The role of next-generation sequencing in detecting gene fusions with known and unknown partners: a single-center experience with methodologies’ integration

Ambrosini-Spaltro, Andrea; Farnedi, Anna; Calistri, Daniele; Rengucci, Claudia; Prisinzano, Giovanna; Chiadini, Elisa; Capelli, Laura; Angeli, Davide; Bennati, Chiara; Valli, Mirca; Luca, Giovanni De; Caruso, Dora; Ulivi, Paola; Rossi, Giulio De

doi:10.1016/j.humpath.2022.02.005

Cited by 7 publications

(4 citation statements)

References 40 publications

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“…Consequently, when NGS is the reference, one can argue that the experimental conditions of the assay comparison can be defined as "optimal". On the other hand, when IHC or FISH are used as the reference methods, the quality of the RNA is unknown, as these "in situ" methods are not RNA-dependent, as also recently demonstrated by Ambrosini-Spaltro et al [27]. So, in our opinion, having used different reference methods is not a limitation, but instead adds some practical observations to previous studies, particularly when considering small samples that fail with or result in inadequate NGS.…”

Section: Discussionmentioning

confidence: 62%

Robust Performance of the Novel Research-Use-Only Idylla GeneFusion Assay Using a Diverse Set of Pathological Samples with a Proposed 1-Day Workflow for Advanced NSCLC Evaluation

Leone

Muscarella

Graziano

et al. 2022

Cancers

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A range of different techniques are available for predictive biomarker testing for non-small-cell lung cancer (NSCLC) clinical management. International guidelines suggest next-generation sequencing (NGS) as the preferred procedure, but other reverse transcriptase-polymerase chain reaction (RT-PCR)-based methods are rapidly evolving. In this study, we evaluated the reliability and accuracy of the IdyllaTM GeneFusion assay, a rapid and fully automated platform able to simultaneously detect ALK, ROS1, RET and NTRK1/2/3 and MET ex14 skipping mutations and compared its performance with routine reference methods. The cohort included thirty-seven NSCLCs plus two parotid gland carcinomas, previously characterized for the above alterations through either IHC, FISH, RT-PCR or NGS. In 36 of 39 cases, the Idylla GeneFusion assay and the reference methods were concordant (overall agreement: 92.3%). Tumor sections stored at room temperature for up to 60 days and 17 cases older than 2 years were successfully characterized. Our results suggest that the Idylla GeneFusion assay is a reliable tool to define gene fusion status and may be a valuable stand-alone diagnostic test when time efficiency is needed or NGS is not feasible.

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Section: Discussionmentioning

confidence: 62%

Robust Performance of the Novel Research-Use-Only Idylla GeneFusion Assay Using a Diverse Set of Pathological Samples with a Proposed 1-Day Workflow for Advanced NSCLC Evaluation

Leone

Muscarella

Graziano

et al. 2022

Cancers

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“…In addition, a few studies analyzed the prevalence and clinical features of pancreatic cystic lesions in a BRCA -tested population in order to establish the risk of pancreatic cysts and cyst-associated cancer, which could have important implications in the context of increasingly accessible genetic testing [ 31 , 32 , 33 ], but there were significant limitations. The use of next-generation-sequencing (NGS)-based technologies is becoming a new gold standard for determining molecular predictive biomarkers and reliable data on the detection of multiple pathogenic variants, allowing for the screening of thousands of affected individuals [ 34 ]. The discovery of new detected variants found in HBOC patients is extremely helpful in aiding clinicians to follow some patients and relatives carrying the same mutations but at a high risk of developing other types of cancer, mostly PDACs.…”

Section: Discussionmentioning

confidence: 99%

Prevalence of a BRCA2 Pathogenic Variant in Hereditary-Breast-and-Ovarian-Cancer-Syndrome Families with Increased Risk of Pancreatic Cancer in a Restricted Italian Area

Zampiga

Cangini

Bandini

et al. 2023

Cancers

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PVs and LPVs in BRCA1/2 genes are correlated to a high risk of developing breast cancer and/or ovarian cancer (Hereditary Breast and Ovarian Cancer syndrome, HBOC); additionally, in recent years, an increasing number of BRCA 1/2 variants have been identified and associated with pancreatic cancer. Epidemiologic studies have highlighted that inherited factors are involved in 10% to 20% of PCs, mainly through deleterious variants of BRCA2. The frequency of BRCA1/2 germline alterations fluctuates quite a lot among different ethnic groups, and the estimated rate of PVs/LPVs variants in Italian HBOC families is not very accurate, according to different reports. The aim of our study is to describe the prevalence of a BRCA2 PV observed in a selected cohort of HBOC patients and their relatives, whose common origin is the eastern coast of Emilia Romagna, a region of Italy. This study provides insight into the frequency of the variant detected in this area and provides evidence of an increased risk of pancreatic and breast cancer, useful for genetic counseling and surveillance programs.

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“…Mutations in affected cells can lead to the expression of immunogenic mutant proteins, the so-called neoantigens, that can be targeted by the immune system. Since neoantigens are not expressed by normal cells, they can be found utilizing genomic deep sequencing of tumor tissues and can represent attractive targets for cancer therapy [ 141 , 142 ]. Importantly, overcoming the peripheral immune tolerance can lead to targeting also of self-antigens, which can be overexpressed in specific cancer subtypes [ 143 ].…”

Section: Tcr and Cancermentioning

confidence: 99%

T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer

Mazzotti

Gaimari

Bravaccini

et al. 2022

IJMS

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The immune system is a dynamic feature of each individual and a footprint of our unique internal and external exposures. Indeed, the type and level of exposure to physical and biological agents shape the development and behavior of this complex and diffuse system. Many pathological conditions depend on how our immune system responds or does not respond to a pathogen or a disease or on how the regulation of immunity is altered by the disease itself. T-cells are important players in adaptive immunity and, together with B-cells, define specificity and monitor the internal and external signals that our organism perceives through its specific receptors, TCRs and BCRs, respectively. Today, high-throughput sequencing (HTS) applied to the TCR repertoire has opened a window of opportunity to disclose T-cell repertoire development and behavior down to the clonal level. Although TCR repertoire sequencing is easily accessible today, it is important to deeply understand the available technologies for choosing the best fit for the specific experimental needs and questions. Here, we provide an updated overview of TCR repertoire sequencing strategies, providers and applications to infectious diseases and cancer to guide researchers’ choice through the multitude of available options. The possibility of extending the TCR repertoire to HLA characterization will be of pivotal importance in the near future to understand how specific HLA genes shape T-cell responses in different pathological contexts and will add a level of comprehension that was unthinkable just a few years ago.

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The role of next-generation sequencing in detecting gene fusions with known and unknown partners: a single-center experience with methodologies’ integration

Cited by 7 publications

References 40 publications

Robust Performance of the Novel Research-Use-Only Idylla GeneFusion Assay Using a Diverse Set of Pathological Samples with a Proposed 1-Day Workflow for Advanced NSCLC Evaluation

Robust Performance of the Novel Research-Use-Only Idylla GeneFusion Assay Using a Diverse Set of Pathological Samples with a Proposed 1-Day Workflow for Advanced NSCLC Evaluation

Prevalence of a BRCA2 Pathogenic Variant in Hereditary-Breast-and-Ovarian-Cancer-Syndrome Families with Increased Risk of Pancreatic Cancer in a Restricted Italian Area

T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer

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