Article
Public, Environmental & Occupational Health
Kathryn Demanelis, Dayana A. Delgado, Lin Tong, Farzana Jasmine, Alauddin Ahmed, Tariqul Islam, Faruque Parvez, Muhammad G. Kibriya, Joseph H. Graziano, Habibul Ahsan, Brandon L. Pierce
Summary: The study found an association between arsenic exposure and somatic loss of the Y chromosome (LoY) in Bangladeshi men, with LoY being linked to an increased risk of developing skin lesions. The percentage of cells with LoY increased with age, suggesting LoY may be a biomarker of susceptibility in populations exposed to arsenic.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
(2023)
Article
Oncology
Samuel Terkper Ahuno, Anna-Lisa Doebley, Thomas U. Ahearn, Joel Yarney, Nicholas Titiloye, Nancy Hamel, Ernest Adjei, Joe-Nat Clegg-Lamptey, Lawrence Edusei, Baffour Awuah, Xiaoyu Song, Verna Vanderpuye, Mustapha Abubakar, Maire Duggan, Daniel G. Stover, Kofi Nyarko, John M. S. Bartlett, Francis Aitpillah, Daniel Ansong, Kevin L. Gardner, Felix Andy Boateng, Anne M. Bowcock, Carlos Caldas, William D. Foulkes, Seth Wiafe, Beatrice Wiafe-Addai, Montserrat Garcia-Closas, Alexander Kwarteng, Gavin Ha, Jonine D. Figueroa, Paz Polak
Summary: ctDNA sequencing studies conducted on patients in sub-Saharan Africa revealed the detection of ctDNA in a majority of patients, despite not being selected for tumor grade and subtype. Additionally, breast cancer driver copy number alterations were observed in the majority of patients.
NPJ PRECISION ONCOLOGY
(2021)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Dermatology
Rachel L. Fulton, David J. Margolis, Patrick G. Sockler, Nandita Mitra, Xuan Fei Colin Cornelius Wong, John E. Common
Summary: Atopic dermatitis is a chronic inflammatory skin condition with a multifactorial pathophysiology. Research has shown that filaggrin gene (FLG) plays a significant role in skin barrier dysfunction and can increase the risk of developing AD. However, a study evaluating FLG CNV in Whites and Blacks found that while racial differences exist, they do not seem to explain the risk of developing AD.
EXPERIMENTAL DERMATOLOGY
(2022)
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Clinical Neurology
Aurelien Perrin, Raul Juntas Morales, Francoise Chapon, Corinne Theze, Delphine Lacourt, Henri Pegeot, Emmanuelle Uro-Coste, Diane Giovannini, Nicolas Leboucq, Martial Mallaret, Emmeline Lagrange, Valerie Rigau, Karen Gaudon, Pascale Richard, Michel Koenig, Corinne Metay, Mireille Cossee
Summary: This study analyzed patients from two distinct families with a novel distal titinopathy phenotype associated with the same CNV in the TTN gene. The CNV reported in this study is the most proximal out-of-frame TTN variant and leads to aberrant splicing transcripts, resulting in frameshift and possibly dominant effects. This data represents a novel phenotype-genotype association and provides hypotheses for its dominant effects.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: The study developed a tool called Montage to enhance the accuracy of detecting mosaic copy number variants, identified numerous mosaic CNVs associated with phenotypes, and presented a novel algorithm for efficient detection of mosaic CNVs.
Article
Oncology
Karen Gambaro, Maud Marques, Suzan McNamara, Mathilde Couetoux du Tertre, Zuanel Diaz, Cyrla Hoffert, Archana Srivastava, Steven Hebert, Benoit Samson, Bernard Lesperance, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sideris, Felix Couture, Ronald Burkes, Mohammed Harb, Errol Camlioglu, Adrian Gologan, Vincent Pelsser, Andre Constantin, Celia M. T. Greenwood, Sabine Tejpar, Petr Kavan, Claudia L. Kleinman, Gerald Batist
Summary: A study on genomic plasticity in liver metastatic samples of colorectal cancer revealed an increased frequency of specific CN in metastatic lesions after first-line treatment. Comparison of CNA profiles in lesions with different treatment responses showed focal genomic divergences in post-treatment resistant lesions but not in responder lesions. Examining metastatic lesions is crucial as 15 out of 18 independently validated CNA regions associated with progression-free survival were only identified in metastatic lesions, not in primary tumors.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Agnieszka Piotrowska-Nowak, Krzysztof Safranow, Jakub G. Adamczyk, Ireneusz Soltyszewski, Pawel Cieszczyk, Katarzyna Tonska, Cezary Zekanowski, Beata Borzemska
Summary: Energy efficiency is crucial for athletic performance. This study investigated the relationship between mitochondrial DNA (mtDNA) variants and athletic performance among Polish male athletes. The analysis revealed no correlation between mtDNA variants and athletic performance, but showed a lower mtDNA copy number in both power and endurance athletes compared to controls.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Aditi Hazra, Andrea O'Hara, Kornelia Polyak, Faina Nakhlis, Beth T. Harrison, Antonio Giordano, Beth Overmoyer, Filipa Lynce
Summary: The goal of this study was to identify biomarkers associated with de novo inflammatory breast cancer (IBC). Through examination of breast biopsies, significant copy number variations (CNVs) on chromosome 7p11.2 and 21 were identified. These findings provide insights into the biology of IBC and may lead to the optimization of treatment strategies.
Article
Multidisciplinary Sciences
Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen
Summary: This paper presents a method called "Chameleolyser" that accurately identifies variants in duplicated genomic regions. Application of this method to a large cohort of exome samples led to the identification of a significant number of rare variants, including those that resulted in direct molecular diagnoses for previously undiagnosed patients.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Heming Wu, Qingyan Huang, Xia Zhang, Zhikang Yu, Zhixiong Zhong
Summary: This study identified a high rate of chromosomal abnormalities in fetuses with miscarriage during early and middle pregnancy, with a significantly higher numerical chromosomal abnormality rate in pregnant women aged >=35 compared to <35. The early fetal chromosomal abnormality rate was higher than the middle fetal rate, and there were 168 genes enriched in the VOUS + pCNV regions, associated with 41 functions and 12 pathways.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
DeElegant Robinson, Elena Vanacloig-Pedros, Ruoyi Cai, Michael Place, James Hose, Audrey P. Gasch
Summary: Copy-number variation in genes can affect gene expression, and the tolerance to such variation can vary with genetic background and environmental conditions. This study explored the interaction between copy-number variation tolerance and sodium chloride stress in four genetically distinct Saccharomyces cerevisiae strains. The results showed strain-specific responses to gene overexpression, indicating the importance of both genetic background and environmental conditions in the response to copy-number variation.
G3-GENES GENOMES GENETICS
(2023)