Article
Oncology
Lucas W. Thornblade, Paul Wong, Daneng Li, Susanne G. Warner, Sue Chang, Mustafa Raoof, Jonathan Kessler, Arya Amini, James Lin, Vincent Chung, Gagandeep Singh, Yuman Fong, Laleh G. Melstrom
Summary: Cholangiocarcinomas are rare cancers with potentially targetable mutations, and a third of patients undergoing resection in the past decade have had tumor genomic profiling, with 89% harboring targetable mutations. While targeted therapies were identified in most sequenced tumors, only 4% of patients received these therapies, highlighting the potential for precision medicine in the future care of cholangiocarcinoma.
Article
Medicine, General & Internal
Su-Jung Park, Narae Lee, Seong-Hee Jeong, Mun-Hui Jeong, Shin-Yun Byun, Kyung-Hee Park
Summary: The prevalence of genetic causes in SGA infants without known risk factors was 22%, and targeted-panel sequencing or whole-exome sequencing was effective in diagnosing the etiology of SGA infants without a known cause.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Lucia Pia Bruno, Gabriella Doddato, Floriana Valentino, Margherita Baldassarri, Rossella Tita, Chiara Fallerini, Mirella Bruttini, Caterina Lo Rizzo, Maria Antonietta Mencarelli, Francesca Mari, Anna Maria Pinto, Francesca Fava, Alessandra Fabbiani, Vittoria Lamacchia, Anna Carrer, Valentina Caputo, Stefania Granata, Elisa Benetti, Kristina Zguro, Simone Furini, Alessandra Renieri, Francesca Ariani
Summary: Intelectual disability (ID) and autism spectrum disorder (ASD) are often associated and characterized by impairments in cognitive processes and daily life tasks. Molecular diagnosis is crucial for improving prognosis and initiating treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Rheumatology
Yiming Luo, Marcela A. Ferrada, Keith A. Sikora, Cameron Rankin, Hugh D. Alessi, Daniel L. Kastner, Zuoming Deng, Mengqi Zhang, Peter A. Merkel, Virginia B. Kraus, Andrew S. Allen, Peter C. Grayson
Summary: This study suggests that rare variants in the DCBLD2 gene may play a role in the development of RP. These findings should be further validated in a larger sample and supported by functional experiments.
ANNALS OF THE RHEUMATIC DISEASES
(2023)
Article
Plant Sciences
Hisashi Udagawa, Hiroyuki Ichida, Takanori Takeuchi, Tomoko Abe, Yoshimitsu Takakura
Summary: In this study, a whole-exome sequencing (WES) procedure was developed in tobacco to characterize EMS-induced mutations in a test population, revealing a high number of single nucleotide variants. The amount of mutations detected by WES was 93.5% of those detected by whole-genome sequencing, while requiring significantly less sequencing data, making it a cost-effective tool for high-throughput mutation identification in tobacco.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Cristina Tous, Carmen Munoz-Redondo, Nereida Bravo-Gil, Angela Gavilan, Raquel Maria Fernandez, Juan Antinolo, Elena Navarro-Gonzalez, Guillermo Antinolo, Salud Borrego
Summary: Thyroid carcinoma (TC) can be classified into medullary (MTC) and non-medullary (NMTC). This study aimed to identify susceptibility genes for familial NMTC and non-RET MTC using whole exome sequencing. Rare candidate segregating variants were found in 12 families, with enriched biological processes related to cell proliferation, differentiation, survival, and adhesion. These findings provide insights into molecular mechanisms underlying familial forms of MTC and NMTC, which may contribute to early detection, tailored therapies, and patient management.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Wenxin Zhang, Ruixia Wang, Huan Fang, Xiangyuan Ma, Dan Li, Tao Liu, Zhenxi Chen, Ke Wang, Shiguang Hao, Zicheng Yu, Zhili Chang, Chenglong Na, Yin Wang, Jian Bai, Yanyan Zhang, Fang Chen, Miao Li, Chao Chen, Liangshen Wei, Jinghua Li, Xiaoyan Chang, Shoufang Qu, Ling Yang, Jie Huang
Summary: This study established a linear model to correlate wesTMB and psTMB. It was found that psTMB could be a representative of wesTMB, and even in samples with low tumor content, psTMB could accurately classify TMB high and low patients.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Julia Horjus, Tineke van Mourik-Banda, Marco A. P. Heerings, Marina Hakobjan, Ward De Witte, Dorothea J. Heersema, Anne J. Jansen, Eva M. M. Strijbis, Brigit A. de Jong, Astrid E. J. Slettenaar, Esther M. P. E. Zeinstra, Erwin L. J. Hoogervorst, Barbara Franke, Wiebe Kruijer, Peter J. Jongen, Leo J. Visser, Geert Poelmans
Summary: This study identified 12 rare genetic variants associated with multiple sclerosis through whole exome sequencing and co-segregation analysis, highlighting the involvement of various biological processes related to (de-/re-)myelination and auto-immunity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Julia Hoeglund, Fatemeh Hadizadeh, Weronica E. Ek, Torgny Karlsson, Asa Johansson
Summary: This study analyzed 200,000 whole-exome sequences from the UK Biobank cohort and identified 220 genes in 55 genomic regions that are associated with eosinophil count. Among these genes, seven are driven by rare variants and two are considered novel eosinophil loci. These findings provide valuable knowledge about the effect of rare variants on eosinophil count and can aid in the identification of therapeutic targets.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Health Care Sciences & Services
Mario Cesare Nurchis, Gian Marco Raspolini, Aurora Heidar Alizadeh, Gerardo Altamura, Francesca Clementina Radio, Marco Tartaglia, Bruno Dallapiccola, Gianfranco Damiani
Summary: This study compares the organizational aspects of whole genome sequencing (WGS) and whole exome sequencing (WES) for pediatric patients with suspected genetic disorders in Italy. The results show that WES requires more genome rearrangement analysis, while WGS has higher data storage and security requirements and is only used for specific research studies. No difference was found in centralization and decentralization issues. Both WES and WGS reduce the need for additional diagnostic analyses, but economic evidence gaps exist for WGS in clinical settings.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Adeline Germain, Jeanne-Marie Perotin, Gonzague Delepine, Myriam Polette, Gaetan Deslee, Valerian Dormoy
Summary: A comparative whole-exome sequencing analysis was performed on bronchial epithelia from COPD and non-COPD subjects, revealing genetic alterations and copy number variations in remodelled epithelia, mainly in COPD patients. Functional analysis highlighted cilia-associated processes, indicating a greater genetic alteration in remodelled epithelia.
Article
Medicine, Research & Experimental
Hong Lian, Shen Song, Wenzheng Chen, Anteng Shi, Haobin Jiang, Shengshou Hu
Summary: This study aimed to characterize the genetic basis of dilated cardiomyopathy (DCM) in heart transplantation (HTx) patients in the Chinese population. The results showed that TTN and FLNC genes harbored a significant number of pathogenic and likely pathogenic variants, and FLNC truncation could lead to severe clinical symptoms in DCM patients.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
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
Genetics & Heredity
Gokalp Celik, Timur Tuncali
Summary: A new strategy was developed in this study to detect Runs of long homozygous (ROH) by examining the X chromosome non-pseudoautosomal region, utilizing genotype probabilities and the hidden Markov model algorithm. Testing on simulated and real population data demonstrated that this method, named ROHMM, performed robustly and with high accuracy, surpassing its natural competitors.
Article
Genetics & Heredity
Parneet Kaur, Michelle C. do Rosario, Malavika Hebbar, Suvasini Sharma, Neethukrishna Kausthubham, Karthik Nair, A. Shrikiran, Y. Ramesh Bhat, Leslie Edward S. Lewis, Sheela Nampoothiri, Siddaramappa J. Patil, Narayanaswami Suresh, Sunita Bijarnia Mahay, Ratna Dua Puri, Shivanand Pai, Anupriya Kaur, K. C. Rakshith, Nutan Kamath, Shruti Bajaj, Ali Kumble, Rajesh Shetty, Rathika Shenoy, Mahesh Kamate, Hitesh Shah, Mamta N. Muranjan, B. L. Yatheesha, K. Shreedhara Avabratha, Girish Subramaniam, Rajagopal Kadavigere, Stephanie Bielas, Katta Mohan Girisha, Anju Shukla
Summary: This study describes the phenotypic and genotypic spectrum of genetic disorders with CNS WMAs in our population. It showed that WES, especially singleton WES, is an efficient tool in the diagnosis of these heterogeneous entities. The study also highlights possible founder events and recurrent disease-causing variants in our population and their implications on the testing strategy.