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

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 cancer. Only one 3'-untranslated region (UTR) insertion variant in the NRAS gene (c.*2010T>AT) was detected in the tumor of the present study, and this was a splice site acceptor. A TP53 intronic mutation (c.782+1G>T) was the only pathogenic splice_donor_variant found in this HBL tumor. The frequency of variants and Phred scores were markedly high, and the p-values were significant for all of the aforementioned mutations. In summary, a total of 15 missense, 10 synonymous, and 19 intronic variants were identified in the HBL tumor. Results of the present study detected one novel insertion in NRAS and one novel deletion in HNF1A genes, a novel missense variant in the TP53 gene, and two novel missense variants of SND1. Hotspot mutations in other cancer driver genes, such as PTEN, ATM, SMAD4, SMARCB1, STK11, NPM1, CDKN2A, and EGFR, which are frequently affected in gliomas, were not found in the tumor of the present study. Future studies should aim to validate oncogenic mutations that may act as novel targets for the treatment of these tumors.

Mutation Profiling of Intracranial Myxopapillary Ependymoma by Next Generation DNA Sequencing.

OBJECTIVES: Primary intracranial myxopapillary ependymomas (MPE) are very rare. In order to determine genomic changes in an intracranial MPE, we analyzed its mutation patterns by next generation DNA sequencing. METHODS: Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6. RESULTS: In this tumor, NGS generated 6,298, 354 mapped reads using the Ion PI v3 Chip. The average reads per amplicon was 29,365, 100% of amplicons had at least 500 reads and the amplicons read end-to-end were 97.58%. In this tumor, NGS data analysis identified 12 variants, of which two were missense mutations, seven were synonymous mutations and three were intronic variants. Missense mutation in c.395G>A; in exon 4 of the IDH1 gene, and a missense mutation in c.215C>G; in exon 4 of the TP53 gene were found in this tumor were previously reported. The known synonymous mutations were found in this tumor were, in exon 14 of FGFR3 in c.1953G>A; in exon 12 of PDGFRA in c.1701A>G; in exon 18 of PDGFRA c.2472C>T; in exon 20 of EGFR in c.2361G>A; in exon 13 of RET in c.2307G>T; in exon 16 of APC in c.4479G>A; and in exon 2 of MET in c.534C>T. Additionally, a known intronic variant was identified in KDR and a known acceptor site splice variant in FLT3 (rs2491231) and a SNP in the 3 ' -UTR of the CSF1R gene (rs2066934) were also identified. Except, the frequency of IDH1 variant, the frequencies of other variants were high, and the p-values were significant and Phred scores were high for all of these mutations. CONCLUSIONS: The variants reported in this tumor have not been detected in myxopapillary grade I ependymoma tumor by NGS analysis previously and we therefore report these variants in this case for the first time.

EGFRvIII expression and isocitrate dehydrogenase mutations in patients with glioma.

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.

Adamantinomatous Craniopharyngioma in an Adult: A Case Report with NGS Analysis.

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.

Next generation DNA sequencing of atypical choroid plexus papilloma of brain: Identification of novel mutations in a female patient by Ion Proton.

Choroid plexus papilloma (CPP) is a rare benign tumor of the central nervous system that is usually confined to the cerebral ventricles. According to the World Health Organization, CPP corresponds to a grade I atypical CPP (a-CPP); however, it can become more aggressive and reach grade II, which can rarely undergo malignant transformation into a choroid plexus carcinoma (grade III). To the best of our knowledge, identification of these tumors mutations by next generation DNA sequencing (NGS) has not been yet reported. In the present study, NGS analysis of an a-CPP case was performed. Data were analyzed using Advaita Bioinformatics i-VariantGuide and Ion Reporter 5.6 programs. The results from NGS identified 12 novel missense mutations in the following genes: NOTCH1, ATM, STK36, MAGI1, DST, RECQL4, NUMA1, THBS1, MYH11, MALT1, SMARCA4 and CDH20. The PolyPhen score of six variants viz., DST, RECQL4, NUMA1, THBS1, MYHI1 and SMARCA4 were high, which suggested these variants represents pathogenic variants. Two novel insertions that caused frameshift were also found. Furthermore, two novel nonsense mutations and 14 novel intronic variants were identified in this tumor. The novel missense mutation detected in ATM gene was situated in c.5808A>T; p. (Leu1936Phe) in exon 39, and a known ATM mutation was in c.5948A>G; p. (Asn1983Ser). These novel mutations had not been reported in previous database. Subsequently, the quality statistics of these variants, including allele coverage, allele ratio, P-value, Phred quality score, sequencing coverage, PolyPhen score and alleles frequency was performed. For all variants, P-value was highly significant and the Phred quality score was high. In addition, the results from sequencing coverage demonstrated that 97.02% reads were on target and that 97.88% amplicons had at least 500 reads. These findings may serve at determining new strategies to distinguish the types of choroid plexus tumor, and at developing novel targeted therapies. Development of NGS technologies in the Kingdom of Saudi Arabia may be used in molecular pathology laboratories.

Quality of life assessment of breast cancer patients in Saudi Arabia.

BACKGROUND: To assess the quality of life (QOL) of females with breast cancer in Saudi Arabia and its association with patients' demographic, social, and clinical data. MATERIALS AND METHODS: This analytical cross-sectional study was conducted among breast cancer patients attending King Abdullah Medical City, Makkah. Participants were asked to complete a self-administered structured questionnaire. We utilized the validated Arabic version of the European Organization for Research and Treatment of Cancer QOL-C30 (EORTC-QOL-C30) and breast cancer module QLQ-BR23 (EORTC-QOL-BR-23). Data were analysed using SPSS; mean and standard deviation computed for continuous variables, and percentages for categorical variables. Student's t-test performed to compare mean scores for various groups. RESULTS: Eighty-eight women participated in the study. The participants had a mean global health score of 64.0, standard deviation (SD) = 27.7. Of the functional scales, role functioning scored the highest (mean 71.2, SD = 31), while social and emotional functioning scored the lowest, (mean 57 SD = 35.8) and (mean 59.5 SD = 32), respectively. On the symptom scales, the most troubling symptoms were fatigue and insomnia, (mean 48.86 SD = 29.4) and (mean = 48, SD = 35), respectively. On the disease-specific tool (QLQ-BR23), body image and future perspective scored the lowest with a mean of 60.2 SD = 35 and 42.0 SD = 39.6, respectively. The most distressing symptom was hair loss (mean 61.56 SD = 41). CONCLUSIONS: Our population showed an acceptable overall global health score. However, they scored low on the important functional and symptoms domains. This study implies that patient age, social, and physical factors were possible determinants of global health and QOL scores. The healthcare system of Saudi Arabia should, therefore, address all these different aspects of QOL of breast cancer survivors.

Perspective of Saudi women in the Makkah region on breast cancer awareness.

OBJECTIVE: To assess the perspective of Saudi women in the Makkah region on breast cancer awareness and early detection. MATERIALS AND METHODS: A mixed method study was conducted among 25-65 years old healthy Saudi females from Makkah region during the awareness campaign in October 2014. The participants were recruited by personal invitations at the women's places of work and social gatherings. The initial invitations were issued by either the research coordinator or the investigator. All women were asked to complete a short questionnaire on basic knowledge on breast cancer. This was followed by focus group discussions. All interviews were carried out by female breast cancer consultant oncologists. All discussion transcripts were summarized and categorized into main themes; data presented as frequencies and percentages. RESULTS: Forty Saudi females, aged 25-65 years, were included in the study. Nearly 38% of them had never attended any awareness campaign on breast cancer. Only 10% of the participants correctly answered all five basic questions on the risk and early detection of breast cancer; 63% of the women had never been taught breast self-examination. Participants' perception was discussed in five focus groups. Four themes were identified during the discussions: knowledge about breast cancer and screening; resources of breast cancer awareness; social support for access to awareness program; and beliefs on breast cancer and early detection. CONCLUSION: We recommend that strategies on breast cancer awareness in our population should focus on early detection by improving the knowledge and skills of women. These strategies should include programs widely accessible through primary health-care centers and other health-care institutions. In addition, we recommend that physicians and family members should be involved in these programs.

Sarcomatoid carcinoma of the cervix.

Sarcomatoid carcinoma is a rare pathological entity of the cervix. A case of FIGO stage III sarcomatoid carcinoma of the cervix is reported. The patient was treated with concurrent radiotherapy and chemotherapy. Despite the initial excellent local response to therapy, she developed an early metastatic disease. In a review of the published studies, only 19 cases were reported on this type of cervical cancer.

Assessment of malignancy rate in thyroid nodules according to the Bethesda system of fine-needle aspiration. Report from a tertiary center in the Southwestern region of Saudi Arabia.

OBJECTIVE: To determine the rates of malignancy of thyroid nodules in each standard cytologic diagnostic category of the Bethesda system. METHODS: In a retrospective cohort study from October 1998 to April 2007 at the Department of Pathology, Aseer Central Hospital, Southwestern region of Saudi Arabia, all cases of thyroid nodules that underwent preoperative cytologic examination by fine-needle aspiration (FNA) and concurrent postoperative histopathologic examination were included. All FNA diagnoses were reclassified using the thyroid FNA Bethesda reporting system, including non-diagnostic (insufficient), benign, atypical follicular lesion of undetermined significance (AFLUS), neoplasm, suspicious of malignancy, and malignant groups. The rate of malignancy based on final histopathologic evaluation was analyzed for each of these cytologic groups. RESULTS: A total of 323 thyroid fine needle aspiration cytology (FNAC) diagnoses were reclassified into non-diagnostic 6.2%, benign 57.3%, AFLUS 13.6%, follicular and Hurthle cell neoplasms 16.1%, suspicious of malignancy 1.5%, and malignant 5.3% groups. The corresponding rate of malignancy on histopathologic examination was as follows: 35% in the non-diagnostic group, 10.3% in the benign group, 15.9% in AFLUS group, 32.7% in follicular and Hurthle cell neoplasms, 60% in the suspicious of malignancy group, and 94% in the malignant group. CONCLUSION: Applying a standard terminology reporting system for thyroid FNA may enhance the communication between pathologists and clinicians, assists them to find out the rate of malignancy in each cytologic group, and facilitating a more consistent approach for patients' management.