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

Butt, M. Majid; 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.18721.1

Cited by 7 publications

(23 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The EGFR synonymous exon 20 mutation (rs1050171) we have reported in this ACP tumor also reported in a case of grade III anaplastic ependymoma. 28 This synonymous EGFR SNP (p. Gln787Gln) was reported in 70% of lung adenocarcinoma tumors. This SNP was not a prognostic marker for anti-EGFR therapy; however, it is associated with improved overall survival (OS) in CRC patients.…”

Section: Discussionmentioning

confidence: 99%

“…This exon 7 variant p. (Ile391Met) was reported in grade III anaplastic ependymoma. 28 This variant is reported as a benign one in ClinVar and in SNP databases with reference numbers VCV000135038.1 and rs2230461, respectively. The intronic variant (rs3729674) also is a benign one, and it was reported in CRC and in endometrial cancer.…”

Section: Discussionmentioning

confidence: 99%

“…For immunohistochemistry, sections were collected on Citoglas adhesion microscope slides (Citotest) and then stained with antibodies according to standard protocols of Ventana BenchMark XT automated Stainer (Ventana, Tucson, AZ) as described previously. 27,28 Images were acquired using NIKON Digital Microscope Camera -DS-Ri1, with image software NIS Elements v.4.0. Histology data of the ACP tumor are shown in Figures 3 and 4.…”

Section: Histology and Radiology Examinationmentioning

confidence: 99%

“…Sequencing was performed using Ion PI v3 chip on Ion Proton instrument. 27,28 Libraries were prepared using Ion AmpliSeq Cancer HotSpot panel v. Figure 6. The Ion sphere particle (ISP) density image is showing the semi-conductor chip percent loading across the wells that contain a live ISP; the total number of bases reported in the output file is 10.2 G ( Figure 6A); ISP summary showing loading, enrichment, clonality and final library quality is shown in Figure 6B; In the histogram, the first row shows 95% of loaded wells and empty wells are 5%, wells with the predicted number of live library ISPs (enrichment) are 100%, clonal ISPs are 74% and 26% ISPs are polyclonal (ISPs carrying clones from two or more templates).…”

Section: Dna Isolation and Ngs Analysis On Ion Protonmentioning

confidence: 99%

See 3 more Smart Citations

<p>Adamantinomatous Craniopharyngioma in an Adult: A Case Report with NGS Analysis</p>

Jastania¹,

Saeed²,

Alkhalidi³

et al. 2020

IMCRJ

Self Cite

View full text Add to dashboard Cite

Purpose: Several recent studies have documented CTNNB1 and BRAF mutations which are mutually exclusive for adamantinomatous craniopharyngioma (ACP) and papillary craniopharyngioma (PCP) tumors. This discovery is helpful in the development of novel targeted therapies in successful clinical trials with BRAF mutations in PCP cases. However, no such targeted therapy is available yet for ACP. Here, we report novel mutations, which are not previously reported, in a case of an adult ACP using NGS analysis. Results: Patient DNA was sequenced using Ion PI v3 chip on Ion Proton. A total of 16 variants were identified in this tumor by NGS analysis, out of which four were missense mutations, seven were synonymous mutations, and five were intronic variants. In CTNNB1 gene a known missense mutation in c.101G>T; in TP53 a known missense mutation in c.215C>G; and two known missense variants in PIK3CA, viz., in c.1173A>G; in exon 7, and in c.3128T>C; in exon 21, were found, respectively. Seven synonymous mutations were detected in this tumor, viz., in IDH1 (rs11554137), in FGFR3 (rs7688609), in PDGFRA (rs1873778), in APC (COSM3760869), in EGFR (rs1050171), in MET (rs35775721), and in RET (rs1800861), respectively. Three known, intronic variants were found in genes, such as PIK3CA, KDR, and JAK3, respectively. Also, a 3'-UTR and a splice site acceptor site variant in CSF1R and FLT3 genes were found in this tumor. We have shown allele coverage, allele ratio, and p-value, for all these mutations. The p-values and Phred quality score were significantly high for these variants. Conclusion: As reported in previous studies, in ACP tumors we found a CTNNB1 mutation by NGS analysis. The PIK3CA variants we detected were not known previously in ACP tumors. Finding the PIK3CA mutations in the ACP tumors may help develop targeted therapy for a subset of craniopharyngiomas with PIK3CA activating mutations. Clinical trials are in progress with specific PIK3CA inhibitors in advanced stages of many cancers.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Histology and Radiology Examinationmentioning

confidence: 99%

Section: Dna Isolation and Ngs Analysis On Ion Protonmentioning

confidence: 99%

See 2 more Smart Citations

<p>Adamantinomatous Craniopharyngioma in an Adult: A Case Report with NGS Analysis</p>

Jastania¹,

Saeed²,

Alkhalidi³

et al. 2020

IMCRJ

Self Cite

View full text Add to dashboard Cite

show abstract

“…The vcf file data were analysed using Ion Reporter v5.6 (Thermo Fisher Scientific, Inc.). True mutations were considered based on a Phred score of >100, and mutation calling was considered significant by Ion Reporter software at P<0.05 (36,37).…”

Section: Validation Of Rt-qpcr Results By Sequencing the Pcr Productmentioning

confidence: 99%

EGFRvIII expression and isocitrate dehydrogenase mutations in patients with glioma

et al. 2020

Self Cite

View full text Add to dashboard Cite

Molecular pathology and personalized medicine are still being evolved in Saudi Arabia, and genetic testing for the detection of mutations as cancer markers have not been established in the diagnostics laboratories in Saudi Arabia. The aim of the present study was to determine the prevalence of isocitrate dehydrogenase (IDH1 and IDH2) mutations and epidermal growth factor receptor variant (EGFRv)III transcript expression in Saudi Arabian patients with glioma. Out of 117 brain tumors tested by reverse transcription-quantitative PCR for EGFRvIII, 41 cases tested positive. In the glioblastoma (GBM) category, 28/55 tumors were positive, in astrocytoma tumors 5/22, and in oligodendrogliomas 4/13 cases were positive respectively. EGFRvIII transcript was sequenced by capillary electrophoresis to demonstrate the presence of EGFRvIII-specific junction where exons 2-7 were deleted. In the present study 106 tumors were sequenced for IDH1 exon-4 mutations using the capillary sequencing method. The most common substitution missense mutation c.395G>A was found in 16 tumors. In the case of adamantinomatous craniopharyngioma, a novel missense mutation in c.472C>T was detected in IDH2 gene. Using next-generation sequencing (NGS), 74 tumors were sequenced for the IDH1 gene, and a total of 8 missense variants were identified in 36 tumors in a population of Saudi Arabia. The missense mutation (c.395G>A) was detected in 29/36 of tumors. A novel intronic mutation in c.414+9T>A was found in 13 cases in the IDH1 gene. In addition, one case exhibited a novel synonymous mutation in c.369A>G. Eleven tumors were found to have compound mutations in the IDH1 gene. In IDH2 gene, out of a total of 16 variants found in 6 out of 45 tumors, nine were missense, five were synonymous and one was intronic. This is the first report from Saudi Arabian laboratories analyzing glioma tumors for EGFRvIII expression, and the first study from Saudi Arabia to analyze IDH mutations in gliomas using the capillary and NGS methods.

show abstract

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

View full text Add to dashboard Cite

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.

show abstract

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

Cited by 7 publications

References 82 publications

<p>Adamantinomatous Craniopharyngioma in an Adult: A Case Report with NGS Analysis</p>

<p>Adamantinomatous Craniopharyngioma in an Adult: A Case Report with NGS Analysis</p>

EGFRvIII expression and isocitrate dehydrogenase mutations in patients with glioma

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

Contact Info

Product

Resources

About