Rare Germline Mutations Identified by Targeted Next-Generation Sequencing of Susceptibility Genes in Pheochromocytoma and Paraganglioma

Background:Melanoma has a complex molecular background and multiple genes are involved in its development and progression. The advent of next generation sequencing platforms has enabled the evaluation of multiple genes at a time, thus unraveling new insights into the genetics of melanoma. We investigated a set of germline mutations able to discriminate the development of multiple primary melanomas (MPM) vs. single site primary melanomas (SPM) using a targeted next generation sequencing panel.Materials and Methods:A total of 39 patients, 20 with SPM and 19 with MPM, were enrolled in our study. Next generation analysis was carried out using a custom targeted sequencing panel that included 32 genes known to have a role in several carcinogenic pathways, such as those involved in DNA repair, pigmentation, regulation of kinases, cell cycle control and senescence.Results:We found a significant correlation between PIK3CA:p.I391M and MPMs, compared to SPMs,p= 0.031 and a trend for the association between CYP1B1: p.N453S and SPMs, compared to MPMs (p= 0.096). We also found that both subgroups shared a spectrum of 9 alterations in 8 genes (CYP1B1: p.N453S, BAP1: p.C39fs, PIK3CA: p.I391M, CDKAL1: c.1226_1227TG, POLE: p.V1161fs, OCA2: p.R419Q, OCA2: p.R305W, MC1R: p.V60L, MGMT: p.L115F), which suggested that these genes may play a role in melanoma development.Conclusions:In conclusion, despite the small cohort of patients, we found that germline mutations, such as those of PIK3CAand CYP1B1, might contribute to the differential development of SPM and MPM.

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Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy

Neuro-Oncology ◽

10.1093/neuonc/now254 ◽

2016 ◽

pp. now254 ◽

Cited By ~ 30

Author(s):

Cassie N. Kline ◽

Nancy M. Joseph ◽

James P. Grenert ◽

Jessica van Ziffle ◽

Eric Talevich ◽

...

Keyword(s):

Targeted Therapy ◽

Next Generation Sequencing ◽

Germline Mutations ◽

Next Generation ◽

Oncology Patients ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Germline Pathogenic Variants Identified by Targeted Next-Generation Sequencing of Susceptibility Genes in Pheochromocytoma and Paraganglioma

Journal of Kidney Cancer and VHL ◽

10.15586/jkcvhl.v8i1.171 ◽

2021 ◽

Vol 8 (1) ◽

pp. 19-24

Author(s):

Sinem Yalcintepe ◽

Hakan Gurkan ◽

Fatma Nur Korkmaz ◽

Selma Demir ◽

Engin Atli ◽

...

Keyword(s):

Next Generation Sequencing ◽

Susceptibility Genes ◽

Next Generation ◽

Clinical Genetic ◽

Targeted Next Generation Sequencing ◽

Clinical Genetic Testing ◽

Pathogenic Variants ◽

Diagnosis Rate ◽

Gene Panels ◽

Generation Sequencing

The aim of this study was to evaluate germline variant frequencies of pheochromocytoma and paraganglioma targeted susceptibility genes with next-generation sequencing method. Germline DNA from 75 cases were evaluated with targeted next-generation sequencing on an Illumina NextSeq550 instrument. KIF1B, RET, SDHB, SDHD, TMEM127, and VHL genes were included in the study, and Sanger sequencing was used for verifying the variants. The pathogenic/likely pathogenic variants were in the VHL, RET, SDHB, and SDHD genes, and the diagnosis rate was 24% in this study. Three different novel pathogenic variants were determined in five cases. This is the first study from Turkey, evaluating germline susceptibility genes of pheochromocytoma and paraganglioma with a detection rate of 24% and three novel variants. All patients with pheochromocytoma and paraganglioma need clinical genetic testing with expanded targeted gene panels for higher diagnosis rates.

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Pilot study of clinical targeted next generation sequencing for prostate cancer: Consequences for treatment and genetic counseling.

Journal of Clinical Oncology ◽

10.1200/jco.2016.34.2_suppl.251 ◽

2016 ◽

Vol 34 (2_suppl) ◽

pp. 251-251

Author(s):

Heather H. Cheng ◽

Nola Klemfuss ◽

Robert B. Montgomery ◽

Celestia S. Higano ◽

Michael Thomas Schweizer ◽

...

Keyword(s):

Prostate Cancer ◽

Clinical Trial ◽

Next Generation Sequencing ◽

Pilot Study ◽

Germline Mutations ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Targeted Ngs ◽

High Penetrance ◽

Generation Sequencing

251 Background: Targeted next generation sequencing (NGS) panels for identification of actionable mutations are increasingly used in oncology for therapeutic decision-making, but have yet to be widely used for prostate cancer.To determine the utility of applying a targeted next generation sequencing to prostate cancer management, we conducted a pilot study using the clinical molecular diagnostic assay, UW-OncoPlex, on primary and metastatic tumors from patients with prostate cancer. Methods: Patients receiving treatment for prostate cancer by a medical oncologist were eligible. After providing informed consent, tumor DNA was extracted from formalin-fixed, paraffin-embedded (FFPE)primary tumors and/or metastatic biopsies. Extracted DNA was analyzed using UW-OncoPlex, a targeted NGS panel designed to assess genomic alterations in 234 cancer-associated genes (PMID: 24189654). Results were discussed at a monthly multidisciplinary precision tumor board prior to communicating results to patients. Results: Forty patients consented to the study and 31 (78%) had reportable results. Findings included frequently observed prostate cancer genomic aberrations, including: TMPRSS2-ERG fusions and copy-number alterations of PTEN, TP53, FOXA1, AR, and SPOP. We also observed potentially actionable alterations in BRAF, MAP2K1 (MEK1), PIK3R1, MET, FGFR1, and FGFR3, which inform future treatment and clinical trial considerations. Notably, 8/31 (25%) patients had suspected high penetrance germline mutations, including in BRCA2 (N = 3), TP53 (N = 2), ATM (N = 1), and CHEK2 (N = 2). These 8 individuals were referred to medical genetics and 7 of 8 mutations were confirmed to be germline. One patient was found to have a hypermutated phenotype associated with bi-allelic MSH6 mutation and microsatellite instability. Conclusions: Targeted NGS panel testing may be useful in informing future treatment approaches and clinical trial selection for patients with prostate cancer. In addition, we observed a high proportion of cases with suspected high-penetrance germline mutations and immediate actionability through referral to medical genetics.

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Mutational landscape by targeted next-generation sequencing in EBV-associated lymphoepithelioma-like cholangiocarcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.4_suppl.269 ◽

2019 ◽

Vol 37 (4_suppl) ◽

pp. 269-269

Author(s):

Nai-Jung Chiang ◽

Ming-Huang Chen ◽

Li-Tzong Chen ◽

Shan Yanshen

Keyword(s):

Next Generation Sequencing ◽

Peripheral Blood ◽

Copy Number ◽

Somatic Mutations ◽

Tumor Tissue ◽

Germline Mutations ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing ◽

Cancer Panel

269 Background: Lymphoepithelioma-like cholangiocarcinoma (LELCC) is a rare variant of intrahepatic cholangiocarcinoma, which is highly associated with EBV infection and abundant lymphoplasmacytic cell infiltration. However, there’s limited data of genetic background in LELCC. Therefore, we want to explore the mutation profiles of LELCC, as well as copy number variations. Methods: Five patients’ tumor tissues diagnosed as LELCC, with positive EBER expression were retrospectively collected and microscopically dissected. Of them, two patients’ peripheral blood mononuclear cell served as background of germline mutations. Targeted next-generation sequencing was performed using the ACTOnco Comprehensive Cancer Panel (Ion AmpliSeq Comprehensive Cancer Panel, Life Technologies) to target all coding exons of 409 cancer-related genes for analysis of tumor tissue and blood. PDL1 immunohistochemistry staining with 22C3 antibody pharmDx was applied. Results: All EBV-associated LELCC showed positive expression of PDL1 staining, with combined positive score from 5% to 30%. Both somatic and germline mutations can be detected in LELCC tissue because diffuse infiltration of lymphocytes over tumor. After adjusting for background germline mutation frequency from peripheral blood, only mutations with allele frequency less than or around 10% were considered as somatic mutations. Overall, 10 nonsynonymous somatic mutations were detected in 4 (80%) patients with a range of 1-5 mutations per sample. Mutations were identified including BARD1, EPHA5, MUC16, TNFAIP3, CD19, PTEN, TET1, RECQL4, CD79B, and KDM5A. Copy number changes were rare in this special population. Interesting, one patient who failed to gemcitabine plus cisplatin got partial response after anti-PD1 inhibitor treatment. Conclusions: LELCC is highly correlated with PDL1 expression in tumor and immune cells. It’s necessary to have both tumor tissue and peripheral blood for next-generation sequencing to identify truly somatic mutations in LELCC.

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