Chromatin remodeling (SWI/SNF) complexes, cancer, and response to immunotherapy by Razelle Kurzrock, Shumei Kato, Nithya Krishnamurthy, Scott Lippman

“…Significantly, ~20% of malignancies harbor alterations in >1 of these subunits, making the genes encoding SWI/SNF family members among the most vulnerable to genomic aberrations in cancer. ARID1A is the largest subunit of the SWI/SNF complex and is altered in ~40%–50% of ovarian clear cell cancers and ~15%–30% of cholangiocarcinomas, in addition to a variety of other malignancies. …”
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Functional analysis of a novel homozygous missense IVD gene variant: a case report with dual genetic diagnoses by Yuying Zhu, Ke Wu, Hanying Wen

“…BackgroundGenomic or exome sequencing is beneficial for identifying more than one pathogenic variation causing blended atypical and/or severe phenotypes. …”
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Localization of the quantitative trait loci related to lodging resistance in spring bread wheat (<i>Triticum aestivum</i> L.) by I. N. Leonova, E. V. Ageeva

“…Quantitative trait loci (QTL) mapping was performed by means of genome-wide association study (GWAS) using 9285 SNP markers. …”
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Cytogenetic Evolution of Human Ovarian Cell Lines Associated with Chemoresistance and Loss of Tumorigenicity by Stéphanie Struski, Martine Doco‐Fenzy, Michael Koehler, Ilse Chudoba, Francis Levy, Linda Masson, Nicole Michel, Evelyne Ulrich, Nadine Gruson, Jean Bénard, Gérard Potron, Pascale Cornillet‐Lefebvre

“…In order to identify genomic changes associated with a resistant phenotype acquisition, we used comparative genomic hybridization (CGH) to compare a human ovarian cell line, Igrov1, and four derived subcell lines, resistant to vincristine and presenting a reversion of malignant properties. …”
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Expert Consensus on Molecular Tumor Boards in Taiwan: Joint Position Paper by the Taiwan Oncology Society and the Taiwan Society of Pathology by Ming-Huang Chen, Wan-Shan Li, Bin-Chi Liao, Chiao-En Wu, Chien-Feng Li, Chia-Hsun Hsieh, Feng-Che Kuan, Huey-En Tzeng, Jen-Fan Hang, Nai-Jung Chiang, Tse-Ching Chen, Tom Wei-Wu Chen, John Wen-Cheng Chang, Yao-Yu Hsieh, Yen-Lin Chen, Yi-Chen Yeh, Yi-Hsin Liang, Yu-Li Su, Chiung-Ru Lai, James Chih-Hsin Yang

“…Results: The joint statement proposes key recommendations: (1) MTB discussions encompass diverse molecular analyses including next-generation sequencing (NGS), RNA sequencing, whole-exon sequencing, and whole-genomic sequencing addressing relevant genomic changes, tumor mutation burden, microsatellite instability, and specific biomarkers for certain cancers. (2) MTB meetings should involve multidisciplinary participants who receive regular updates on NGS-related clinical trials. (3) Prioritize discussing cases with unique clinical needs, gene alterations lacking treatments, untreatable neoplasms, or oncogenes unresponsive to targeted therapies. (4) Base MTB discussions on comprehensive patient data, including genetics, pathology, timing of specimen collection, and NGS outcomes. (5) MTBs offer treatment recommendations: standard therapies, off-label use, clinical trials, genetic counseling, and multidisciplinary reviews. (6) MTB effectiveness can be gauged by member composition, case reviews, treatment suggestions, and patient outcomes. …”
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Relationship between the anthocyanin content values in the leaf sheath base of barley cultivars and in the grain of the hybrids derived from them by O. Yu. Shoeva, T. V. Kukoeva

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Systematic Analysis of Environmental Chemicals That Dysregulate Critical Period Plasticity-Related Gene Expression Reveals Common Pathways That Mimic Immune Response to Pathogen by Milo R. Smith, Priscilla Yevoo, Masato Sadahiro, Ben Readhead, Brian Kidd, Joel T. Dudley, Hirofumi Morishita

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Influence of allelic polymorphism in the 3’ untranslated region of the <i>StTCP23</i> gene on the tolerance of potato cultivars to the potato spindle tuber viroid by N. V. Mironenko, A. V. Kochetov, O. S. Afanasenko

“…Cultivars with the A allele (‘Gala’, ‘Colomba’, ‘Favorit’, and ‘Fioletovy’) identical to the reference genome or a high dose of the C allele with a deletion of four nucleotides (cv. …”
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Molecular Detection and Determination of Phylogenetic Position of Watermelon Chlorotic Stunt Virus Khouzestan Isolate Based on Coat Protein Gene by Samira Pakbaz, Zahra Jelavi, Ehsan Hasanvand, Hossein Mirzaei Najafgholi

“…PCR was performed using two primer pairs of Begomovirus related to AV1 and also AV2 genomic region. The sequencing results confirmed WmCSV infection in the samples. …”
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Machine Learning Enabled Prediction of Biologically Relevant Gene Expression Using CT‐Based Radiomic Features in Non‐Small Cell Lung Cancer by Shrey S. Sukhadia, Christoph Sadée, Olivier Gevaert, Shivashankar H. Nagaraj

“…The emerging field of radiogenomics utilizes statistical methods to correlate radiographic tumor features with genomic characteristics from biopsy samples. Radiomic techniques automate the precise extraction of imaging features from tumor regions in radiographic scans, which are subjected to machine learning (ML) to predict genomic attributes. …”
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Redox proteomics reveal a role for peroxiredoxinylation in stress protection by Gerhard Seisenbacher, Zrinka Raguz Nakic, Eva Borràs, Eduard Sabidó, Uwe Sauer, Eulalia de Nadal, Francesc Posas

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The mitochondrial gene order and CYTB gene evolution in insects by F. S. Sharko, A. V. Nedoluzhko, S. M. Rastorguev, S. V. Tsygankova, E. S. Boulygina, A. A. Polilov, E. B. Prokhortchouk, K. G. Skryabin

“…It is known that molecular evolution goes by the way of not only single nucleotide substitutions, but also by larger genomic reorganizations, such as insertion or deletion of large genome fragments, and even changing the order of genes. …”
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Evaluation for Retinal Therapy for RPE65 Variation Assessed in hiPSC Retinal Pigment Epithelial Cells by Benjamin M. Nash, To Ha Loi, Milan Fernando, Amin Sabri, James Robinson, Anson Cheng, Steven S. Eamegdool, Elizabeth Farnsworth, Bruce Bennetts, John R. Grigg, Seo-Kyung Chung, Anai Gonzalez-Cordero, Robyn V. Jamieson

“…In our cohort of patients, we identified siblings with early-onset severe retinal degeneration where genomic studies revealed compound heterozygous variants in RPE65, one a known pathogenic missense variant and the other a novel synonymous variant of uncertain significance. …”
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Prevalence and methodologies for detection, characterization and subtyping of Listeria monocytogenes and L. ivanovii in foods and environmental sources by Jin-Qiang Chen, Patrick Regan, Pongpan Laksanalamai, Stephanie Healey, Zonglin Hu

“…In this review, we (A) described L. monocytogenes and L. ivanovii, world-wide incidence of listeriosis, and prevalence of various L. monocytogenes strains in food and environmental sources; (B) comprehensively reviewed different types of traditional and newly developed methodologies, including culture-based, antigen/antibody-based, LOOP-mediated isothermal amplification, matrix-assisted laser desorption ionization-time of flight-mass spectrometry, DNA microarray, and genomic sequencing for detection and characterization of L. monocytogenes in foods and environmental sources; (C) comprehensively summarized different subtyping methodologies, including pulsed-field gel electrophoresis, multi-locus sequence typing, ribotyping, and phage-typing, and whole genomic sequencing etc. for subtyping of L. monocytogenes strains from food and environmental sources; and (D) described the applications of these methodologies in detection and subtyping of L. monocytogenes in foods and food processing facilities.…”
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Differences in Transcriptional Activation by the Two Allelic (L162V Polymorphic) Variants of PPARα after Omega-3 Fatty Acids Treatment by Iwona Rudkowska, Mélanie Verreault, Olivier Barbier, Marie-Claude Vohl

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Role of sirtuins in epigenetic regulation and aging control by E. M. Samoilova, S. E. Romanov, D.  A. Chudakova, P. P. Laktionov

“…Additionally, experimental data obtained in animal models, as well as data from population genomic studies, suggest a SIRT effect on life expectancy. …”
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Bi-allelic variants in WDR47 cause a complex neurodevelopmental syndrome by Efil Bayam, Peggy Tilly, Stephan C Collins, José Rivera Alvarez, Meghna Kannan, Lucile Tonneau, Elena Brivio, Bruno Rinaldi, Romain Lecat, Noémie Schwaller, Ludovica Cotellessa, Sateesh Maddirevula, Fabiola Monteiro, Carlos M Guardia, João Paulo Kitajima, Fernando Kok, Mitsuhiro Kato, Ahlam A A Hamed, Mustafa A Salih, Saeed Al Tala, Mais O Hashem, Hiroko Tada, Hirotomo Saitsu, Mariano Stabile, Paolo Giacobini, Sylvie Friant, Zafer Yüksel, Mitsuko Nakashima, Fowzan S Alkuraya, Binnaz Yalcin, Juliette D Godin

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Low & Anaplastic Grade Glioma Umbrella Study of MOlecular Guided TherapieS (LUMOS-2): study protocol for a phase 2, prospective, multicentre, open-label, multiarm, biomarker-direct... by Marshall Pitz, Eng-Siew Koh, Elizabeth H Barnes, Lucille Sebastian, Mandy L Ballinger, David M Thomas, Christopher O'Callaghan, John Simes, Hui K Gan, Sonia Yip, Hao-Wen Sim, Desma Spyridopoulos, Richard De Abreu Lourenco, Cynthia Hawkins, Kristen McParland, Benjamin Kong, Subotheni Thavaneswaran, Patrick J Wheeler

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Shared genetic risk and causal associations between Post-traumatic stress disorder and migraine with antithrombotic agents and other medications by Charlotte K. Bainomugisa, Dagmar Bruenig, Heidi G. Sutherland, Lyn R. Griffiths, Dale R. Nyholt, Divya Mehta

“…There are proposed biological, genetic and environmental factors associated with both PTSD and migraine suggesting shared etiology. Genome-Wide Association Studies (GWAS) have been used to identify genomic risk loci associated with various disorders and to investigate genetic overlap between traits. …”
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Sharing of cmeRABC alleles between C. coli and C. jejuni associated with extensive drug resistance in Campylobacter isolates from infants and poultry in the Peruvian Amazon by Kerry K. Cooper, Evangelos Mourkas, Francesca Schiaffino, Craig T. Parker, Tackeshy N. Pinedo Vasquez, Paul F. Garcia Bardales, Pablo Peñataro Yori, Maribel Paredes Olortegui, Katia Manzanares Villanueva, Lucero Romaina Cachique, Hermann Silva Delgado, Matthew D. Hitchings, Steven Huynh, Samuel K. Sheppard, Ben Pascoe, Margaret N. Kosek

“…Publicly accessible global genomic data from 16,120 Campylobacter genomes identified these mutations in approximately 6% of C. jejuni and C. coli isolates globally, with higher prevalence in samples from poultry in many countries, including Peru. …”
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