Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

doi:10.1007/s13577-017-0168-8

Cited by 163 publications

(129 citation statements)

References 47 publications

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“…Short-read NGS approaches are not ideally suited for mutational and neoantigen profiling of MSI cancers (19)(20)(21), showing a high variability in mutation frequency regarding the detection of mutations in different cMS candidates like i.e. TGFBR2, SLC35F5 or TFAM (Table S1).…”

Section: Cms Mutation Frequencies In Msi Crc and Ecmentioning

confidence: 99%

The sharedneoantigen landscape of MSI cancers reflects immunoediting during tumor evolution

Ballhausen

Przybilla

Jendrusch

et al. 2019

Preprint

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Glossary TermMeaning ELS Epitope likelihood score GELS General epitope likelihood score IRS Immune relevance score, based on the mutation frequency (ReFrame) and the GELS M1Reading frame resulting from the deletion of one nucleotide or insertions of two nucleotides M2Reading frame resulting from the deletions of two nucleotides or insertion of one nucleotide m1, m2, m3, etc.Minus one, two, three base pair deletions p1, p2, p3, etc.Plus one, two, three base pair insertions ReFrameREgression-based FRAMEshift quantification Abbreviations B2M Beta2-microglobulin cMS Coding microsatellites CRC Colorectal cancer MMR Mismatch repair EC Endometrium cancer FSP neoantigens Frameshift peptide neoantigens HLA Human leukocyte antigen ICB Immune checkpoint blockade MSI Microsatellite instability, microsatelliteunstable NGSNext generation sequencing Abstract:The immune system can recognize and attack cancer cells, especially those with a high load of mutation-induced neoantigens. Such neoantigens are particularly abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and to neoantigen-inducing translational frameshifts. The abundance of mutational neoantigens renders MSI cancers sensitive to immune checkpoint blockade. However, the neoantigen landscape of MMR-deficient cancers has not yet been systematically mapped. In the present study, we used a novel tool to monitor neoantigen-inducing indel mutations in MSI colorectal and endometrial cancer. Our results show that MSI cancers share several highly immunogenic neoantigens that result from specific, recurrent indel mutation events.Notably, the frequency of such indel mutations was negatively correlated to the predicted immunogenicity of the resulting neoantigens. These observations suggest continuous immunoediting of emerging MMR-deficient cells during tumor evolution. Main text:DNA MMR deficiency is a major mechanism causing genomic instability in human cancer. MMR-deficient cancers accumulate an exceptionally high number of somatic mutations. These mutations encompass certain types of single nucleotide alterations, but mostly insertion/deletion (indel) mutations at repetitive sequence stretches termed microsatellites (microsatellite instability, MSI) (1, 2). About 15% of colorectal cancers (CRC), up to 30% of endometrial cancers (EC) and multiple other tumors display the MSI phenotype (3). MSI tumors can develop sporadically or in the context of Lynch syndrome, the most common inherited cancer predisposition syndrome. Due to this very specific process of genomic instability, the pathogenesis of MSI cancers can be precisely dissected (4): Indel mutations affecting coding microsatellites (cMS), predominantly coding mononucleotide repeats, in genomic regions encoding tumor suppressor genes are considered major drivers of MSI tumorigenesis (5-7). Importantly, the same indels that inactivate tumor suppressor genes simultaneously cause translational frameshi...

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Section: Cms Mutation Frequencies In Msi Crc and Ecmentioning

confidence: 99%

The sharedneoantigen landscape of MSI cancers reflects immunoediting during tumor evolution

Ballhausen

Przybilla

Jendrusch

et al. 2019

Preprint

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“…Hence, the used annotation can constrain especially gene expression studies if the unmapped reads are discarded without proper inspection. Long-read sequencing is often used to improve the reference genome as this can overcome the repeat area and GC-issues [58].…”

Section: Gc Content Features Of Missing Genes Identified and Try1 Genmentioning

confidence: 99%

Exploring the unmapped DNA and RNA reads in a songbird genome

Laine

Gossmann

Oers

et al. 2018

Preprint

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“…For example, single-molecule sequencing technologies are gaining importance in de novo assembly projects and structural variation screenings (Lu, Giordano, & Ning, 2016;Nakano et al, 2017;Rhoads & Au, 2015). PacBio is moving to the SAM specifications in their current pipeline version (Pacific Biosciences, 2015), but data sets generated with the PacBio RS platforms are stored in the HDF5 format (The HDF Group, 2000).…”

Section: Further Developmen T and Extensionmentioning

confidence: 99%

ReadTools: A universal toolkit for handling sequence data from different sequencing platforms

Gómez-Sánchez¹,

Schlötterer²

2017

Molecular Ecology Resources

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Sequencing whole genomes has become a standard research tool in many disciplines including Molecular Ecology, but the rapid technological advances in combination with several competing platforms have resulted in a confusing diversity of formats. This lack of standard formats causes several problems, such as undocumented preprocessing steps or the loss of information in downstream software tools, which do not account for the specifics of the different available formats. ReadTools is an open-source Java toolkit designed to standardize and preprocess read data from different platforms. It manages FASTQ- and SAM-formatted inputs while dealing with platform-specific peculiarities and provides a standard SAM compliant output. The code and executable are available at https://github.com/magicDGS/ReadTools.

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Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

Cited by 163 publications

References 47 publications

The sharedneoantigen landscape of MSI cancers reflects immunoediting during tumor evolution

The sharedneoantigen landscape of MSI cancers reflects immunoediting during tumor evolution

Exploring the unmapped DNA and RNA reads in a songbird genome

ReadTools: A universal toolkit for handling sequence data from different sequencing platforms

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