Next generation sequencing of non-muscle invasive bladder cancer to reveal potential biomarkers and rational therapeutic targets.

2017 ◽  
Vol 35 (6_suppl) ◽  
pp. 302-302
Author(s):  
Eugene J. Pietzak ◽  
Eugene K. Cha ◽  
Aditya Bagrodia ◽  
Esther N. Drill ◽  
Gopa Iyer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cox Regression ◽  
Clinical Laboratory ◽  
Genetic Alterations ◽  
Gene Panel ◽  
Next Generation ◽  
Cox Regression Analysis ◽  
Bcg Therapy ◽  
Pre Treatment ◽  
Generation Sequencing

302 Background: We examined a cohort of index pre-treatment NMIBC tumors using Next Generation Sequencing to identify genetic alterations with potential clinical implications. Methods: 105 patients on a prospective IRB-approved protocol had their pre-treatment index NMIBC tumor and matched germline DNA sequenced with a 341 cancer-associated gene panel in a CLIA-certified clinical laboratory. A genitourinary pathologist reviewed representative H&E slides to confirm grade, stage, and urothelial histology. Restaging TUR was performed in all HGT1 tumors. Results: To characterize the genomic landscape of NMIBC, we analyzed 105 tumors across the disease spectrum including LGTa (n = 23), HGTis (n = 12), HGTa (n = 32) and HGT1 (n = 38). The most frequently altered genes in NMIBC were the TERT promoter (74%), FGFR3 (50%), KDM6A (47%), ARID1A (28%), PIK3CA (27%), KMT2D (24%), STAG2 (21%), and CDKN2A (17%). 81% of tumors had inactivating alterations in a chromatin-modifying gene. Alterations in the RTK/RAS/PIK3 pathway occurred in 83% of tumors, including 58% of high-grade NMIBC having alterations in either ERBB2 or FGFR3. Of the 105 patients, 62 were treated uniformly with a 6-week induction course of BCG without maintenance. We investigated all genes altered on the 341-gene panel in at least 5 patients for their association with recurrence after BCG therapy in this 62 patient cohort. On cox-regression analysis, only truncating mutations in the chromatin-modifying gene ARID1A were associated with recurrence after BCG (HR = 3.14 [95%CI = 1.51, 6.51] p = 0.002). This remained significant when adjusting for multiple comparisons (p = 0.04) and when including ARID1A missense mutations of unknown significance (p = 0.002). Conclusions: Next Generation Sequencing of index pre-treatment NMIBC tumors identified an association between ARID1A mutations and recurrence after BCG therapy. Further investigation is needed to determine whether ARID1A mutations are a potential predictive/prognostic biomarker or therapeutic target. Moreover, most NMIBC tumors had at least one potentially “actionable” alteration that could serve as a target in rationally designed trials of intravesical or systemic therapy.

Concurrent genetic alterations identified by next-generation sequencing in pre-treatment, metastatic EGFR-mutant lung cancers.

2016 ◽  
Vol 34 (15_suppl) ◽  
pp. 9053-9053 ◽  
Author(s):  
Helena Alexandra Yu ◽  
Emmet Jordan ◽  
Ai Ni ◽  
Daniel Feldman ◽  
Christopher Rodriguez ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Alterations ◽  
Next Generation ◽  
Lung Cancers ◽  
Pre Treatment ◽  
Egfr Mutant ◽  
Generation Sequencing

scholarly journals Analytical Validation and Performance of a 7-gene Next-generation Sequencing Panel in Uveal Melanoma

2020 ◽  
Author(s):  
Katherina Maria Alsina ◽  
Lauren M Sholl ◽  
Kyle R Covington ◽  
Suzette M Arnal ◽  
Michael M Durante ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Uveal Melanoma ◽  
Clinical Laboratory ◽  
Limit Of Detection ◽  
Gene Panel ◽  
Biopsy Sample ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Mutational Profiling ◽  
Generation Sequencing

Abstract Background: A 15-gene expression profiling (GEP) test is widely used for prognostication of metastatic risk in uveal melanoma (UM) patients. Because the amount of tumor tissue that can be safely obtained by biopsy from UM is limited, it is critical to obtain as much individualized genomic information as possible from each biopsy sample. Mutational profiling of UM tumors using next generation sequencing (NGS) in combination with GEP allows for analysis of both DNA and RNA from a single tumor sample, offers additional prognostic value, and can potentially inform therapy selection. This study evaluated the analytical performance of a targeted custom NGS panel for mutational profiling of the seven genes known to be commonly mutated in primary UM.Methods: 105 primary UM samples were analyzed, including 37 formalin-fixed paraffin embedded (FFPE) specimens and 68 fine needle aspiration biopsy (FNAB) specimens obtained with a 25- or 27-gauge needle. Sequencing was performed on the Ion GeneStudio S5 platform to an average read depth of greater than 500X per region of interest in a clinical laboratory accredited by the College of American Pathologists (CAP) and certified under the Clinical Laboratory Improvement Amendments (CLIA).Results: The 7-gene panel assay achieved a positive percent agreement (PPA) of 100% for detection of both single nucleotide variants (SNVs) and insertions/deletions (INDELs), with a technical positive predictive value (TPPV) of 99.4% and 100%, respectively. Intra-assay and inter-assay concordance studies confirmed the reproducibility and repeatability of the assay. The limit of detection was determined to be 5% variant allele frequency (VAF) for both SNVs and INDELs, with a minimum DNA input requirement of 1.5ng for FNAB and 5ng for FFPE samples.Conclusions: The 7-gene panel is a robust, highly accurate NGS test that can be successfully performed, along with GEP, from a single small gauge needle biopsy sample.

SAT0531 NEXT GENERATION SEQUENCING AND AUTOINFLAMMATORY SYNDROMES: CLINICAL AND GENETICAL CORRELATION ON AN ADULT POPULATION FROM A REFERRAL THIRD-CARE CENTRE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1223-1223
Author(s):  
J. R. Marques Soares ◽  
M. Antolin Mate ◽  
E. Garcia Arumi ◽  
E. Tizzano Ferrari ◽  
S. Bujan Rivas
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Data ◽  
Clinical Suspicion ◽  
Gene Panel ◽  
Adult Patients ◽  
Next Generation ◽  
Related Gene ◽  
Unknown Significance ◽  
Level Hospital ◽  
Generation Sequencing

Background:Systemic autoinflammatory diseases (sAID) are a group of conditions with recurrent episodes of inflammation in absence of infection or autoimmune response. Its physiopathology mainly lies on mono/poligenic mutations involving genes related to the innate immune system response. Next Generation Sequencing (NGS) platformss have been a big step forward on sAID diagnosis, although a clinical and genetic correlation is still needed.Objectives:To review the sAID related gene panel variants identified using NGS sAID gene panel on a cohort of adult patients screened for sAID from a referral third-level hospital.To correlate genetic and clinical findings for sAID related variants identified in order to the clinical suspicion diagnosis of sAID.Methods:A retrospective review of a cohort of adult (≥ 16 yo) patients with available NGS sAID related gene panel (MiSeq Illumina sequencing platform including intron and exon variants from up to 17 sAID genes, with coverage depth > x100) among 2014 and 2019 was performed.Demographic, clinical and genetic data were collected in a database.Genetic variants were classified according to the American College of Medical Genetics/Association for Molecular Pathology classification as benign/likely benign/variable of unknown significance (VUS)/likely pathogenic/pathogenic. In case of polymorphisms or lack of genetic data, the variants were named as unclassified.A description of the cohort and an analysis of the correlation assessment between clinical data and genetic findings were performed.Results:246 out of 299 (82%) patients with NGS sAID gene panel had clinical data available. 170/246 (69%) were adult patients. The medium age was 48 yo, and the M/F ratio was 2.46. 87/170 (51%) adult patients presented 122 variants involving sAID genes (60/87 patients with a single variant). All the variants out of 7 seven were heterozygous variants.Variants were classified according to ACMG/AMP as follow: pathogenic/probably pathogenic: 22/122 (18%), unknown significance: 74/122 (60.6%), benign/probably benign: 6/122 (4.91%). 20/122 (16.4%) were unclassified variants or polymorphisms.The most frequent variants identified involved MEFV (54/122), NOD2/CARD15 (18/122) and TNFRSF1A (17/122 including 12 p.Arg121Gln variants) genes.37/122 (30%) variants correlated with the clinical picture in 33 patients, allowing to confirm the suspected diagnosis. Among the 122 variants, 7 not previously communicated variants were identified.No somatic variants were found.Conclusion:NGS sAID related gene panel is a useful tool for sAID diagnosis. In this cohort of 170 adult patients from a referral third-level hospital, genetic tests identified sAID related variants in almost half of them.20% of patients who underwent genetic NGS sAID related gene panel studies were finally diagnosed with sAID.The identification of a genetic variant (even pathogenic / likely pathogenic variant) is not diagnostic for sAID if there is not a suggestive clinical picture.Despite genetic findings, a careful evaluation of clinical – genetic correlation is needed to confirm the suspicion diagnosis, especially for low penetrance variants like TNFRSF1A p. Arg121Gln.References:Diagnostic utility of a targeted next-generation sequencing gene panel in the clinical suspicion of systemic autoinflammatory diseases: a multi-center study. Karacan I, Balamir A, Uğurlu S, et al. . Rheumatol Int. 2019 May;39(5):911-919. doi: 10.1007/s00296-019-04252-5. Epub 2019 Feb 19.Disclosure of Interests:None declared

scholarly journals Next generation sequencing-based gene panel tests for the management of solid tumors

2018 ◽  
Vol 110 (1) ◽  
pp. 6-15 ◽  
Author(s):  
Masayuki Nagahashi ◽  
Yoshifumi Shimada ◽  
Hiroshi Ichikawa ◽  
Hitoshi Kameyama ◽  
Kazuaki Takabe ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solid Tumors ◽  
Gene Panel ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing Approach to Non–Small Cell Lung Carcinoma Yields More Actionable Alterations

2017 ◽  
Vol 142 (3) ◽  
pp. 353-357 ◽  
Author(s):  
Mitra Mehrad ◽  
Somak Roy ◽  
Humberto Trejo Bittar ◽  
Sanja Dacic
Keyword(s):  
Next Generation Sequencing ◽  
Lung Adenocarcinoma ◽  
Small Cell ◽  
Gene Panel ◽  
Next Generation ◽  
Small Cell Lung ◽  
Genomic Alterations ◽  
Generation Sequencing ◽  
Gene Alterations ◽  
Cancer Panel

Context.— Different testing algorithms and platforms for EGFR mutations and ALK rearrangements in advanced-stage lung adenocarcinoma exist. The multistep approach with single-gene assays has been challenged by more efficient next-generation sequencing (NGS) of a large number of gene alterations. The main criticism of the NGS approach is the detection of genomic alterations of uncertain significance. Objective.— To determine the best testing algorithm for patients with lung cancer in our clinical practice. Design.— Two testing approaches for metastatic lung adenocarcinoma were offered between 2012–2015. One approach was reflex testing for an 8-gene panel composed of DNA Sanger sequencing for EGFR, KRAS, PIK3CA, and BRAF and fluorescence in situ hybridization for ALK, ROS1, MET, and RET. At the oncologist's request, a subset of tumors tested by the 8-gene panel was subjected to a 50-gene Ion AmpliSeq Cancer Panel. Results.— Of 1200 non–small cell lung carcinomas (NSCLCs), 57 including 46 adenocarcinomas and NSCLCs, not otherwise specified; 7 squamous cell carcinomas (SCCs); and 4 large cell neuroendocrine carcinomas (LCNECs) were subjected to Ion AmpliSeq Cancer Panel. Ion AmpliSeq Cancer Panel detected 9 potentially actionable variants in 29 adenocarcinomas that were wild type by the 8-gene panel testing (9 of 29, 31.0%) in the following genes: ERBB2 (3 of 29, 10.3%), STK11 (2 of 29, 6.8%), PTEN (2 of 29, 6.8%), FBXW7 (1 of 29, 3.4%), and BRAF G469A (1 of 29, 3.4%). Four SCCs and 2 LCNECs showed investigational genomic alterations. Conclusions.— The NGS approach would result in the identification of a significant number of actionable gene alterations, increasing the therapeutic options for patients with advanced NSCLCs.

scholarly journals Targeted next generation sequencing with an extended gene panel does not impact variant detection in mitochondrial diseases

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Morgane Plutino ◽  
Annabelle Chaussenot ◽  
Cécile Rouzier ◽  
Samira Ait-El-Mkadem ◽  
Konstantina Fragaki ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mitochondrial Diseases ◽  
Gene Panel ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Variant Detection ◽  
Generation Sequencing

scholarly journals Co-occurrence of immature T-lymphoblastic lymphoma and acute myeloid leukemia—microenvironment-dependent lineage differentiation derived from a common progenitor?

2021 ◽  
Author(s):  
Edit Porpaczy ◽  
Wolfgang R. Sperr ◽  
Renate Thalhammer ◽  
Gerlinde Mitterbauer-Hohendanner ◽  
Leonhard Müllauer ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Genetic Alterations ◽  
Lymphoblastic Lymphoma ◽  
Simultaneous Occurrence ◽  
Next Generation ◽  
T Lymphoblastic Lymphoma ◽  
Generation Sequencing ◽  
Acute Myeloid

AbstractMixed phenotype acute leukemia (MPAL) is an uncommon disease characterized by currently only limited knowledge concerning biology, clinical presentation, and treatment outcome. We here describe a most unusual case of simultaneous occurrence of T-lymphoblastic lymphoma in cervical and mediastinal lymph nodes and acute myeloid leukemia in the bone marrow (BM) successfully treated with allogeneic stem cell transplantation (SCT). Although the blasts in both locations showed additional aberrant expression of other lineage markers (even B-cell markers), diagnostic criteria of MPAL were not fulfilled either in the LN or in the BM. We performed next generation sequencing (NGS) with the objective to look for common genetic aberrations in both tissues. Histology, immunohistochemistry, flow cytometry, AML-associated genetic alterations (FLT3, NPM1, KIT D816V, CEPBA), and clonal T-cell receptor β and γ gene rearrangements were performed according to routine diagnostic workflows. Next generation sequencing and Sanger sequencing were additionally performed in BM and LN. Somatic mutation in the EZH2 gene (p.(Arg684Cys)) was detected in the BM by NGS, and the same mutation was found in the LN. Since an identical genetic aberration (EZH2 mutation) was detected in both locations, a common progenitor with regional dependent differentiation may be involved.

scholarly journals Next-generation sequencing as a clinical laboratory tool for describing different microbiotas: an urgent need for future paediatric practice

2021 ◽  
pp. archdischild-2021-321683
Author(s):  
Richard Hansen ◽  
Mona Bajaj-Elliott ◽  
Georgina L Hold ◽  
Konstantinos Gerasimidis ◽  
Tariq H Iqbal ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Laboratory ◽  
Next Generation ◽  
Paediatric Practice ◽  
Laboratory Tool ◽  
Generation Sequencing
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