Article
Medical Laboratory Technology
Yingdi Liu, Yanling Teng, Zhuo Li, Jingyi Cui, Desheng Liang, Lingqian Wu
Summary: By reanalyzing whole-exome sequencing data with updated algorithms and databases, optimizing processes and strategies, the diagnostic yield can be improved and missed diagnoses reduced.
CLINICA CHIMICA ACTA
(2021)
Article
Oncology
Gabriella Doddato, Floriana Valentino, Annarita Giliberti, Filomena Tiziana Papa, Rossella Tita, Lucia Pia Bruno, Sara Resciniti, Chiara Fallerini, Elisa Benetti, Maria Palmieri, Maria Antonietta Mencarelli, Alessandra Fabbiani, Mirella Bruttini, Alfredo Orrico, Margherita Baldassarri, Francesca Fava, Diego Lopergolo, Caterina Lo Rizzo, Vittoria Lamacchia, Sara Mannucci, Anna Maria Pinto, Aurora Curro, Virginia Mancini, Francesca Mari, Alessandra Renieri, Francesca Ariani
Summary: This study identified pathogenic and potentially pathogenic genes in HBOC patients through whole exome sequencing and MLPA testing, expanding the spectrum of causative variants. This helps to improve personalized risk assessment and clinical surveillance in HBOC families.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemical Research Methods
Jianteng Zhou, Jianing Gao, Huan Zhang, Daren Zhao, Ao Li, Furhan Iqbal, Qinghua Shi, Yuanwei Zhang
Summary: Researchers have reviewed existing linkage analysis tools and introduced PedMiner, a web-based application designed to narrow down candidate variants from family-based whole-exome sequencing (WES) data through linkage analysis. PedMiner integrates linkage analysis, variant annotation, and prioritization in an automated pipeline, providing comprehensive annotation of variants and genes within linked regions. This efficient application will benefit the scientific community studying Mendelian inherited disorders using family-based WES data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Richa Malhotra, Vyomesh Javle, Nishtha Tanwar, Pooja Gowda, Linu Varghese, K. Anju, Nandhitha Madhusudhan, Nupur Jaiswal, K. S. Bhargavi, Manjima Chatterjee, Kumar Prabhash, Peddagangannagari Sreekanthreddy, Kshitij D. D. Rishi, Hitesh M. M. Goswami, Vidya H. H. Veldore
Summary: This study aims to validate a whole exome-based tumor molecular profiling method, which allows for the extraction of DNA and RNA from formalin-fixed paraffin-embedded tumor tissue. The results demonstrate that this method can accurately detect clinically relevant gene variants and provide clinical assistance in tumor diagnosis and progression.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yaxuan Liu, Hafdis T. Helgadottir, Pedram Kharaziha, Jungmin Choi, Francesc Lopez-Giraldez, Shrikant M. Mane, Veronica Hoiom, Carl Christofer Juhlin, Catharina Larsson, Svetlana Bajalica-Lagercrantz
Summary: This study aimed to identify new predisposing genes for hereditary breast cancer (HBC) using whole-exome sequencing, but no pathogenic variants in known hereditary cancer-related genes were found. Further analysis suggested that a combination of low- and intermediate-genetic-risk variants might contribute to breast cancer susceptibility in these families.
Article
Oncology
Migle Gabrielaite, Mathias Husted Torp, Malthe Sebro Rasmussen, Sergio Andreu-Sanchez, Filipe Garrett Vieira, Christina Bligaard Pedersen, Savvas Kinalis, Majbritt Busk Madsen, Miyako Kodama, Guel Sude Demircan, Arman Simonyan, Christina Westmose Yde, Lars Ronn Olsen, Rasmus L. Marvig, Olga ostrup, Maria Rossing, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger
Summary: Copy-number variations (CNVs) have significant clinical implications for various diseases and cancers, but detecting relevant CNVs accurately remains challenging. Our study found diverse performance levels among different CNV calling tools, suggesting that combining the best tools could be a potential solution.
Article
Oncology
Chuang Zhou, Song Chen, Fei Xu, Jinwang Wei, Xiaoyu Zhou, Zhiqiang Wu, Longshuan Zhao, Jun Liu, Wenbo Guo
Summary: The study found that there may be differences in TMB threshold criteria among different cancer types, leading to variations in predicting the efficacy of ICI therapy. TMB was shown to predict clinical benefit in patients with colorectal cancer, but was not able to accurately predict outcomes in other cancer types.
ANNALS OF TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Raffaele Gaeta, Mariangela Morelli, Francesca Lessi, Chiara Maria Mazzanti, Michele Menicagli, Rodolfo Capanna, Lorenzo Andreani, Luca Coccoli, Paolo Aretini, Alessandro Franchi
Summary: This study aims to identify gene alterations in high-grade osteosarcoma (OS) patients using whole exome sequencing (WES) to find new potential prognostic biomarkers and therapeutic targets. Mutations in ARID1A, CREBBP, BRCA2 and RAD50 genes were found to be significantly correlated with poor response to neoadjuvant therapy and negatively influenced the progression-free survival time. Moreover, higher tumor mutational burden values were associated with worse prognosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Geriatrics & Gerontology
Lin Sun, Jianye Zhang, Ning Su, Shaowei Zhang, Feng Yan, Xiang Lin, Jie Yu, Wei Li, Xia Li, Shifu Xiao
Summary: By conducting whole exome sequencing on 84 patients with degenerative dementia, new pathogenic and likely pathogenic gene variants were identified, indicating heterogeneity in the etiology and phenotype of dementia.
FRONTIERS IN AGING NEUROSCIENCE
(2021)
Article
Multidisciplinary Sciences
Juan Cao, An'er Chen, Liyun Tian, Lulu Yan, Haibo Li, Bihua Zhou
Summary: This study investigated the role of whole exome sequencing (WES) technology in diagnosing fetuses with skeletal abnormalities. Several novel heterozygous mutations were identified, expanding the mutation spectrum for prenatal diagnosis. WES technology is essential for accurate diagnosis of skeletal abnormalities in fetuses.
Article
Medicine, General & Internal
Ylenia D'Agostino, Domenico Palumbo, Maria Rosaria Rusciano, Oriana Strianese, Sonia Amabile, Domenico Di Rosa, Elena De Angelis, Valeria Visco, Fabio Russo, Elena Alexandrova, Annamaria Salvati, Giorgio Giurato, Giovanni Nassa, Roberta Tarallo, Gennaro Galasso, Michele Ciccarelli, Alessandro Weisz, Francesca Rizzo
Summary: Dilated cardiomyopathy (DCM) is a complex disease with genetic and environmental factors contributing to its development. Early identification of causative gene mutations is important for genetic diagnosis, pre-symptomatic interventions, and prognosis prediction. Whole-exome sequencing (WES) has emerged as a promising method to identify causal variants in known genes and novel disease-related candidates in DCM.
Article
Oncology
Maria Gonzalez-Tablas, Carlos Prieto, Daniel Arandia, Maria Jara-Acevedo, Alvaro Otero, Daniel Pascual, Laura Ruiz, Ivan Alvarez-Twose, Andres Celestino Garcia-Montero, Alberto Orfao, Maria Dolores Tabernero
Summary: Our study examined the genetic variants in 32 WHO grade 1 meningiomas using whole exome sequencing, revealing a diverse mutational profile with NF2 gene being the most affected. Based on NF2 mutations and tumor cytogenetics, four genetic profiles were defined, showing an impact on patient recurrence-free survival.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Olga Levchenko, Elena Dadali, Ludmila Bessonova, Nina Demina, Galina Rudenskaya, Galina Matyushchenko, Tatiana Markova, Inga Anisimova, Natalia Semenova, Olga Shchagina, Oxana Ryzhkova, Rena Zinchenko, Varvara Galkina, Victoria Voinova, Sabina Nagieva, Alexander Lavrov
Summary: Intellectual development disorder (IDD) is characterized by deficits in intellectual and adaptive functioning. This study investigated the genetic structure of IDD, particularly in patients with non-specific IDD. Hereditary forms of IDD accounted for a significant portion of non-specific IDD cases, with monogenic forms being the most common. Variants in genes associated with the BAF (SWI/SNF) complex were frequently identified. Whole-exome sequencing was found to be an efficient diagnostic method after standard examination of patients with IDD in Russia.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Zhengyu Wu, Fang Zhang, Chengzhu Liu, Shuhong Shen, Jinhua Chu, Linhai Yang, Zhiwei Xie, Yu Liu, Kangkang Liu, Ningling Wang
Summary: This study reports two cases of TCF4-ZNF384 fusion in pediatric acute lymphoblastic leukemia patients, highlighting the importance of identifying ZNF384 rearrangement in ALL patients for understanding the clinical features and prognosis. Developing methods to detect ZNF384 specific translocation partners and leukemia specific targeting agents is crucial for improving the outcomes of ALL with ZNF384-rearrangement.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Yufen Xu, Di Che, Xiaoyu Zuo, Lanyan Fu, Lei Pi, Huazhong Zhou, Yaqian Tan, Kejian Wang, Xiaoqiong Gu
Summary: Kawasaki disease is an autoimmune disease that causes acquired heart disease in children. It is more common in males, but the reason for this sex bias is unknown. A study using whole-exome sequencing identified several genetic variants associated with male and female Kawasaki disease patients, and further validation showed that four of these variants were associated with Kawasaki disease susceptibility. These findings provide insight into the sex bias in Kawasaki disease and may contribute to the development of sex-specific precision therapies.