Translational Cancer Genomics by Next Generation Sequencing and Molecular-Barcoding Technique

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (22 November 2020) | Viewed by 7968

Special Issue Editors


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Guest Editor
Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi 400-8506, Japan
Interests: lung cancer; sequencing; immunotherapy; thoracic surgery; liquid biopsy; microbiome; genome analysis
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Genome Analysis Center, Yamanashi Central Hospital, Yamanashi 400-8506, Japan
Interests: cancer genomics; familial cancer; immunotherapy; tumor heterogeneity

Special Issue Information

Dear Colleagues,

In the past decade, there have been incredible advances that have improved clinical management of cancer and the disease outcome in the field of molecular oncology. Despite this, the drug therapy cure rate at the advanced stage for many types of cancers remains inadequately high, and development of further innovative therapeutic strategies is currently desired. Recent advances in sequencing technology, notably the introduction of next-generation sequencing and molecular barcoding techniques, have enabled rapid, efficient, low-cost, and precise sequencing. Furthermore, extensive application of these latest technologies to basic cancer research has facilitated the in-depth molecular characterization of cancer from various perspectives (oncogenesis, tumor phylogeny, progression, metastasis, treatment response, etc.) with higher precision than before.

This Special Issue aims to publish original research papers and review articles related to advances in basic research on cancer genomics that are very close to the stage of clinical application. A particular focus will be given to research using sequencing data expected to contribute to the development of novel cancer diagnostics and treatment techniques (including gene therapies) as well as new medical devices and drugs, such as studies on circulating tumor DNA, fusion gene, intratumor heterogeneity, tumor mutation burden, and the microbiome. Furthermore, papers discussing cancer cell responses to immunotherapy based on sequence data will also be considered.

Dr. Taichiro Goto
Dr. Yosuke Hirotsu
Guest Editors

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Keywords

  • cancer
  • intratumor heterogeneity
  • tumor mutation burden
  • gene mutation
  • immune checkpoint
  • biomarker
  • circulating tumor DNA
  • microbiome
  • fusion gene
  • sequencing

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Published Papers (2 papers)

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Research

11 pages, 1081 KiB  
Article
The Study of the Expression of CGB1 and CGB2 in Human Cancer Tissues
by Piotr Białas, Aleksandra Śliwa, Anna Szczerba and Anna Jankowska
Genes 2020, 11(9), 1082; https://doi.org/10.3390/genes11091082 - 17 Sep 2020
Cited by 5 | Viewed by 3444
Abstract
Human chorionic gonadotropin (hCG) is a well-known hormone produced by the trophoblast during pregnancy as well as by both trophoblastic and non-trophoblastic tumors. hCG is built from two subunits: α (hCGα) and β (hCGβ). The hormone-specific β subunit is encoded by six allelic [...] Read more.
Human chorionic gonadotropin (hCG) is a well-known hormone produced by the trophoblast during pregnancy as well as by both trophoblastic and non-trophoblastic tumors. hCG is built from two subunits: α (hCGα) and β (hCGβ). The hormone-specific β subunit is encoded by six allelic genes: CGB3, CGB5, CGB6, CGB7, CGB8, and CGB9, mapped to the 19q13.32 locus. This gene cluster also encompasses the CGB1 and CGB2 genes, which were originally considered to be pseudogenes, but as documented by several studies are transcriptionally active. Even though the protein products of these genes have not yet been identified, based on The Cancer Genome Atlas (TCGA) database analysis we showed that the mutual presence of CGB1 and CGB2 transcripts is a characteristic feature of cancers of different origin, including bladder urothelial carcinoma, cervical squamous cell carcinoma, esophageal carcinoma, head and neck squamous cell carcinoma, ovarian serous cystadenocarcinoma, lung squamous cell carcinoma, pancreatic adenocarcinoma, rectum adenocacinoma, testis germ cell tumors, thymoma, uterine corpus endometrial carcinoma and uterine carcinosarcoma. Full article
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12 pages, 2009 KiB  
Article
Analysis of HBV Genomes Integrated into the Genomes of Human Hepatoma PLC/PRF/5 Cells by HBV Sequence Capture-Based Next-Generation Sequencing
by Tomotaka Ishii, Akinori Tamura, Toshikatsu Shibata, Kazumichi Kuroda, Tatsuo Kanda, Masaya Sugiyama, Masashi Mizokami and Mitsuhiko Moriyama
Genes 2020, 11(6), 661; https://doi.org/10.3390/genes11060661 - 18 Jun 2020
Cited by 19 | Viewed by 4114
Abstract
Hepatitis B virus (HBV) infection is a leading cause of hepatocellular carcinoma (HCC) worldwide. The integration of HBV genomic DNA into the host genome occurs randomly, early after infection, and is associated with hepatocarcinogenesis in HBV-infected patients. Therefore, it is important to analyze [...] Read more.
Hepatitis B virus (HBV) infection is a leading cause of hepatocellular carcinoma (HCC) worldwide. The integration of HBV genomic DNA into the host genome occurs randomly, early after infection, and is associated with hepatocarcinogenesis in HBV-infected patients. Therefore, it is important to analyze HBV genome integration. We analyzed HBV genome integration in human hepatoma PLC/PRF/5 cells by HBV sequence capture-based next-generation sequencing (NGS) methods. We confirmed the results by using Sanger sequencing methods. We observed that HBV genotype A is integrated into the genome of PLC/PRF/5 cells. HBV sequence capture-based NGS is useful for the analysis of HBV genome integrants and their locations in the human genome. Among the HBV genome integrants, we performed functional analysis and demonstrated the automatic expression of some HBV proteins encoded by HBV integrants from chromosomes 3 and 11 in Huh7 cells transfected with these DNA sequences. HBV sequence capture-based NGS may be a useful tool for the assessment of HBV genome integration into the human genome in clinical samples and suggests new strategies for hepatocarcinogenesis in HBV infection. Full article
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