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J. Mol. Pathol., Volume 4, Issue 2 (June 2023) – 5 articles

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19 pages, 2681 KiB  
Article
Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors
by Catherine I. Dumur, Ramakrishnan Krishnan, Jorge A. Almenara, Kathleen E. Brown, Kailyn R. Dugan, Christiana Farni, Fatima Z. Ibrahim, Naomi A. Sanchez, Sumra Rathore, Dinesh Pradhan and Jonathan H. Hughes
J. Mol. Pathol. 2023, 4(2), 109-127; https://doi.org/10.3390/jmp4020012 - 07 Jun 2023
Cited by 2 | Viewed by 3437
Abstract
The detection of driver oncogenic variants and the recent identification of tumor-agnostic genomic biomarkers has driven the use of comprehensive genomic profiling (CGP) for disease diagnosis, prognosis, and treatment selection. The Oncomine™ Comprehensive Assay Plus (OCA+) panel uses DNA and RNA to detect [...] Read more.
The detection of driver oncogenic variants and the recent identification of tumor-agnostic genomic biomarkers has driven the use of comprehensive genomic profiling (CGP) for disease diagnosis, prognosis, and treatment selection. The Oncomine™ Comprehensive Assay Plus (OCA+) panel uses DNA and RNA to detect single nucleotide variants (SNVs), small insertions/deletions (Indels), and structural variants (SVs) across 501 genes. Moreover, microsatellite instability (MSI), tumor mutational burden (TMB), and homologous recombination deficiency (HRD) status are assessed in a single workflow. Herein, we present the analytical validation and clinical utilization of OCA+. By using commercial reference materials, we found good analytical sensitivity, specificity, and precision for all biomarkers analyzed. The limit of detection (LoD) was validated for SNVs and Indels at 4%, except for Indels located in homopolymeric regions, where the LoD was 10%. An additional set of 81 tumor samples, including cytology smears, were sequenced to assess the clinical utility of the OCA+ across different tumor types. Among the clinical cohort, OCA+ demonstrated 100% accuracy, sensitivity, and specificity for all biomarkers analyzed, except for MSI assessment of endometrial cancer cases, where 83% accuracy and 67% sensitivity were achieved, compared to PCR and IHC. The validation of accuracy and robustness of this assay supports the OCA+’s utility for solid tumor CGP. Full article
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10 pages, 2424 KiB  
Review
Different Subtypes of Osteosarcoma: Histopathological Patterns and Clinical Behaviour
by Emel Rothzerg, Jiake Xu and David Wood
J. Mol. Pathol. 2023, 4(2), 99-108; https://doi.org/10.3390/jmp4020011 - 16 May 2023
Cited by 2 | Viewed by 4240
Abstract
Osteosarcoma (OS) is a primary malignant bone tumour that usually occurs in children and adolescents. OS is a highly aggressive tumour type with a propensity for local invasion and systemic early metastasis to the lungs or other bones. According to the World Health [...] Read more.
Osteosarcoma (OS) is a primary malignant bone tumour that usually occurs in children and adolescents. OS is a highly aggressive tumour type with a propensity for local invasion and systemic early metastasis to the lungs or other bones. According to the World Health Organization, there are different subtypes of OS, including conventional OS (osteoblastic, chondroblastic, fibroblastic), telangiectatic OS, low-grade OS, small-cell OS, parosteal OS, periosteal OS, and high-grade surface OS. In this mini review, we will discuss the background of OS and histopathological patterns and clinical behaviour of the disease. Understanding the subtypes of OS and their pathogenesis is crucial for developing more precise and effective therapies for OS patients. Full article
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10 pages, 4110 KiB  
Article
Sinonasal Hyalinizing Adenoid Cystic Carcinoma Is Molecularly Different from Its Salivary and Breast Counterparts
by Ebtissam Alerraqi, Essam Mandour and Mariz Faltas
J. Mol. Pathol. 2023, 4(2), 89-98; https://doi.org/10.3390/jmp4020010 - 15 May 2023
Viewed by 1555
Abstract
Adenoid cystic carcinoma (AdCC) is known to behave differently based on its location, histologic features, and molecular profile. Despite this understanding, efforts to use these molecular findings to develop personalized treatments have not yet been successful. The purpose of this retrospective study is [...] Read more.
Adenoid cystic carcinoma (AdCC) is known to behave differently based on its location, histologic features, and molecular profile. Despite this understanding, efforts to use these molecular findings to develop personalized treatments have not yet been successful. The purpose of this retrospective study is to examine the molecular characteristics of AdCC with various histologic features in three different locations. A reference group of 20 classic cribriform AdCC cases from the parotid gland was included, along with 10 salivary AdCCs (Group 1), 10 sinonasal AdCCs with hyalinization (Group 2), and 10 solid mammary AdCCs with basaloid features (Group 3). Tissue samples were processed and tested using various molecular techniques, and the Wilcoxon signed-rank test was used to compare the different groups. Molecular data were obtained for both common and rare cases of sinonasal, salivary, and mammary AdCCs, revealing differences in molecular features depending on the tumor’s location. The molecular profile of the AdCCs in the experimental group varied depending on the site, with MYB gene rearrangements being common in all cases. We report the first MYB::KMT2C/D fusions in a subset of salivary AdCCs and sinonasal AdCCs but not in mammary adenoid cystic carcinoma with basaloid features. We conclude that co-occurring genetic alterations may vary among different sites and may have implications for the prognosis and treatment plan of AdCC. More research is needed to fully understand the mechanisms of KMT2C and KMT2D mutations in the development and progression of head and neck cancer, including their interactions with the NOTCH pathway. Full article
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8 pages, 276 KiB  
Opinion
Liquid Biopsy in EGFR-Mutated Advanced NSCLC from T790M to MET Amplification: Clinical Implications and Possibilities in the Resistance Setting
by Luigi Della Gravara, Ciro Battiloro, Aniello Avellino, Francesca Caputo, Carmine D’Aniello and Danilo Rocco
J. Mol. Pathol. 2023, 4(2), 81-88; https://doi.org/10.3390/jmp4020009 - 30 Apr 2023
Viewed by 1398
Abstract
According to the ESMO and ASCO clinical guidelines, the main role of liquid biopsy in EGFR+ advanced NSCLC patients is represented by T790M detection after erlotinib/gefitinib/afatinib progression. However, the general international expert consensus regards osimertinib as the preferred upfront treatment in this [...] Read more.
According to the ESMO and ASCO clinical guidelines, the main role of liquid biopsy in EGFR+ advanced NSCLC patients is represented by T790M detection after erlotinib/gefitinib/afatinib progression. However, the general international expert consensus regards osimertinib as the preferred upfront treatment in this setting; therefore, this role has been scaled back in recent years. As of today, liquid biopsy has no ASCO or ESMO recommendation following first-line osimertinib; in the same vein, no targeted therapy has received ASCO or ESMO recommendation following post upfront Osimertinib progression. However, this standard could change in the near future. Therefore, adopting a clinical point of view, this paper aims to provide a comprehensive review on the previous, the current and the possible future role of liquid biopsy in the framework of the diagnostic–therapeutic algorithm of EGFR+ advanced NSCLC. Full article
(This article belongs to the Special Issue Liquid Biopsy in Solid Tumors)
12 pages, 596 KiB  
Article
Performance of a 7-Type HPV mRNA Test in Triage of HPV DNA Primary Screen Positive Women Compared to Liquid-Based Cytology
by Sveinung Wergeland Sørbye, Bente Marie Falang and Mona Antonsen
J. Mol. Pathol. 2023, 4(2), 69-80; https://doi.org/10.3390/jmp4020008 - 25 Mar 2023
Cited by 3 | Viewed by 2398
Abstract
Background: A plethora of data supports HPV-based screening to be the preferred strategy for cervical cancer prevention. The shift to a more sensitive first-line test brings the need of effective triage up for discussion. Currently, most algorithms apply cytology as a triage of [...] Read more.
Background: A plethora of data supports HPV-based screening to be the preferred strategy for cervical cancer prevention. The shift to a more sensitive first-line test brings the need of effective triage up for discussion. Currently, most algorithms apply cytology as a triage of HPV-DNA positive women. This study compared the performance of a 7-type HPV-mRNA test to cytology. Methods: From 1 January 2019 until 31 December 2021, cervical samples from 58,029 women were examined at the University Hospital of North Norway. A total of 30.5% (17,684/58,029) fulfilled the criteria for HPV-DNA primary screening. All positive samples were triaged by cytology and followed-up according to national guidelines through 2022. Additionally, a 7-type HPV-mRNA test was applied. The study endpoint was a histologically confirmed high-grade lesion (CIN2+). Results: A total of 5.6% (990/17,684) had positive HPV-DNA test, 97.2% (962/990) with valid HPV-mRNA results. A total of 55.5% (534/962) had abnormal cytology (ASC-US+), and 35.1% (338/962) had a positive HPV-mRNA test. A total of 13.9% (134/962) had CIN2+. The sensitivity (CIN2+) of cytology versus the HPV-mRNA test was 76.1% (102/134) versus 73.1% (98/134), p = 0.67. The specificity was 47.8% (396/828) versus 71.0% (588/624), p < 0.001. PPV was 19.1% (102/534) and 29.0% (98/338), p < 0.001, respectively. The number of colposcopies per CIN2+ detected by cytology and HPV-mRNA test was 5.2 and 3.1. Conclusion: The 7-type HPV mRNA test was significantly more specific than cervical cytology in a triage of HPV-DNA positive women. Using this biomarker as the threshold for colposcopy may better balance the benefits and harms of screening. Full article
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