Full-Length Transcript Phasing with Third-Generation Sequencing

Svrzikapa, Nenad; Boyanapalli, Ramakrishna

doi:10.1007/978-1-0716-2819-5_3

“…Different reviews, such as the one conducted by Mantere et al, have demonstrated the utility of LRS technologies by identifying novel elements of genomic alterations in known diseases (50)(51)(52). LRS has been employed to detect and map novel structural variants (52)(53)(54)(55)(56)(57), sequence repetitive genomic regions (58)(59)(60)(61)(62)(63), solve haplotype phasing (64)(65)(66)(67), and discriminate pseudogenes (68)(69)(70). The versatility of LRS makes this technology invaluable for a range of genetic studies as this platform can be of significant utility in the creation of high-resolution genomic assemblies due to its long-read mechanism, which can accurately characterize a genome.…”

Section: Lrs Applicationsmentioning

confidence: 99%

Long-read sequencing for brain tumors

Shelton,

Zandpazandi,

Nix

et al. 2024

Front. Oncol.

0

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Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.

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“…With the continuous development of Nanopore sequencing technology, the error rate and fragment length are also constantly changing. For instance, the average fragment length of Nanopore long reads can reach hundreds of kb, and the average error rate has also been reduced from 15% of 1D to 13% of 2D and 5% of 1D2 technologies ( Wang et al, 2021 ; Jain et al, 2022 ; Svrzikapa and Boyanapalli, 2022 ; Gao et al, 2023 ; Kovaka et al, 2023 ). The average length of full-length transcripts is approximately 1.5 kb.…”

Section: Introductionmentioning

confidence: 99%

LCAT: an isoform-sensitive error correction for transcriptome sequencing long reads

Zhu

¹

,

Liao

²

2023

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As the carrier of genetic information, RNA carries the information from genes to proteins. Transcriptome sequencing technology is an important way to obtain transcriptome sequences, and it is also the basis for transcriptome research. With the development of third-generation sequencing, long reads can cover full-length transcripts and reflect the composition of different isoforms. However, the high error rate of third-generation sequencing affects the accuracy of long reads and downstream analysis. The current error correction methods seldom consider the existence of different isoforms in RNA, which makes the diversity of isoforms a serious loss. Here, we introduce LCAT (long-read error correction algorithm for transcriptome sequencing data), a wrapper algorithm of MECAT, to reduce the loss of isoform diversity while keeping MECAT’s error correction performance. The experimental results show that LCAT can not only improve the quality of transcriptome sequencing long reads but also retain the diversity of isoforms.

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“…Different reviews, such as the one conducted by Mantere et al, have demonstrated the utility of LRS technologies by identifying novel elements of genomic alterations in known diseases (50)(51)(52). LRS has been employed to detect and map novel structural variants (52)(53)(54)(55)(56)(57), sequence repetitive genomic regions (58)(59)(60)(61)(62)(63), solve haplotype phasing (64)(65)(66)(67), and discriminate pseudogenes (68)(69)(70). The versatility of LRS makes this technology invaluable for a range of genetic studies as this platform can be of significant utility in the creation of high-resolution genomic assemblies due to its long-read mechanism, which can accurately characterize a genome.…”

Section: Lrs Applicationsmentioning

confidence: 99%

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Full-Length Transcript Phasing with Third-Generation Sequencing

Cited by 3 publications

References 17 publications

Long-read sequencing for brain tumors

Long-read sequencing for brain tumors

LCAT: an isoform-sensitive error correction for transcriptome sequencing long reads

Table_1.docx

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