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Ion AmpliSeq™ Cancer Hotspot Panel v2

This study demonstrates the feasibility of localized tumor-normal sequencing in Nigerian BC patients, revealing actionable variants with clinical relevance. These findings highlight the need to integrate genomic profiling into routine cancer care and establish molecular tumor boards to advance precision oncology in Nigeria.

Co-occurrence of GNAQ, GNAS, and IDH1 mutations may represent a molecular signature of recurrence. Further validation in larger cohorts is needed to define optimal gene panels and VAF thresholds for clinical use.

Our study highlights STK11 as a key deleterious mutation in Bangladeshi bladder cancer patients, suggesting its potential role in tumor progression and patient prognosis.

The scalability of Bridge Capture was validated using an expanded panel and synthetic DNA targets, showing a strong linear correlation between observed and expected VAF values. This study demonstrates the scalability and accuracy of the Bridge Capture platform, and its potential to enhance mutation detection and clinical decision-making using ctDNA samples from patients with mCRC.

The detection of tumor imprints and heterogeneity in cfDNA samples highlights the potential of liquid biopsy as a valuable tool for monitoring therapeutic responses in OSCC. The identification of recurrently mutated genes and pathogenic variants provides insights into potential therapeutic targets.

Several definite genetic mutations involved in GC were observed. Mutations were less frequent in post-eradication differentiated GC. However, because of small number of cases analyzed to identify carcinogenic differences, further analysis with a large number of cases and with strictly grading GC samples is needed.

Thus, for variants within the MET gene in patients with NSCLC, particular attention is required to assess for possible intronic variants that may lead to the METex14, especially if only sequencing DNA. The novelty of the intronic variant herein identified is heightened by being a net insertion rather than a deletion, as all reported intronic variants in the Catalogue of Somatic Mutations in Cancer (COSMIC) within this region are deletions. If sequencing DNA and RNA, both the intronic variant and RNA consequence should be used synergistically as evidence for the presence of METex14 skipping variant.

"This report emphasis the importance of molecular testing in the differential diagnosis between PEComa and melanoma, especially when the tumor arises in a site typical of melanoma but showing an unusual morphology and immunophenotype. The detection of TFE3 fusion transcripts suggested the diagnosis of SNT PEComa, although it cannot be excluded that this and similar tumors represent a distinct diagnostic category."

Secondly, the presence of the rare pathogenic variants R201S, p.R201G and p.Q227E in 26% (5 out of 19) of myxomas with GNAS pathogenic variants shows that methodologies designed to detect only the common "hotspot" of p.R201C and p.R201H will give false negative results. Finally, a comparison between Ion AmpliSeq Cancer Hotspot Panel v2 and direct cycle Sanger sequencing showed that direct cycle Sanger sequencing provides a quick, reliable, and relatively cheap method to detect GNAS pathogenic variants, matching even the most cutting-edge sequencing methods.

These findings may help the understanding of the molecular mechanism(s) of PMP and contribute to the development of therapeutic strategies for this life-threatening disease.

Taken together, our comparison ofIon PGMTM Dx system and GenexusTM integrated sequencer indicates that the latter exhibits superior performance with significantly higher total reads, mapped reads, and mean depth, leading to a faster turnaround time and improved detection of clinically relevant variants. This underscores its potential for enhanced precision in clinical applications.

"Conclusions NGS data correlate well with histology and may aid in diagnosis and risk stratification of pancreatic cysts. Cyst wall biopsy performs well in diagnosing cysts but was inadequate in five of 24 patients."