Detection of Disease-specific Fusion Genes of Soft Tissue Tumors Using Formalin-fixed Paraffin-embedded Tissues; Its Diagnostic Usefulness and Factors Affecting the Detection Rates

Matsushige, Takahiro; Kuwamoto, Satoshi; Matsushita, Michiko; Wardhani, Lusi Oka; Horie, Yasushi; Hayashi, Kazuhiko; Kitamura, Yukisato

doi:10.33160/yam.2019.03.016

Cited by 3 publications

(3 citation statements)

References 21 publications

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“…The accumulation of fusion genes is one of the patterns commonly found in tumor tissues ( Matsushige et al, 2019 ). However, how the fusion genes contribute to or are formed during cancer progression is barely documented.…”

Section: Resultsmentioning

confidence: 99%

Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing

Long

et al. 2022

Front. Cell Dev. Biol.

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Background: Structural variations (SVs) are common genetic alterations in the human genome that could cause different phenotypes and diseases, including cancer. However, the detection of structural variations using the second-generation sequencing was limited by its short read length, which restrained our understanding of structural variations.Methods: In this study, we developed a 28-gene panel for long-read sequencing and employed it to Oxford Nanopore Technologies and Pacific Biosciences platforms. We analyzed structural variations in the 28 breast cancer-related genes through long-read genomic and transcriptomic sequencing of tumor, para-tumor, and blood samples in 19 breast cancer patients.Results: Our results showed that some somatic SVs were recurring among the selected genes, though the majority of them occurred in the non-exonic region. We found evidence supporting the existence of hotspot regions for SVs, which extended our previous understanding that they exist only for single nucleotide variations.Conclusion: In conclusion, we employed long-read genomic and transcriptomic sequencing to identify SVs from breast cancer patients and proved that this approach holds great potential in clinical application.

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Section: Resultsmentioning

confidence: 99%

Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing

Long

et al. 2022

Front. Cell Dev. Biol.

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“…The accumulation of fusion genes is one of the patterns commonly found in tumor tissues 17 . However, how the fusion genes contribute to or are formed during cancer progression is barely documented.…”

Section: Gene Fusions With Both Genomic and Transcriptomic Evidencementioning

confidence: 99%

Detection of structural variations and fusion genes in breast cancer samples using third-generation sequencing

Hu¹,

Li²,

Long³

et al. 2021

Preprint

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Structural variations (SVs) are common genetic alterations in the human genome that could cause different phenotypes and various diseases including cancer. However, the detection of structural variations using the second-generation sequencing was limited by its short read-length which in turn restrained our understanding of structural variations. In this study, we analyzed structural variations in 28 breast cancer-related genes through long-read genomic and transcriptomic sequencing of tumor, para-tumor and blood samples in 19 breast cancer patients. Our results showed that some somatic SVs were recurring among the selected genes, though the majority of them occurred in the non-exonic region. We found evidence supporting the existence of hotspot regions for SVs, which extended our previous understanding that they exist only for single nucleotide variations. In conclusion, we employed long-read genomic and transcriptomic sequencing in identifying SVs from breast cancer patients and proved that this approach holds great potential in clinical application.

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“…5,6,7 In hard tissues, histological staining can be preceded by softening bones or decalcification process using the EDTA method 5 and the Plank Rychlo's solution. 8 Another non-softening method is grown in methyl methacrylate (MMA). 7 This bone softening action before processing is intended to facilitate slicing the bones into thin slices, thus making staining easier and perfecting the result.…”

Section: Introductionmentioning

confidence: 99%

A histological evaluation of cellular response on bone regeneration scaffold

Dewi

Listyarifah

Ardhani

et al. 2023

Majalah Kedokteran Gigi Indonesia

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Biocompatibility testing for a new implant material is necessary before clinical use. The materials for bone scaffolding must also go through biocompatibility tests both in vitro and in vivo. The purpose of this study was to compare different staining methods in histological preparations to assess the biocompatibility of the material to tissues. Twenty Wistar rats (n= 20), aged 4 months, males, weighing about 250-350 g were divided into 2 research groups, namely sub-cutaneous and bone implantation for 3, 14, and 30 days. The sample was a biodegradable material with gypsum and calcium carbonate as the basic ingredients. Histological stains were prepared in several ways using Hematoxylin Eosin (HE), Mallory, Toluidine Blue, Tartrate-resistant acid phosphatase polyclonal antibody (TRAP), and Chromogen 3,3 diaminobenzidine (DAB) after pre-performing a decalcification process with ethylenedinitril-o-tetra-acetic acid (EDTA). The observation was done using magnification ranging from 10X10 to 100X10 with a light microscope (Nikon eclipse E600) and OptiLab viewer. The results were displayed in the form of descriptions of images generated from different staining methods. Staining by the HE method is most often chosen because it is cheap and easy but the other staining methods such as Toluidine Blue, Mallory, and TRAP show better contrast. Tissue staining techniques with immunohistochemistry (DAB, VEGF) are used to evaluate cell and tissue responses by identifying specific proteins present.

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Detection of Disease-specific Fusion Genes of Soft Tissue Tumors Using Formalin-fixed Paraffin-embedded Tissues; Its Diagnostic Usefulness and Factors Affecting the Detection Rates

Cited by 3 publications

References 21 publications

Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing

Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing

Detection of structural variations and fusion genes in breast cancer samples using third-generation sequencing

A histological evaluation of cellular response on bone regeneration scaffold

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