Article
Multidisciplinary Sciences
Sho Uedaa, Satoshi Yamashita, Miho Nakajima, Tadashi Kumamoto, Chitose Ogawa, Yu-Yu Liu, Harumi Yamada, Emi Kubo, Naoko Hattori, Hideyuki Takeshima, Mika Wakabayashi, Naoko Iida, Yuichi Shiraishi, Masayuki Noguchi, Yukio Sato, Toshikazu Ushijima
Summary: This study developed a cost-effective pipeline called EcoSeq, which utilizes duplex sequencing to accurately count somatic mutations in single DNA molecules. The researchers used this method to analyze normal blood cells from pediatric sarcoma patients and found that the mutation frequency significantly increased in patients who received chemotherapy, with the increased frequency persisting even months after chemotherapy. This suggests that mutation accumulation poses a risk of secondary leukemia.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Dermatology
Satyamaanasa Polubothu, Nicole Bender, Siobhan Muthiah, Davide Zecchin, Charalambos Demetriou, Sara Barberan Martin, Sony Malhotra, Jana Travnickova, Zhiqiang Zeng, Markus Boehm, Sebastien Barbarot, Catherine Cottrell, Olivia Davies, Eulalia Baselga, Nigel P. Burrows, Virginie Carmignac, Joey Santiago Diaz, Christine Fink, Holger A. Haenssle, Rudolf Happle, Mark Harland, Jacquelyn Majerowski, Pierre Vabres, Marie Vincent, Julia A. Newton-Bishop, D. Tim Bishop, Dawn Siegel, E. Elizabeth Patton, Maya Topf, Neil Rajan, Beth Drolet, Veronica A. Kinsler
Summary: Phakomatosis pigmentovascularis is a condition characterized by the presence of specific types of pigmentary and vascular birthmarks, along with various systemic involvements and a risk of developing malignancy. This study reveals that clonal mosaic variants in the PTPN11 gene can cause phakomatosis pigmentovascularis type III or spilorosea. The same variant is found in different pigmentary and vascular birthmarks within an individual, but not in the blood. These findings improve our understanding of nevus spilus and capillary malformation syndromes, potentially leading to better clinical management.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Review
Endocrinology & Metabolism
Kazutaka Nanba, William E. Rainey, Aaron M. Udager
Summary: Aldosterone production is regulated by circulating potassium, angiotensin II, and other secretagogues, while aldosterone synthase is crucial for its synthesis. Primary aldosteronism is commonly caused by adrenal aldosterone-producing adenomas and hyperaldosteronism, with advances in genetic profiling revealing mutations leading to renin-independent aldosterone production. Utilizing formalin-fixed paraffin-embedded tissue sections for determining tumor mutations can aid in studying adrenal disorders.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Orsolya Pipek, Donat Alpar, Orsolya Rusz, Csaba Bodor, Zoltan Udvarnoki, Anna Medgyes-Horvath, Istvan Csabai, Zoltan Szallasi, Lilla Madaras, Zsuzsanna Kahan, Gabor Cserni, Bence Kovari, Janina Kulka, Anna Maria Tokes
Summary: This study conducted whole-genome sequencing on 63 samples from 29 Hungarian breast cancer patients, revealing common pathogenic genes and mutational signatures related to homologous recombination deficiency. This highlights the importance of comprehensive genomic characterization in breast cancer patient populations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Li-Han Lin, Chung-Hsien Chou, Hui-Wen Cheng, Kuo-Wei Chang, Chung-Ji Liu
Summary: Understanding genomic alterations in oral carcinogenesis is crucial for the diagnosis and treatment of OSCC. The study used WES to uncover mutational spectrum in OSCC samples, revealing associations between tumor mutation burden and clinical parameters. Several high frequency false positive mutation genes were identified, along with known and novel genes frequently mutated in OSCC. Pathway analysis showed associations with OSCC prognosis, and a catalog of targetable genomic alterations was defined, showing potential for targeted therapies in OSCC patients. Analysis also revealed molecular subgroups in OSCC correlated with etiology and prognosis, providing valuable information for clinical trial design and patient stratification.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Georgia Kontogianni, Konstantinos Voutetakis, Georgia Piroti, Katerina Kypreou, Irene Stefanaki, Efstathios Iason Vlachavas, Eleftherios Pilalis, Alexander Stratigos, Aristotelis Chatziioannou, Olga Papadodima
Summary: This study aimed to characterize patients with primary cutaneous melanoma (CM) by analyzing both germline and somatic variations as well as alterations at the gene expression level. Oncogenic alterations were identified and phenotypic cell states were inferred from transcriptomic data. Integrating mutational and transcriptomic data could provide insights into genes and pathways involved in the maintenance of phenotypic states in primary melanomas.
Article
Multidisciplinary Sciences
Duo Wang, Yuanfeng Zhang, Rui li, Jinming Li, Rui Zhang
Summary: This study developed paired tumor-normal reference materials using CRISPR-Cas9 technology and evaluated the performance of 56 panels in detecting somatic mutations. The results showed variations in accuracy and reproducibility among different panels, with filtering errors, low-quality detection, cross-contamination, and other sequencing errors as major sources of false discoveries. The study provides an integrated practice to assess onco-panels and quantitatively reveals the sources of detection errors.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Oncology
Jie Liu, Chengwen Gao, Liping Wang, Xuemin Jian, Mingdi Ma, Tong Li, XiWei Hao, Qian Zhang, Yuanbin Chen, Jing Zhao, Haitao Niu, Chengzhan Zhu, Jie Zhao, Nan Xia, Zhiqiang Li, Qian Dong
Summary: This study analyzed data from 16 patients and compared data from whole-exome sequencing studies, finding genetic differences in HB among different races in children. Furthermore, the study verified the function of specific candidate genes.
FRONTIERS IN ONCOLOGY
(2021)
Article
Endocrinology & Metabolism
Lei Li, Qixuan Sheng, Huajin Zeng, Wei Li, Qiang Wang, Guanjun Ma, Xinyun Xu, Ming Qiu, Wei Zhang, Chengxiang Shan
Summary: This study provides a comprehensive analysis of the genetic characteristics of hyperplastic parathyroids in THPT, finding multiple driver mutations and enriched pathways involved in the development and progression of the disease.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Review
Oncology
Kai Liu, Yunlong Cui, Hua Li, Jiahui Mi, Hailong Wang, Yan Zhuang, Liang Tang, Jia Liu, Caijuan Tian, Zhenzhen Zhang, Jiang Zhou, Haijing Shi, Xin Tian, Pengfei Liu
Summary: This study analyzed the somatic mutations and pathways associated with liver and lung metastasis of CRC using next-generation sequencing. They identified genes and pathways related to CRC metastasis, such as IRS1, BRCA2, EphA5, PTPRD, BRAF, and PTEN. These findings provide new insights for understanding the pathogenesis of CRC metastasis and potential targets for diagnosis and treatment.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2023)
Correction
Multidisciplinary Sciences
Argyri Mathioudaki, Viktor Ljungstroem, Malin Melin, Maja Louise Arendt, Jessika Nordin, Asa Karlsson, Eva Muren, Pushpa Saksena, Jennifer R. S. Meadows, Voichita D. Marinescu, Tobias Sjoeblom, Kerstin Lindblad-Toh
Summary: An updated version of the paper has been published and is accessible through a link at the top of the paper.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Haoling Xie, Wen Li, Yuqiong Hu, Cheng Yang, Jiansen Lu, Yuqing Guo, Lu Wen, Fuchou Tang
Summary: This study achieved high continuity human genome assembly using single-cell genome long-read sequencing technology and explored the impact of different assemblers and sequencing strategies on genome assembly. It is of great significance for the practice of single-cell genome de novo assembly.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Pathology
Eunji Kim, Dong-Jin Han, Byoung Hyuck Kim, Jinseon Yoo, Hak Jae Kim, Hong-Gyun Wu, Kyung Su Kim, Han-Soo Kim, Ilkyu Han, Kyung Chul Moon, Jeong Hwan Park, Sanghyuk Song, Tae-Min Kim, Ji Hyun Chang
Summary: Radiation-induced sarcoma (RIS) is a rare and serious late complication of radiotherapy. This study analyzed the genomes of 11 RIS tumors and identified somatic alterations potentially associated with RIS development. The results revealed different types of genomic alterations in cancer-related genes and the prevalence of nonhomologous end joining pathway in RIS genomes. The findings provide valuable insights for the diagnosis and treatment of RIS.
Article
Oncology
Sofia Birkealv, Mark Harland, Larissa Satiko Alcantara Sekimoto Matsuyama, Mamun Rashid, Ishan Mehta, Jonathan P. Laye, Kerstin Haase, Tracey Mell, Vivek Iyer, Carla Daniela Robles-Espinoza, Ultan McDermott, Peter van Loo, Marieke L. Kuijjer, Patricia A. Possik, Silvya Stuchi Maria Engler, D. Timothy Bishop, Julia Newton-Bishop, David J. Adams
Summary: This study conducted sequence profiling of 524 American Joint Committee on Cancer Stage I-III primary tumors, revealing recurrent driver mutations, mutually exclusive genetic interactions, and an absence of co-occurring genetic events. By intersecting copy number calls with CRISPR screening data, the transcription factor IRF4 was identified as a melanoma-associated dependency.
JOURNAL OF PATHOLOGY
(2023)
Article
Genetics & Heredity
Yuanqing Yan, Rebecca Martinez, Maria N. Rasheed, Joshua Cahal, Zhen Xu, Yanning Rui, Krista J. Qualmann, John P. Hagan, Dong H. Kim
Summary: The study elucidated rare variants and germline gene mutations in pineal cysts under different inheritance modes, as well as the impact of somatic mutations on biological processes such as gene expression, epigenetic regulation, immune response modulation, and transferase activity. These molecular profiles provide novel insights for investigators interested in pineal cysts.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2021)