Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing

Butt, Ejaz; Alyami, Sabra; Nageeti, T.; Saeed, Muhammad; Alquthami, Khalid; Bouazzaoui, Abdellatif; Athar, Mohammad; Abduljaleel, Zainularifeen; Al‐Allaf, Faisal A.; Taher, Mohiuddin M.

doi:10.12688/f1000research.18721.2

Cited by 6 publications

(9 citation statements)

References 83 publications

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“…Results of a previous study demonstrated a KDR mutation, namely, c.1416A>T; p. (Gln472His) in exon 11, in an anaplastic ependymoma Grade III tumor. In the HBL tumor in this study, c.862T>C; p. (Phe288Leu) was present in exon 7 [20].…”

Section: Gene Name Genotypementioning

confidence: 45%

“…In the ABL1 gene, a mutation c.864C>T; p. (Ala288Ala; COSM9802919) was detected in the skin, and in the HBL tumor in this study, another mutation in c.864A>T was found that caused the same synonymous change p. (Ala288Ala). Results of a previous study reported intronic PIK3CA (rs3729674) and missense KDR (rs1870377) variants in anaplastic ependymoma Grade III [20]. Notably, synonymous variants found in this tumor were detected in other tumors, such as APC (rs41115) variant in MPE [31], FGFR3 (rs7688609), PDGFRA (rs1873778), and RET (rs1800861) in anaplastic ependymoma Grade III tumor, a-CPP, and myxopapillary ependymoma (MPE) tumors [20,22,23].…”

Section: Gene Name Genotypementioning

confidence: 70%

“…Results of a previous study reported intronic PIK3CA (rs3729674) and missense KDR (rs1870377) variants in anaplastic ependymoma Grade III [20]. Notably, synonymous variants found in this tumor were detected in other tumors, such as APC (rs41115) variant in MPE [31], FGFR3 (rs7688609), PDGFRA (rs1873778), and RET (rs1800861) in anaplastic ependymoma Grade III tumor, a-CPP, and myxopapillary ependymoma (MPE) tumors [20,22,23].…”

Section: Gene Name Genotypementioning

confidence: 70%

“…Details of histopathological and immunological methods were published by us previously [20,21]. The formalin-fixed paraffin-embedded (FFPE) tumor tissue used in this NGS analysis was obtained from the Al-Noor Specialty Hospital, Makkah.…”

Section: Histopathological and Immunological Examinationmentioning

confidence: 99%

“…56404; Qiagen GmbH). As described previously [20], DNA (10 ng) was sequenced using the Ion PI v3 Chip kit (cat no. A25771) with the Ion Proton system (Thermo Fisher Scientific, Inc.) [21][22][23].…”

Section: Next-generation Dna Sequencing Analysismentioning

confidence: 99%

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Supratentorial Sporadic Hemangioblastoma: A Case Report With Mutation Profiling Using Next-Generation DNA Sequencing

Taher¹,

Bantan²,

Alwalily³

et al. 2023

Cureus

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The present study aimed to determine genomic changes in sporadic intracranial hemangioblastoma (HBL), and the mutation patterns were analyzed using next-generation DNA sequencing (NGS). In this NGS analysis of the HBL tumor, 67 variants of 41 genes were identified. Of these, 64 were single-nucleotide variants (SNVs), two were exonic insertions and deletions (INDEL), and one was an intronic INDEL. In total, 15 were missense exonic variants, including an insertion variant in the NRAS gene, c.1_2insA, and a deletion variant, c.745delT, in the HNF1A gene, both of these mutations produced a termination codon. Other exonic missense variants found in the tumor were CTNNB1 , FGFR3 , KDR , SMO , HRAS , RAI1 , and a TP53 variant (c.430C>G). Moreover, the results of the present study revealed a novel variant, c.430C>G, in TP53 and two missense variants of SND1 (c.1810G>C and c.1814G>C), which were also novel. ALK (rs760315884) and FGFR2 (rs1042522) missense variants were reported previously. Notably, a total of 10 previously reported single-nucleotide polymorphisms (SNPs) were found in this tumor in genes including MLH1 (rs769364808), FGFR3 (rs769364808), two variants (rs1873778 and rs2228230) in PDGFRA , KIT (rs55986963), APC (rs41115), and RET (rs1800861). The results of this study revealed a synonymous mutation (SNP) in c.1104 G>T; p. (Ser368Ser) in the MLH1 gene. In this amino acid (AA) codon, two other variants are also known to cause missense substitutions, c.1103C>G; p. (Ser368Trp); COSM6986674) and c.1103C>T; p.(Ser368Leu; COSM3915870), were found in hematopoietic and urinary tract tissue, respectively. However, three SNPs found in genes such as ALK , KDR , and ABL1 in the HBL tumor in this study were not reported in UCSC, COSMIC, and ClinVar databases. Additionally, 19 intronic variants were identified in this tumor. One intronic SNV was present in each of the following genes: EGFR , ERBB4 , KDR , SMO , CDKN2B , PTEN , PTPN11 , RB1 , AKT1 , and ERBB2 . In PIK3CA and FBXL18 genes, two intronic variants were present, and in the SND1 gene, three intronic variants were detected in the HBL tumor presented in this study. Notably, only one of these was reported in the catalog of somatic mutations in canc...

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Section: Gene Name Genotypementioning

confidence: 45%

Section: Gene Name Genotypementioning

confidence: 70%

Section: Gene Name Genotypementioning

confidence: 70%

Section: Histopathological and Immunological Examinationmentioning

confidence: 99%

Section: Next-generation Dna Sequencing Analysismentioning

confidence: 99%

See 3 more Smart Citations

Supratentorial Sporadic Hemangioblastoma: A Case Report With Mutation Profiling Using Next-Generation DNA Sequencing

Taher¹,

Bantan²,

Alwalily³

et al. 2023

Cureus

Self Cite

View full text Add to dashboard Cite

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Synonymous Variants: Necessary Nuance in Our Understanding of Cancer Drivers and Treatment Outcomes

Kaissarian

Meyer

Kimchi-Sarfaty³

2022

JNCI: Journal of the National Cancer Institute

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Once called “silent mutations” and assumed to have no effect on protein structure and function, synonymous variants are now recognized to be drivers for some cancers. There have been significant advances in our understanding of the numerous mechanisms by which synonymous single nucleotide variants (sSNVs) can affect protein structure and function by affecting pre-mRNA splicing, mRNA expression, stability, folding, miRNA binding, translation kinetics, and co-translational folding. This review highlights the need for considering sSNVs in cancer biology to gain a better understanding of the genetic determinants of human cancers and to improve their diagnosis and treatment. We surveyed the literature for reports of sSNVs in cancer and found numerous studies on the consequences of sSNVs on gene function with supporting in vitro evidence. We also found reports of sSNVs that have statistically significant associations with specific cancer types but for which in vitro studies are lacking to support the reported associations. Additionally, we found reports of germline and somatic sSNVs that were observed in numerous clinical studies and for which in silico analysis predicts possible effects on gene function. We provide a review of these investigations and discuss necessary future studies to elucidate the mechanisms by which sSNVs disrupt protein function and are play a role in tumorigeneses, cancer progression, and treatment efficacy. As splicing dysregulation is one of the most well recognized mechanisms by which sSNVs impact protein function, we also include our own in silico analysis for predicting which sSNVs may disrupt pre-mRNA splicing.

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Multifocal intradural extramedullary ependymoma, MYCN amplified: illustrative case

Shields

Sun

Highfield³

et al. 2022

Journal of Neurosurgery: Case Lessons

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BACKGROUND Ependymomas are the most frequent tumors of the adult spinal cord, representing 1.9% of all central nervous system tumors and 60% of spinal cord tumors. Spinal ependymomas are usually solitary, intramedullary lesions. While intradural extramedullary (IDEM) ependymomas are infrequent, multifocal IDEM ependymomas are exceptionally rare. OBSERVATIONS The authors reported the first case in the literature of a patient diagnosed with multifocal IDEM ependymomas who was treated with tumor resection and brain and spinal radiotherapy. The patient presented with a 10-day history of bilateral leg numbness extending to the umbilicus and gait instability. Magnetic resonance imaging (MRI) studies revealed multiple enhancing nodular nodules throughout the entire spinal canal. Brain MRI revealed no abnormal lesions. A World Health Organization grade II ependymoma was confirmed histologically. At 31 months postoperatively, the patient remained clinically asymptomatic. Although cervical and thoracic MRI revealed stable intradural nodules and several areas of leptomeningeal enhancement, no malignant cells were seen in the cerebrospinal fluid (CSF). He underwent genetic testing to determine the appropriate chemotherapeutic agent if activation of the tumor should arise. LESSONS Because complete resection of multifocal IDEM ependymomas is not feasible, continued monitoring with brain and spine MRI is warranted to detect potential tumor dissemination in the CSF.

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Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing

Cited by 6 publications

References 83 publications

Supratentorial Sporadic Hemangioblastoma: A Case Report With Mutation Profiling Using Next-Generation DNA Sequencing

Supratentorial Sporadic Hemangioblastoma: A Case Report With Mutation Profiling Using Next-Generation DNA Sequencing

Synonymous Variants: Necessary Nuance in Our Understanding of Cancer Drivers and Treatment Outcomes

Multifocal intradural extramedullary ependymoma, MYCN amplified: illustrative case

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