Targeted Long-Read Sequencing Decodes the Transcriptional Atlas of the Founding RAS Gene Family Members

Adamopoulos, Panagiotis G.; Tsiakanikas, Panagiotis; Boti, Michaela A.; Scorilas, Andreas

doi:10.3390/ijms222413298

Cited by 3 publications

(1 citation statement)

References 52 publications

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“…A touchdown PCR-based assay was conducted to amplify the PTEN transcript variants with increased sensitivity, specificity, and PCR yield [ 37 , 38 ]. For this purpose, two gene-specific primers (GSPs) were designed.…”

Section: Methodsmentioning

confidence: 99%

Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies

Boti,

Adamopoulos,

Vassilacopoulou

et al. 2023

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Background: Phosphatase and tensin homolog, widely known as PTEN, is a major negative regulator of the PI3K/AKT/mTOR signaling pathway, involved in the regulation of a variety of important cellular processes, including cell proliferation, growth, survival, and metabolism. Since most of the molecules involved in this biological pathway have been described as key regulators in cancer, the study of the corresponding genes at several levels is crucial. Objective: Although previous studies have elucidated the physiological role of PTEN under normal conditions and its involvement in carcinogenesis and cancer progression, the transcriptional profile of PTEN has been poorly investigated. Methods: In this study, instead of conducting the “gold-standard” direct RNA sequencing that fails to detect less abundant novel mRNAs due to the decreased sequencing depth, we designed and implemented a multiplexed PTEN-targeted sequencing approach that combined both short- and longread sequencing. Results: Our study has highlighted a broad spectrum of previously unknown PTEN mRNA transcripts and assessed their expression patterns in a wide range of human cancer and non-cancer cell lines, shedding light on the involvement of PTEN in cell cycle dysregulation and thus tumor development. Conclusion: The identification of the described novel PTEN splice variants could have significant implications for understanding PTEN regulation and function, and provide new insights into PTEN biology, opening new avenues for monitoring PTEN-related diseases, including cancer.

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Section: Methodsmentioning

confidence: 99%

Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies

Boti,

Adamopoulos,

Vassilacopoulou

et al. 2023

Self Cite

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AI and precision oncology in clinical cancer genomics: From prevention to targeted cancer therapies-an outcomes based patient care

Dlamini

Skepu

Kim

et al. 2022

Informatics in Medicine Unlocked

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Leveraging the power of long reads for targeted sequencing

Iyer,

Goodwin,

McCombie

2024

Genome Res.

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Long-read sequencing technologies have improved the contiguity and, as a result, the quality of genome assemblies by generating reads long enough to span and resolve complex or repetitive regions of the genome. Several groups have shown the power of long reads in detecting thousands of genomic and epigenomic features that were previously missed by short-read sequencing approaches. While these studies demonstrate how long reads can help resolve repetitive and complex regions of the genome, they also highlight the throughput and coverage requirements needed to accurately resolve variant alleles across large populations using these platforms. At the time of this review, whole-genome long-read sequencing is more expensive than short-read sequencing on the highest throughput short-read instruments; thus, achieving sufficient coverage to detect low-frequency variants (such as somatic variation) in heterogenous samples remains challenging. Targeted sequencing, on the other hand, provides the depth necessary to detect these low-frequency variants in heterogeneous populations. Here, we review currently used and recently developed targeted sequencing strategies that leverage existing long-read technologies to increase the resolution with which we can look at nucleic acids in a variety of biological contexts.

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Targeted Long-Read Sequencing Decodes the Transcriptional Atlas of the Founding RAS Gene Family Members

Cited by 3 publications

References 52 publications

Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies

Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies

AI and precision oncology in clinical cancer genomics: From prevention to targeted cancer therapies-an outcomes based patient care

Leveraging the power of long reads for targeted sequencing

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