PLAG1 Immunohistochemical Staining Is a Surrogate Marker for PLAG1 Fusions in Lipoblastomas

2021 ◽  
pp. 109352662110433
Author(s):  
Mikako Warren ◽  
Nishant Tiwari ◽  
Sabrina Sy ◽  
Gordana Raca ◽  
Ryan J Schmidt ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gold Standard ◽  
Immunohistochemical Staining ◽  
Surrogate Marker ◽  
Molecular Testing ◽  
Protein Overexpression ◽  
Conventional Cytogenetics ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Lipomatous Tumors

Background The hallmark of lipoblastoma is a PLAG1 fusion. PLAG1 protein overexpression has been reported in sporadic PLAG1-rearranged lipoblastomas. Methods We evaluated the utility of PLAG1 immunohistochemical staining (IHC) in 34 pediatric lipomatous tumors, correlating the results with histology and conventional cytogenetics, FISH and/or next generation sequencing (NGS) results. Results The study included 24 lipoblastomas, divided into 2 groups designated as “Lipoblastoma 1” with both lipoblastoma histology and PLAG1 rearrangement (n = 16) and “Lipoblastoma 2” with lipoblastoma histology but without PLAG1 cytogenetic rearrangement (n = 8), and 10 lipomas with neither lipoblastoma histology nor a PLAG1 rearrangement. Using the presence of a fusion as the “gold standard” for diagnosing lipoblastoma (Lipoblastoma 1), the sensitivity of PLAG1 IHC was 94%. Using histologic features alone (Lipoblastoma 1 + 2), the sensitivity was 96%. Specificity, as defined by the ability to distinguish lipoma from lipoblastoma, was 100%, as there were no false positives in the lipoma group. Conclusions Cytogenetics/molecular testing is expensive and may not be ideal for detecting PLAG1 fusions because PLAG1 fusions are often cytogenetically cryptic and NGS panels may not include all partner genes. PLAG1 IHC is an inexpensive surrogate marker of PLAG1 fusions and may be useful in distinguishing lipoblastomas from lipomas.

scholarly journals Synchronous Pulmonary Adenocarcinomas

2020 ◽  
Vol 154 (1) ◽  
pp. 57-69
Author(s):  
Carlos A Pagan ◽  
Catherine A Shu ◽  
John P Crapanzano ◽  
Galina G Lagos ◽  
Mark B Stoopler ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gene Panel ◽  
Driver Mutations ◽  
Molecular Testing ◽  
Next Generation ◽  
Synchronous Tumors ◽  
Targeted Next Generation Sequencing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Objectives To determine concordance/discordance between morphology and molecular testing (MT) among synchronous pulmonary carcinomas using targeted next generation sequencing (NGS), with and without comprehensive molecular review (CMR), vs analyses of multiple singe genes (non-NGS). Methods Results of morphologic and MT assessment were classified as concordant, discordant, or indeterminate. For discordant cases, comprehensive histologic assessment (CHA) was performed. Results Forty-seven cases with 108 synchronous tumors were identified and underwent MT (NGS, n = 23 and non-NGS, n = 24). Histology and MT were concordant, discordant, and indeterminate in 53% (25/47), 21% (10/47), and 26% (12/47) of cases, respectively. CHA of the 10 discordant cases revised results of three cases. Conclusions There is discordance between histology and MT in a subset of cases and MT provides an objective surrogate for staging synchronous tumors. A limited gene panel is sufficient for objectively assessing a relationship if the driver mutations are distinct. Relatedness of mutations require CMR with a larger NGS panel (eg, 50 genes).

scholarly journals Evaluating Pancreatic and Biliary Neoplasms with Small Biopsy-Based Next Generation Sequencing (NGS): Doing More with Less

Cancers ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 397
Author(s):  
Ilias P. Nikas ◽  
Giannis Mountzios ◽  
Guy I. Sydney ◽  
Kalliopi J. Ioakim ◽  
Jae-Kyung Won ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Risk ◽  
Pancreatic Juice ◽  
Response To Therapy ◽  
Biliary Duct ◽  
Molecular Testing ◽  
Cystic Lesions ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Pancreatic cancer and cholangiocarcinoma are lethal diseases mainly diagnosed at an inoperable stage. As pancreatobiliary surgical specimens are often unavailable for further molecular testing, this review aimed to highlight the diagnostic, prognostic, and therapeutic impact of next-generation sequencing (NGS) performed on distinct small biopsies, including endoscopic ultrasound fine-needle aspirations and biopsies of pancreatic solid and cystic lesions, biliary duct brushings, and also “liquid biopsies” such as the pancreatic juice, bile, and blood. NGS could clarify indeterminate pancreatic lesions or biliary strictures, for instance by identifying TP53 or SMAD4 mutations indicating high-grade dysplasia or cancer. It could also stratify pancreatic cystic lesions, by distinguishing mucinous from non-mucinous cysts and identifying high-risk cysts that should be excised in surgically fit patients, whereas the combination of cytology, elevated cystic CEA levels and NGS could improve the overall diagnostic accuracy. When NGS is performed on the pancreatic juice, it could stratify high-risk patients under surveillance. On the plasma, it could dynamically monitor the disease course and response to therapy. Notably, the circulating tumor DNA (ctDNA) levels have been associated with staging, grading, and survival. Lastly, NGS has shown potential in identifying potentially actionable molecular alterations. In conclusion, NGS applied on small biopsies could carry significant diagnostic, prognostic, and therapeutic value.

scholarly journals Duplex RTqPCRs for detection and relative quantification of SARS-CoV-2 variants of concern (VOC)

2021 ◽  
Author(s):  
Albert Carcereny ◽  
David Garcia-Pedemonte ◽  
Albert Bosch ◽  
Rosa M Pintó ◽  
Susana Guix
Keyword(s):  
Public Health ◽  
Next Generation Sequencing ◽  
Gold Standard ◽  
Relative Proportion ◽  
N Gene ◽  
Relative Quantification ◽  
Allelic Discrimination ◽  
Serious Disease ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract During the evolution of the SARS-CoV-2 pandemic, new variants of the virus have emerged and spread worldwide. The increased transmissibility and proclivity of some of these variants to cause more serious disease threatens public health responses against the virus, and they are classified as variants of concern (Variants of Concern, VOCs). While Next-Generation-Sequencing (NGS) is the gold standard to identify VOC, it cannot always be rapidly implemented in some settings to provide information as an early warning tool. Duplex quantitative real time RTqPCR assays offer a sensitive and easy-to-use tool to detect, discriminate, and estimate relative proportions of SARS-CoV-2 variants containing VOC-specific signature mutations from variants lacking it, using allelic discrimination probes. We developed three multiplexed RTqPCR assays that can detect Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2) VOCs by targeting 22281_22289DelCTTTACTTG, 28262_28263InsAACA and 22029_22034DelAGTTCA deletions/insertions in their genomes, respectively. Beta and Delta deletions are mapped to the S gene (residues 241/243 and 157/158, respectively), while Gamma insertion is located between the end of ORF8 and the beginning of N gene. Our specific duplex RTqPCR assays have been adapted from a previously designed duplex RTqPCR assay used to estimate the relative proportion of genomes containing 21765-21770DelTACATG mutation affecting residues HV69/70, a signature mutation of Alpha VOC (Carcereny et al., 2021). All duplex RTqPCR assays targeting signature mutations of VOCs may be used as a complementary tool to NGS for rapid variant tracking and surveillance in wastewater-based epidemiology.

Development of Plant Genetic Diversity by Biotechnology and Genomics

2014 ◽  
Vol 522-524 ◽  
pp. 1047-1050
Author(s):  
He Qi Wu ◽  
Zheng Hong Li ◽  
Xuan Zhou ◽  
Hong Dao Zhang ◽  
Ji Lin Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Gold Standard ◽  
Soil Productivity ◽  
Agricultural Crops ◽  
Irreversible Loss ◽  
Local Species ◽  
Genetic Pool ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Interactions between civilizations and ethnic groups have generated a fusion of customs and lifestyles, with an important effect on plant genetic diversity. The loss of local species and varieties usually results in irreversible loss of the genetic diversity they contain, this has dangerously shrunk the genetic pool that is available for natural selection and art selection, and has consequently increased the vulnerability of agricultural crops to sudden changes in climate, and to the appearance of new pests. Currently, biotechnology and genomic selection have enabled the genetic alteration of crops, improved soil productivity, and enhanced weed and pest control, and benefit to the development of plant genetic diversity. For example, next generation sequencing (NGS) and bioinformatics, as the gold standard, they provide a powerful tool for discovery of domestication genes in crop plants and their wild relatives.The objectives of this article are to review the development of plant genetic diversity and summarize the research of biotechnology and genomics for plant. Then, we look forward and consider the significant of development of plant genetic diversity by biotechnology and genomics.

scholarly journals What’s new in molecular genetic pathology 2021: solid tumors and NGS panel selection

2021 ◽  
Vol 55 (6) ◽  
pp. 421-422
Author(s):  
Guoli Chen ◽  
Patricia C. Tsang
Keyword(s):  
Next Generation Sequencing ◽  
Solid Tumors ◽  
Digestive System ◽  
Molecular Genetic ◽  
Genomic Testing ◽  
Molecular Testing ◽  
Next Generation Sequencing Ngs ◽  
To Receive ◽  
Generation Sequencing ◽  
Therapeutic Responses

The linchpin of precision medicine is molecular genetic and genomic testing. Molecular biomarkers are important for establishing precise diagnoses and for predicting therapeutic responses that enable cancer patients to receive personalized and targeted treatment. Below are highlights of the current considerations in next generation sequencing (NGS) panel selection, and in molecular testing of solid tumors of the lung, digestive system, thyroid and soft tissue.

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