scholarly journals The puzzling mutational landscape of the SARS‐2‐variant Omicron

2022 ◽  
Author(s):  
Jacques Fantini ◽  
Nouara Yahi ◽  
Philippe Colson ◽  
Henri Chahinian ◽  
Bernard La Scola ◽  
...  
Keyword(s):  
Mutational Landscape

scholarly journals Mutational landscape of Gastric Adenocarcinoma in Latin America: A genetic approach for precision medicine

2021 ◽  
Author(s):  
Dennis Cerrato-Izaguirre ◽  
Yolanda I. Chirino ◽  
Claudia M. García-Cuellar ◽  
Miguel Santibáñez-Andrade ◽  
Diddier Prada ◽  
...  
Keyword(s):  
Latin America ◽  
Precision Medicine ◽  
Gastric Adenocarcinoma ◽  
Genetic Approach ◽  
Mutational Landscape

Mutational landscape of Juvenile Myelomonocytic Leukemia (JMML)—A real‐world context

2021 ◽  
Author(s):  
Shrinidhi Nathany ◽  
Gaurav Chatterjee ◽  
Shruti Ghai ◽  
Nirmalya Roy Moulik ◽  
Dhanalaxmi Shetty ◽  
...  
Keyword(s):  
Real World ◽  
Juvenile Myelomonocytic Leukemia ◽  
Mutational Landscape ◽  
Myelomonocytic Leukemia

scholarly journals GE-34 * THE MUTATIONAL LANDSCAPE AND TEMPORAL AND SPATIAL CLONAL EVOLUTION TO PROGRESSION IN 351 LOW-GRADE GLIOMAS

2014 ◽  
Vol 16 (suppl 5) ◽  
pp. v103-v104
Author(s):  
H. Suzuki ◽  
K. Aoki ◽  
F. Ohka ◽  
K. Motomura ◽  
M. Fujii ◽  
...  
Keyword(s):  
Clonal Evolution ◽  
Low Grade ◽  
Low Grade Gliomas ◽  
Mutational Landscape ◽  
Temporal And Spatial

Mutational landscape of HCC—the end of the beginning

2014 ◽  
Vol 11 (2) ◽  
pp. 73-74 ◽  
Author(s):  
Augusto Villanueva ◽  
Josep M. Llovet
Keyword(s):  
Mutational Landscape

An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus

2005 ◽  
Vol 37 (4) ◽  
pp. 441-444 ◽  
Author(s):  
Darin R Rokyta ◽  
Paul Joyce ◽  
S Brian Caudle ◽  
Holly A Wichman
Keyword(s):  
Empirical Test ◽  
Landscape Model ◽  
Dna Virus ◽  
Single Stranded Dna ◽  
Mutational Landscape

Characterization of microsatellite instability (dMMR/MSI-H) and mutational landscape in a large contemporary cohort of upper tract urothelial cancer (UTUC) patients.

2021 ◽  
Vol 39 (6_suppl) ◽  
pp. 465-465
Author(s):  
Arpit Rao ◽  
Julie Elaine McGrath ◽  
Joanne Xiu ◽  
Andre Luiz De Souza ◽  
Shuchi Gulati ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Chromatin Remodeling ◽  
Statistical Significance ◽  
Small Sample ◽  
Biological Pathways ◽  
High Rate ◽  
Chi Square ◽  
Mutational Landscape ◽  
Comparison Results ◽  
Small Sample Sizes

465 Background: UTUC is a rare genitourinary malignancy and a number of studies, limited by small sample sizes, have attempted to characterize its mutational landscape. Because immunotherapy is commonly used for this disease type, we evaluated the prevalence of microsatellite instability and characterized the mutational landscapes of UTUC in a large contemporary patient cohort. Methods: UTUC tumor samples were analyzed using next generation sequencing (NGS) (NextSeq, 592 gene panel) or whole exome sequencing (WES) (NovaSeq) (Caris Life Sciences, Phoenix, AZ). Mismatch repair status (deficient [dMMR] or proficient [pMMR]) and microsatellite instability status (MSI-high or stable [MSS]) were detected by immunohistochemistry (IHC), fragment analysis, and NGS. Tumor mutational burden (TMB) was measured by counting all somatic mutations found per tumor (high cutoff ≥ 10 mutations per MB). PD-L1 expression was tested by IHC using PD-L1 antibody clones 22c3 (Agilent; positive cutoff CPS ≥ 10) and SP142 (Ventana; positive cutoff ≥ 5% IC). Pathogenic fusion events were detected using whole transcriptome sequencing (NovaSeq). Statistical significance was determined using the Chi-square test and adjusted for multiple comparison. Results: 538 patients with included – median (range) age 71.5 (30-89) years and 37.5% female/62.5% male. Prevalence of dMMR/MSI-H was 3.9% (21/538) and TMB-high was 22.7% (96/423). Significant molecular differences were not detected in primary vs metastatic disease or in male vs female cases. dMMR/MSI-H tumors had higher frequency of TMB-high compared to MSS tumors (100% vs. 19%, p = 0.00003). dMMR/MSI-H tumors also had a higher frequency than MSS tumors for mutations in genes involved in chromatin remodeling (ASXL 82.4%, CREBBP 60%, SMARCA4 40%, KMT2D 95%, ARIDIA 100%, KMT2A 20%, KMT2C 35.3%, NSD1 20%), DNA-damage repair (FANCG 10%, ATM 45%, ATRX 40%) and other biological pathways (RNF43 10%, PTCH1 21.4%, ERBB3 30%, CDKN2A 25%, TSC2 15%, FLNC 15%, HNF1A 20%, CIC 15%, DNMT3A 17.6%); all adjusted p < 0.05. Pathogenic fusions were detected in 3.8% (17/443) cases, with FGFR3 fusion being the most common, occurring in 2.7% (12/443) cases. PD-L1 positivity was identified in 33.2% (133/400) cases tested by 22c3 antibody and 28.4% (89/313) cases tested by SP142 antibody. No difference was seen in PD-L1 positivity between MSI-H/dMMR vs. MSS tumors. Conclusions: In the largest analysis to date, we found a 3.9% prevalence of dMMR/MSI-high rate in UTUC. All dMMR/MSI-H tumors displayed TMB-high. PD-L1 positivity was comparable between dMMR/MSI-H and MSS tumors. dMMR/MSI-H tumors had a significantly higher rate of mutations in genes involved in chromatin remodeling and DDR biological pathways. These results could inform design of targeted therapy trials in UTUC.

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