3 The gene analysis of the tumor. (A) No EWSR1 gene breaks and rearrangements were detected, and 200 interphase cells were analyzed. Green spectrum labeled 3'EWSR1(22q12) probe; red spectrum labeled 5'EWSR1 probe. The normal signal mode is 2F, and the typical positive signal mode is 1G1R1F (Note: G represents the green signal, R represents the red signal, F represents the yellow signal or green and red superimposed signals). (B) Tumor sequencing analysis process. (C) Results of the GO pathway enrichment analysis.

Table 1

Detected fusion gene probe in the common soft tissue tumor

Fusion gene 5' gene transcript number 5' genetic testing range 3' gene transcript number 3' genetic testing range
ACTB-GLI1 NM_001101.3 Exon2/3 NM_005269.3 Exon5-7
ASPSCR1-TFE3 NM_024083.4 Exon7 NM_006521.6 Exon5/6
ATIC-ALK NM_004044.7 Exon7 NM_004304.5 Exon20
BCOR-CCNB3 NM_017745.6 Exon15 NM_033031.2 Exon5
CARS-ALK NM_001751.6 Exon17 NM_004304.5 Exon20
CDH11-USP6 NM_001797.4 Exon1/2 NM_004505.4 Exon1/2
CIC-DUX4 NM_005258673.2 Exon20 NM_033178.4 Exon1
CIC-FOXO4 NM_005258673.2 Exon19/20 NM_005938.4 Exon2
CLTC-ALK NM_004859.4 Exon30 NM_004304.5 Exon20
COL1A1-PDGFB NM_000088.4 Full coding region NM_002608.4 Exon2
COL1A1-USP6 NM_000088.4 Exon1 NM_004505.4 Exon1/2
COL1A2-PLAG1 NM_000089.4 Exon1 NM_002655.3 Exon2/3
CNBP-USP6 NM_003418.5 Exon1 NM_004505.4 Exon1/2
EPC1-PHF1 NM_025209.5 Exon10 NM_024165.3 Exon2
ETV6-NTRK3 NM_001987.5 Exon4/5 NM_002530.4 Exon15
EWSR1-ATF1 NM_005243.4 Exon5-10 NM_005171.5 Exon4/5/7-10
EWSR1-CREB1 NM_005243.4 Exon7 NM_134442.5 Exon7
EWSR1-DDIT3 NM_005243.4 Exon7/9/10/13 NM_001195057.1 Exon2
EWSR1-ERG NM_005243.4 Exon6/7/9/10 NM_004449.4 Exon8-11
EWSR1-ETV1 NM_005243.4 Exon7 NM_004956.5 Exon12
EWSR1-ETV4 NM_005243.4 Exon7 NM_001079675.5 Exon8/9
EWSR1-FEV NM_005243.4 Exon7/9/10 NM_017521.3 Exon2
EWSR1-FLI1 NM_005243.4 Exon7-10 NM_002017.5 Exon4-9
EWSR1-NFATC2 NM_005243.4 Exon8 NM_173091.4 Exon3
EWSR1-NR4A3 NM_005243.4 Exon11-13 NM_006981.4 Exon1-3
EWSR1-PBX1 NM_005243.4 Exon7/8 NM_002585.4 Exon5
EWSR1-POU5F1 NM_005243.4 Exon6/7 NM_002701.6 Exon2
EWSR1-PATZ1 NM_005243.4 Exon8 NM_032051.2 Exon1
EWSR1-SMARCA5 NM_005243.4 Exon7 NM_003601.4 Exon5
EWSR1-SP3 NM_005243.4 Exon7/8 NM_003111.4 Exon6
EWSR1-WT1 NM_005243.4 Exon8-10 NM_000378.6 Exon8-10
EWSR1-ZNF444 NM_005243.4 Exon8 NM_018337.4 Exon5
FUS-ATF1 NM_004960.4 Exon5 NM_005171.5 Exon5
FUS-CREB3L2 NM_004960.4 Exon5-7 NM_194071.4 Exon5/6
FUS-DDIT3 NM_004960.4 Exon3/5-9/11-13 NM_001195057.1 Exon2/3
FUS-ERG NM_004960.4 Exon5-8 NM_004449.4 Exon8-11
HAS2-PLAG1 NM_005328.3 Exon1 NM_002655.3 Exon2
HEY1-NCOA2 NM_012258.4 Exon4 NM_006540.4 Exon13
HMGA2-LPP NM_003483.6 Exon2/3 NM_005578.3 Exon7/9
LMNA-NTRK1 NM_170707.4 Exon2 NM_001007792.1 Exon10
MEAF6-PHF1 NM_022756.6 Exon5 NM_024165.3 Exon2
MYH9-USP6 NM_002473.6 Exon1 NM_001304284.2 Exon9/10
NAB2-STAT6 NM_005967.4 Exon2-7 NM_003153.5 Exon2-7/16-19
OMD-USP6 NM_005014.2 Exon1 NM_004505.4 Exon1
PAX3-FOXO1 NM_181459.4 Exon7 NM_002015.4 Exon2
PAX3-NCOA1 NM_181459.4 Exon6/7 NM_005264625.1 Exon14/15
PAX3-NCOA2 NM_181459.4 Exon7 NM_006540.4 Exon12
PAX7-FOXO1 NM_002584.3 Exon7 NM_002015.4 Exon2
RANBP2-ALK NM_006267.5 Exon18 NM_004304.5 Exon20
SERPINE1-FOSB NM_000602.5 Exon1 NM_006732.3 Exon1/2
SFPQ-TFE3 NM_005066.3 Exon7/9 NM_006521.6 Exon5/6
SS18-SSX1 NM_001007559.3 Exon9/10 NM_005635.4 Exon4-6
SS18-SSX2 NM_001007559.3 Exon10 NM_003147.5 Exon6
SS18-SSX4 NM_001007559.3 Exon10 NM_005636.3 Exon3/6/7
TAF15-NR4A3 NM_207037.1 Exon6/7 NM_006981.4 Exon3
TCF12-NR4A3 NM_207036.2 Exon5 NM_006981.4 Exon3
TFG-NR4A3 NM_006070.6 Exon7 NM_006981.4 Exon3
THRAP3-USP6 NM_005119.4 Exon1 NM_004505.4 Exon1
TPM3-ALK NM_153649.4 Exon6/7 NM_004304.5 Exon20
TPM3-NTRK1 NM_153649.4 Exon6/7 NM_001007792.1 Exon10
TPM4-ALK NM_003290.2 Exon6/7 NM_004304.5 Exon20
TPR-NTRK1 NM_003292.3 Exon21 NM_001007792.1 Exon10
WWTR1-CAMTA1 NM_015472.6 Exon4 NM_015215.4 Exon8/9
ZC3H7B-BCOR NM_017590.6 Exon10 NM_001123385.2 Exon7

Follow up

However, 6 months postoperatively, a series of follow-up CT scans revealed an increase in the liver metastasis size, with the appearance of new metastases; the metastases on the rib did not change significantly. Targeted therapy and immunotherapy (camrelizumab 200 mg and anlotinib 12 mg) were then administered to treat the patient. The liver metastases were reduced during treatment, and no new metastases appeared.


In this article, we described a rare case of a woman presenting with a malignant gastrointestinal neuroectodermal tumor without common gene fusion in a soft tissue tumor. To the best of our knowledge, this is the first case report of a GNET mutation analysis.

GNET was first discovered in 1985 by Alpert and Beckstead (5). Zambrano et al. (6) reported 6 cases in 2003 and identified the similarities between GNET and CCS. In 2012, Stockman et al. (3) differentiated GNET from CCS using the immunohistochemical and ultrastructural evidence of 16 cases. The question of whether CCS and GNET are distinct tumors or whether GNET is a subtype of CCS has been debated for a long time. As related research became more thorough, GNET and CCS came to be considered and are now widely accepted to be two distinct entities. Most GNETs occur in the muscularis propria of the small intestine, with focal extensions into the serosa. Similar to some soft tissue sarcomas, the diagnosis of GNET remains a clinical challenge, and its diagnosis requires histological, immunohistochemical, and molecular evidence.

There are microscopic morphological and molecular similarities between GNET and CCS. The GNET and CCS tumor cells are characteristically composed of epithelioid, polygonal, or round cells with eosinophilic cytoplasm and vesicular nuclei with prominent nucleoli. However, CD68-positive, multinucleated osteoclast-like giant cells have been reported to occur in 50% of GNET cases (1,2). Such cells provide an important clue for distinguishing GNET from CCS (1,2). We did not find any osteoclast-like giant cells in the present case.

Immunohistochemically, GNET and CCS are positive for S100. However, most GNET cases are negative for melanocytic markers, such as HMB-45 and Melan-A. Additionally, many cases of GNET have shown evidence of neuroectodermal differentiation and have often shown focal reactivities for SOX10, synaptophysin, neuron-specific enolase, neurofilament, CD56, and CD57 at the immunophenotypic level (3). Gastrointestinal stromal tumors (GISTs) should also be considered for differential diagnosis. CD117 and DOG1 markers are positive in GISTs but negative in GNETs. The multinucleated osteoclast-like giant cells are rare in GIST, while c-kit fusion is common in GISTs genetically. Additionally, while granular cell tumors are also positive for S100 and CD56, their morphology under the microscope differs. The cytoplasm of granulosa cell tumors are more abundant than those of GNETs, and the cytoplasm of granular cell tumors contain augulate bodies.

Gene analysis plays an important role in diagnosing GNET. A molecular genetic study of most GNETs has found EWSR1 gene rearrangements, usually fused with ATF1 or CREB1 (4). EWSR1 has a propensity for fusing (as the 5’ partner) with a host of different genes, with its product being a member of the FET (FUS/EWSR1/TAF15) family of transcription factors (7). More than 70% of GNETs show EWSR1-ATF1 fusions, with 20–30% of cases showing EWSR1-CREB1 fusions. However, in our case, common gene rearrangements, including EWSR1, were not identified. For EWSR1 fusion-negative GNETs, there is currently less diagnostic evidence at the genetic level, so we performed further genetic analysis in this case.

Then we used next-generation sequencing technology to improve our understanding of the genetic mutations in this case. The somatic SNP mutation findings in our case revealed 374 gene locus mutations in our patient’s tumor. By comparing widely accepted cancer-associated mutated genes in the Cancer Gene Census database, we identified 15 genes involved in the mechanisms of the tumor. The Gene Ontology (GO) pathway enrichment analysis showed that 36 genes were involved in 17 pathways that regulated tumor growth (see Figure 3C). Combined with the results of The Cancer Gene Census database and the GO pathway enrichment analysis, 11 genes in this case were involved in the occurrence and development of soft tissue sarcoma, including APEX1, ATRX, TET1, POLQ, FGFR4, MEN1, MUC4, NELL1, KMT2C, PALB2, and ROCK1.

Among these, ATRX and PALB2 mutations are important in the pathogeneses of various kinds of sarcoma, such as dedifferentiated liposarcoma and leiomyosarcoma (8,9). MUC4 encodes transmembrane mucin 4 proteins, which are overexpressed in a variety of cancers (10). In our case, MUC4 was mutated at multiple sites, and may have been associated with the proliferation and metastasis of the tumor (11). FGFR4 is associated with a poor prognosis of rhabdomyosarcoma and may be a potential therapeutic target for sarcoma (12). APEX1, TET1, NELL1, KMT2C, and ROCK1 are related to the occurrence, development, and prognosis of osteosarcoma (13-15). Alterations in the POLQ gene could contribute to dendritic cell sarcoma formation but more evidence is needed (16). MEN1 mutations can be found in pulmonary carcinosarcoma (17). These genes require further study to reveal their role in the diagnosis and mechanism of GNET occurrence and development.

Driver genes play an important role in the modification and activation of cell functions. The identification of driver genes provides important mechanistic, diagnostic, and therapeutic insights (18). We identified the driving mutations in the tumor genes of our patient and compared them to the mutant genes in the latest versions of the Cancer Gene Census database (which contained 125 mutation driver genes) (18,19). We found that 6 genes had the following missense mutations: NEB, PALB2, ATRX, PWP1, GRIN3A, and ARID1B. The ATRX and PALB2 genes are closely related to sarcomas. ARID1B regulates the expression of the SWI/SWF complex, which may be potentially related to the mechanism of GNET formation (20). This provide more valuable clues for the diagnosis of GNET; however, the role of these genes in the occurrence and progression of neoplasms has not yet been clarified.


We reported a case of GNET lacking any common gene fusion in soft tissue tumors and analyzed the gene mutations of GNET. To date, few studies have been conducted on this rare type of GNET, but next-generation sequencing technologies can help us understand this disease. 11 genes included known cancer genes PALB2, ATRX were mutated in the case and were closely related to the development of soft tissue sarcomas. The genes identified in our case may contribute to the study of GNET genes.


Funding: None.


Reporting Checklist: The authors have completed the CARE reporting checklist. Available at https://jgo.amegroups.com/article/view/10.21037/jgo-22-387/rc

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://jgo.amegroups.com/article/view/10.21037/jgo-22-387/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work, including ensuring that any questions related to the accuracy or integrity of any part of the work have been appropriately investigated and resolved. All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee(s) and with the Declaration of Helsinki (as revised in 2013). Written informed consent was obtained from the patient for publication of this case report and accompanying images. A copy of the written consent is available for review by the editorial office of this journal.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.


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(English Language Editor: L. Huleatt)

Cite this article as: Liu ZL, Zhou B, Zhao YJ, Yu MQ, Liang J, Li Y. A case report of malignant neuroectodermal tumor of the gastrointestinal tract without common gene fusion in a soft tissue tumor. J Gastrointest Oncol 2022;13(3):1489-1498. doi: 10.21037/jgo-22-387

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