Comparing Clonality Between Components of Combined Hepatocellular Carcinoma and Cholangiocarcinoma by Targeted Sequencing

Jeon, Jong Up; Maeng, Lee-So; Bae, Yoon Jin; Lee, Eui Jin; Yoon, Young Chul; Yoon, Nara

doi:10.21873/cgp.20087

Cited by 15 publications

(21 citation statements)

References 28 publications

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“…DNA and RNA were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific). DNA and RNA libraries were prepared as previously described (24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35). These DNA libraries were generated from 20 ng of DNA per sample using an Ion AmpliSeq Library Kit 2.0 (Thermo Fisher Scientific) and the Oncomine Comprehensive Assay v1 (OCA v1) panel (Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

“…Analysis of the sequencing data was performed using the Torrent Suite Software v5.2.2 (Thermo Fisher Scientific). This workflow was created by adding a custom hotspot Browser Extensible Data file to report mutations of interest and a custom CNA baseline (described below) using the manufacturer's default workflow, as described previously (24,25,35). The pipeline used included signaling processing, base calling, quality score assignment, adapter trimming, read mapping to the human genome assembly GRCh37, quality control of mapping, coverage analysis with downsampling, and variant calling.…”

Section: Methodsmentioning

confidence: 99%

“…Gene fusions were detected using the fusion detection module within the Ion Reporter Software (Thermo Fisher Scientific) workflow. This pipeline only reported fusions that were annotated previously, as defined in a reference file preloaded into the workflow (24,25,35).…”

Section: Methodsmentioning

confidence: 99%

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Targeted Genomic Sequencing Reveals Different Evolutionary Patterns Between Locally and Distally Recurrent Glioblastomas

Yoon

Kim

Lee

et al. 2020

Cancer Genomics Proteomics

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Background/Aim: Glioblastoma is the most malignant form of astrocytoma. The purpose of this study was to analyze the genetic characteristics of primary and recurrent glioblastomas using targeted sequencing and investigate the differences in mutational profiles between the locations of tumor recurrence. Materials and Methods: Fourteen glioblastoma patients who developed local (n=10) or distal (n=4) recurrence were included in the study. Targeted sequencing analysis was performed using the primary (n=14) and corresponding recurrent (n=14) tumor tissue samples. Results: The local and distal recurrence groups showed different genetic evolutionary patterns. Most of the locally recurrent glioblastomas demonstrated concordant mutational profiles between the primary and recurrent tumors, suggesting a linear evolution. In contrast, all cases of distally recurrent glioblastomas showed changes in mutational profiles with newly acquired mutations when compared to the corresponding primary tumors, suggesting a branching evolution. Conclusion: Locally and distally recurrent glioblastomas exhibit different evolutionary patterns. Glioblastoma is the most common malignant tumor of the central nervous system (1-9). The current standard treatment for glioblastoma involves surgical resection, followed by concurrent chemoradiation therapy and adjuvant chemotherapy using temozolomide (8-12). Due to the invasive nature of glioblastoma, surgical resection rarely eliminates all tumor cells, and postoperative treatment is usually necessary to prevent disease recurrence. Despite the advances made in therapeutic strategies, the prognosis of patients with glioblastoma remains very poor, with an average survival of 15 months (13-15) and disease recurrence being the major cause of mortality (16-18). Recurrent glioblastomas tend to be more invasive and resistant to chemotherapy than primary tumors. An understanding of the genetic characteristics of recurrent glioblastoma is crucial for identifying potential targets for drug discovery, stratifying patients for diagnosis, and optimizing an effective treatment strategy. Previous studies have shown the molecular features of recurrent glioblastomas. In particular, the mutational profiles observed in recurrent glioblastomas were compared to those of the corresponding primary tumors (19-21). However, there is a lack of studies exploring the differences in mutational profiles between recurrent glioblastomas at different sites (21, 22). In this study, we investigated the mutational profiles of primary and recurrent glioblastomas using 803 This article is freely accessible online.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Targeted Genomic Sequencing Reveals Different Evolutionary Patterns Between Locally and Distally Recurrent Glioblastomas

Yoon

Kim

Lee

et al. 2020

Cancer Genomics Proteomics

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“…Just as the histological aspects in cHCC-CCA vary, so does the molecular profile. 31,32,34,[36][37][38][39][40][41][42] Previous studies found that the genetics of cHCC-CCA were closer to iCCA than HCC. 42 However, the recent study performed by Joseph et al showed that the genetics of cHCC-CCA, classical type, are distinct from iCCA but similar to HCC, for example, alterations in TERT, TP53, cell cycle genes (CCND1, CCNE1, CDKN2A), receptor tyrosine kinase/Ras/PI3-kinase pathway genes (MET, ERBB2, KRAS, PTEN).…”

Section: Molecular Profiles (►Table 2)mentioning

confidence: 99%

A Review on the Update of Combined Hepatocellular Cholangiocarcinoma

Komuta

Yeh

2019

Semin Liver Dis

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Combined hepatocellular-cholangiocarcinoma (cHCC-CCA) is a primary liver tumor with neoplastic components of both hepatocytic and cholangiocytic differentiation. This unique neoplasm is gaining increasing recognition due to the intriguing pathology, tumor biology, and clinical behavior. It also poses challenges in diagnosis, treatment, and research, largely because of its histological and phenotypic diversity that lead to confusion in terminology and classification. There have been efforts attempting to unify the terminology of this neoplasm recently. Advances in investigation in various aspects have also been made. This review aims to update the terminology, classification, and clinical and pathological characteristics of cHCC-CCA.

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“…DNA and RNA were quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific). DNA and RNA libraries were prepared as previously described (6,(13)(14)(15)(16)(17)(18)(19)(20)(21)(22). These DNA libraries were generated from 20 ng of DNA per sample using an Ion AmpliSeq Library Kit 2.0 (Thermo Fisher Scientific) and Oncomine Comprehensive Assay (OCA) v1 panel (Thermo Fisher Scientific).…”

Section: Materials and μEthodsmentioning

confidence: 99%

Atypical Mesonephric Hyperplasia of the Uterus Harbors Pathogenic Mutation of Kirsten Rat Sarcoma 2 Viral Oncogene Homolog (KRAS) and Gain of Chromosome 1q

Kim

Yoon

Woo

et al. 2020

Cancer Genomics Proteomics

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Background/Aim: Mesonephric carcinoma (MNC) is a rare but notable entity of the female genital tract. While many researchers have acknowledged and studied MNC, much remains unknown on the characteristics of mesonephric remnant (MNR) or hyperplasia (MNH). There has not been any study examining the molecular features of MNR and MNH so far. The aim of this study was to investigate the clinicopathological and molecular characteristics of ten uterine mesonephric lesions, including two MNRs without atypia, four MNHs without atypia, and three MNHs with atypia. Materials and Methods: We reviewed the electronic medical records and all available slides of ten cases from multiple institutions. Targeted sequencing and array comparative genomic hybridization were performed. Results: Three atypical MNHs displayed nuclear enlargement, mild-tomoderate nuclear pleomorphism, and nuclear membrane irregularity, and harbored pathogenic Kirsten rat sarcoma 2 viral oncogene homolograt sarcoma 2 viral oncogene homolog (KRAS) mutation. Two of those that co-existed with MNC harbored the same sequence alterations as each of their adjacent MNC. One of the three atypical MNHs harbored chromosome 1q gain. Conclusion: Atypical MNH is a potential premalignant lesion in which KRAS mutation and chromosome 1q gain play an important role in the early stage of mesonephric carcinogenesis. The mesonephric duct is a precursor of the male genital tract present during human embryogenesis (1). In males, it gives rise to the internal genitalia, including the epididymides, vasa deferentia, seminal vesicles, and efferent ductules of the testes, whereas in females, it regresses with some remnants persisting in the broad ligament and the uterine cervix (2). Mesonephric remnant (MNR) and hyperplasia (MNH) are not uncommon findings in specimens of conizations and hysterectomies, being reported in up to one-third of resected adult uterine cervices (1). They might also be present within the wall of the vagina and uterine body, as well as the ovarian hilum and mesosalpinx (3). Mesonephric carcinoma (MNC) is a rare malignant neoplasm thought to arise from the embryonal remnants of mesonephric tubules and ducts, comprising less than 1% of all gynecological tract malignancies (4). MNC arises 813 This article is freely accessible online.

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Comparing Clonality Between Components of Combined Hepatocellular Carcinoma and Cholangiocarcinoma by Targeted Sequencing

Abstract: Abstract. Background

Cited by 15 publications

References 28 publications

Targeted Genomic Sequencing Reveals Different Evolutionary Patterns Between Locally and Distally Recurrent Glioblastomas

Targeted Genomic Sequencing Reveals Different Evolutionary Patterns Between Locally and Distally Recurrent Glioblastomas

A Review on the Update of Combined Hepatocellular Cholangiocarcinoma

Atypical Mesonephric Hyperplasia of the Uterus Harbors Pathogenic Mutation of Kirsten Rat Sarcoma 2 Viral Oncogene Homolog (KRAS) and Gain of Chromosome 1q

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