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JOURNAL ARTICLE
Yupeng Liu, Xue Ma, Zhehui Chen, Ruxuan He, Yao Zhang, Hui Dong, Yanyan Ma, Tongfei Wu, Qiao Wang, Yuan Ding, Xiyuan Li, Dongxiao Li, Jinqing Song, Mengqiu Li, Ying Jin, Jiong Qin, Yanling Yang
BACKGROUND: Clinicians traditionally aim to identify a singular explanation for the clinical presentation of a patient; however, in some cases, the diagnosis may remain elusive or fail to comprehensively explain the clinical findings. In recent years, advancements in next-generation sequencing, including whole-exome sequencing, have led to the incidental identification of dual diagnoses in patients. Herein we present the cases of five pediatric patients diagnosed with dual rare genetic diseases...
April 12, 2024: Orphanet Journal of Rare Diseases
#22
JOURNAL ARTICLE
Bryson M F Sjodin, Danielle A Schmidt, Kurt E Galbreath, Michael A Russello
Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range...
April 13, 2024: Scientific Reports
#23
JOURNAL ARTICLE
Rosa Celia Poquita-Du, Danwei Huang, Peter A Todd
Characterisation of genomic variation among corals can help uncover variants underlying trait differences and contribute towards genotype prioritisation in coastal restoration projects. For example, there is growing interest in identifying resilient genotypes for transplantation, and to better understand the genetic processes that allow some individuals to survive in specific conditions better than others. The coral species Pocillopora acuta is known to survive in a wide range of habitats, from reefs artificial coastal defences, suggesting its potential use as a starter species for ecological engineering efforts involving coral transplantation onto intertidal seawalls...
April 12, 2024: Scientific Reports
#24
JOURNAL ARTICLE
Anthony M Musolf, Cristina M Justice, Zeynep Erdogan-Yildirim, Seppe Goovaerts, Araceli Cuellar, John R Shaffer, Mary L Marazita, Peter Claes, Seth M Weinberg, Jae Li, Craig Senders, Marike Zwienenberg, Emil Simeonov, Radka Kaneva, Tony Roscioli, Lorena Di Pietro, Marta Barba, Wanda Lattanzi, Michael L Cunningham, Paul A Romitti, Simeon A Boyadjiev
Craniosynostosis (CS) is a major birth defect resulting from premature fusion of cranial sutures. Nonsyndromic CS occurs more frequently than syndromic CS, with sagittal nonsyndromic craniosynostosis (sNCS) presenting as the most common CS phenotype. Previous genome-wide association and targeted sequencing analyses of sNCS have identified multiple associated loci, with the strongest association on chromosome 20. Herein, we report the first whole-genome sequencing study of sNCS using 63 proband-parent trios...
April 12, 2024: Scientific Reports
#25
JOURNAL ARTICLE
Mauricio Andrade-Marcial, Ramón Pacheco-Arjona, Sara Hernández-Castellano, Ligia Che-Aguilar, Clelia De-la-Peña
Albino plants display partial or complete loss of photosynthetic pigments and defective thylakoid membrane development, consequently impairing plastid function and development. These distinctive attributes render albino plants excellent models for investigating chloroplast biogenesis. Despite their potential, limited exploration has been conducted regarding the molecular alterations underlying these phenotypes, extending beyond photosynthetic metabolism. In this study, we present a novel de novo transcriptome assembly of an albino somaclonal variant of Agave angustifolia Haw...
2024: Physiologia Plantarum
#26
JOURNAL ARTICLE
Weicheng Chen, Zhuoyao Guo, Mengru Li, Wei Sheng, Guoying Huang
UNLABELLED: Primary ciliary dyskinesia (PCD) is a rare disorder characterized by extensive genetic heterogeneity. However, in the genetic pathogenesis of PCD, copy number variation (CNV) has not received sufficient attention and has rarely been reported, especially in China. Next-generation sequencing (NGS) followed by targeted CNV analysis was used in patients highly suspected to have PCD with negative results in routine whole-exome sequencing (WES) analysis. Quantitative real-time polymerase chain reaction (qPCR) and Sanger sequencing were used to confirm these CNVs...
February 2024: Phenomics
#27
JOURNAL ARTICLE
Niels Vos, Lotte Kleinendorst, Liselot van der Laan, Jorrit van Uhm, Philip R Jansen, Agnies M van Eeghen, Saskia M Maas, Marcel M A M Mannens, Mieke M van Haelst
The 16p11.2 deletion syndrome is a clinically heterogeneous disorder, characterized by developmental delay, intellectual disability, hyperphagia, obesity, macrocephaly and psychiatric problems. Cases with 16p11.2 duplication syndrome have similar neurodevelopmental problems, but typically show a partial 'mirror phenotype' with underweight and microcephaly. Various copy number variants (CNVs) of the chromosomal 16p11.2 region have been described. Most is known about the 'typical' 16p11.2 BP4-BP5 (29.6-30.2 Mb; ~600 kb) deletions and duplications, but there are also several published cohorts with more distal 16p11...
April 11, 2024: European Journal of Human Genetics: EJHG
#28
JOURNAL ARTICLE
Andrew Fleming, Miranda Galey, Lizi Briggs, Matthew Edwards, Claire Hogg, Shibu John, Sam Wilkinson, Ellie Quinn, Ranjit Rai, Tom Burgoyne, Andy Rogers, Mitali P Patel, Paul Griffin, Steven Muller, Siobhan B Carr, Michael R Loebinger, Jane S Lucas, Anand Shah, Ricardo Jose, Hannah M Mitchison, Amelia Shoemark, Danny E Miller, Deborah J Morris-Rosendahl
Primary ciliary dyskinesia (PCD), a disorder of the motile cilia, is now recognised as an underdiagnosed cause of bronchiectasis. Accurate PCD diagnosis comprises clinical assessment, analysis of cilia and the identification of biallelic variants in one of 50 known PCD-related genes, including HYDIN. HYDIN-related PCD is underdiagnosed due to the presence of a pseudogene, HYDIN2, with 98% sequence homology to HYDIN. This presents a significant challenge for Short-Read Next Generation Sequencing (SR-NGS) and analysis, and many diagnostic PCD gene panels do not include HYDIN...
April 11, 2024: European Journal of Human Genetics: EJHG
#29
JOURNAL ARTICLE
Edoardo Errichiello, Mauro Lecca, Chiara Vantaggiato, Zoraide Motta, Nicoletta Zanotta, Claudio Zucca, Sara Bertuzzo, Luciano Piubelli, Loredano Pollegioni, Maria Clara Bonaglia
Copy number variants (CNVs) represent the genetic cause of about 15-20% of neurodevelopmental disorders (NDDs). We identified a ~67 kb de novo intragenic deletion on chromosome 2q22.3 in a female individual showing a developmental encephalopathy characterised by epilepsy, severe intellectual disability, speech delay, microcephaly, and thin corpus callosum with facial dysmorphisms. The microdeletion involved exons 5-6 of GTDC1, encoding a putative glycosyltransferase, whose expression is particularly enriched in the nervous system...
April 11, 2024: European Journal of Human Genetics: EJHG
#30
JOURNAL ARTICLE
Thomas W Laver, Matthew N Wakeling, Richard C Caswell, Benjamin Bunce, Daphne Yau, Jonna M E Männistö, Jayne A L Houghton, Jasmin J Hopkins, Michael N Weedon, Vrinda Saraff, Melanie Kershaw, Engela M Honey, Nuala Murphy, Dinesh Giri, Stuart Nath, Ana Tangari Saredo, Indraneel Banerjee, Khalid Hussain, Nick D L Owens, Sarah E Flanagan
Persistent congenital hyperinsulinism (HI) is a rare genetically heterogeneous condition characterised by dysregulated insulin secretion leading to life-threatening hypoglycaemia. For up to 50% of affected individuals screening of the known HI genes does not identify a disease-causing variant. Large deletions have previously been used to identify novel regulatory regions causing HI. Here, we used genome sequencing to search for novel large (>1 Mb) deletions in 180 probands with HI of unknown cause and replicated our findings in a large cohort of 883 genetically unsolved individuals with HI using off-target copy number variant calling from targeted gene panels...
April 11, 2024: European Journal of Human Genetics: EJHG
#31
JOURNAL ARTICLE
George J Burghel, Jamie M Ellingford, Ronnie Wright, Lauren Bradford, Jake Miller, Christopher Watt, Jonathan Edgerley, Farah Naeem, Siddharth Banka
BACKGROUND: Reanalysis of exome/genome data improves diagnostic yield. However, the value of reanalysis of clinical array comparative genomic hybridisation (aCGH) data has never been investigated. Case-by-case reanalysis can be challenging in busy diagnostic laboratories. METHODS AND RESULTS: We harmonised historical postnatal clinical aCGH results from ~16 000 patients tested via our diagnostic laboratory over ~7 years with current clinical guidance. This led to identification of 37 009 copy number losses (CNLs) including 33 857 benign, 2173 of uncertain significance and 979 pathogenic...
April 11, 2024: Journal of Medical Genetics
#32
JOURNAL ARTICLE
Linlin Wang, Ping Liang, Pingshan Pan, Jiasun Su, Jiayi Qin, Zhaoxia Chen, Dongbing Huang, Weijia Sun, Pengshu Song, Hongwei Wei
OBJECTIVES: To evaluate the the diagnostic yield of chromosomal microarray analysis (CMA) in fetuses with isolated CPC (iCPC). METHODS: A total of 315 fetuses with iCPC (iCPC group) and 364 fetuses without abnormal ultrasound findings (control group) were recruited between July 2014 to March 2018. RESULTS: The overall diagnostic yield of chromosomal abnormalities by CMA and karyotyping in iCPC group was up to 4.1 %, higher than 1.4 % in the control group, p < 0...
April 6, 2024: European Journal of Obstetrics, Gynecology, and Reproductive Biology
#33
JOURNAL ARTICLE
Simone Weiss, Philippe Lamy, Maria Rusan, Maibritt Nørgaard, Benedicte Parm Ulhøi, Michael Knudsen, Christine Gaasdal Kassentoft, Leila Farajzadeh, Jørgen Bjerggaard Jensen, Jakob Skou Pedersen, Michael Borre, Karina Dalsgaard Sørensen
Treatment resistance remains a major issue in aggressive prostate cancer (PC), and novel genomic biomarkers may guide better treatment selection. Circulating tumor DNA (ctDNA) can provide minimally invasive information about tumor genomes, but the genomic landscape of aggressive PC based on whole-genome sequencing (WGS) of ctDNA remains incompletely characterized. Thus, we here performed WGS of tumor tissue (n = 31) or plasma ctDNA (n = 10) from a total of 41 aggressive PC patients, including 11 hormone-naïve, 15 hormone-sensitive, and 15 castration-resistant patients...
April 11, 2024: International Journal of Cancer. Journal International du Cancer
#34
JOURNAL ARTICLE
Maria Mabyalwa Mudau, Bronwyn Dillon, Clarice Smal, Candice Feben, Engela Honey, Nadia Carstens, Amanda Krause
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic condition with complete age-dependent penetrance, variable expressivity and a global prevalence of ∼1/3,000. It is characteriszed by numerous café-au-lait macules, skin freckling in the inguinal or axillary regions, Lisch nodules of the iris, optic gliomas, neurofibromas, and tumour predisposition. The diagnostic testing strategy for NF1 includes testing for DNA single nucleotide variants (SNVs), copy number variants (CNVs) as well as RNA analysis for deep intronic and splice variants, which can cumulatively identify the causative variant in 95% of patients...
2024: Frontiers in Genetics
#35
Yongxue Lyu, Tao Wang, Meifang Lin, Fengfeng Qi
BACKGROUND: Infantile neuroaxonal dystrophy (INAD) is an ultra-rare early-onset autosomal recessive neurodegenerative disorder due to PLA2G6 variants. The clinical symptoms of INAD patients display considerable diversity, and many PLA2G6 variants are still not thoroughly investigated in relation to their associated clinical presentations. CASE DESCRIPTION: A 16-month-old boy was admitted to our hospital due to regression of acquired motor and speech abilities that had persisted for 4 months...
March 27, 2024: Translational Pediatrics
#36
JOURNAL ARTICLE
Urszula N Wasko, Jingjing Jiang, Tanner C Dalton, Alvaro Curiel-Garcia, A Cole Edwards, Yingyun Wang, Bianca Lee, Margo Orlen, Sha Tian, Clint A Stalnecker, Kristina Drizyte-Miller, Marie Menard, Julien Dilly, Stephen A Sastra, Carmine F Palermo, Marie C Hasselluhn, Amanda R Decker-Farrell, Stephanie Chang, Lingyan Jiang, Xing Wei, Yu C Yang, Ciara Helland, Haley Courtney, Yevgeniy Gindin, Karl Muonio, Ruiping Zhao, Samantha B Kemp, Cynthia Clendenin, Rina Sor, William P Vostrejs, Priya S Hibshman, Amber M Amparo, Connor Hennessey, Matthew G Rees, Melissa M Ronan, Jennifer A Roth, Jens Brodbeck, Lorenzo Tomassoni, Basil Bakir, Nicholas D Socci, Laura E Herring, Natalie K Barker, Junning Wang, James M Cleary, Brian M Wolpin, John A Chabot, Michael D Kluger, Gulam A Manji, Kenneth Y Tsai, Miroslav Sekulic, Stephen M Lagana, Andrea Califano, Elsa Quintana, Zhengping Wang, Jacqueline A M Smith, Matthew Holderfield, David Wildes, Scott W Lowe, Michael A Badgley, Andrew J Aguirre, Robert H Vonderheide, Ben Z Stanger, Timour Baslan, Channing J Der, Mallika Singh, Kenneth P Olive
Broad-spectrum RAS inhibition holds the potential to benefit roughly a quarter of human cancer patients whose tumors are driven by RAS mutations1,2 . RMC-7977 is a highly selective inhibitor of the active GTP-bound forms of KRAS, HRAS, and NRAS, with affinity for both mutant and wild type (WT) variants (RAS(ON) multi-selective)3 . As >90% of human pancreatic ductal adenocarcinoma (PDAC) cases are driven by activating mutations in KRAS4 , we assessed the therapeutic potential of the RAS(ON) multi-selective inhibitor RMC-7977 in a comprehensive range of PDAC models...
April 8, 2024: Nature
#37
JOURNAL ARTICLE
Malek Bouassida, Denise Molina-Gomes, Fairouz Koraichi, Bérénice Hervé, Morgane Lhuilier, Clémence Duvillier, Jessica Le Gall, Marion Gauthier-Villars, Valérie Serazin, Thibaud Quibel, Rodolphe Dard, François Vialard
BACKGROUND: Despite recent advances in prenatal genetic diagnosis, medical geneticists still face considerable difficulty in interpreting the clinical outcome of copy-number-variant duplications and defining the mechanisms underlying the formation of certain chromosomal rearrangements. Optical genome mapping (OGM) is an emerging cytogenomic tool with proved ability to identify the full spectrum of cytogenetic aberrations. METHODS: Here, we report on the use of OGM in a prenatal diagnosis setting...
April 2024: Molecular Genetics & Genomic Medicine
#38
JOURNAL ARTICLE
Emilia Stahlbom, Jesper Molin, Claes Lundstrom, Anders Ynnerman
Genomics is at the core of precision medicine, and there are high expectations on genomics-enabled improvement of patient outcomes in the years to come. Around the world, initiatives to increase the use of DNA sequencing in clinical routine are being deployed, such as the use of broad panels in the standard care for oncology patients. Such a development comes at the cost of increased demands on throughput in genomic data analysis. In this paper, we use the task of copy number variant (CNV) analysis as a context for exploring visualization concepts for clinical genomics...
April 8, 2024: IEEE Transactions on Visualization and Computer Graphics
#39
JOURNAL ARTICLE
Oscar Crisafulli, Angela Berardinelli, Giuseppe D'Antona
Hereditary proximal 5q Spinal Muscular Atrophy (SMA) is a severe neuromuscular disorder with onset mainly in infancy or childhood. The underlying pathogenic mechanism is the loss of alpha motor neurons in the anterior horns of spine, due to deficiency of the survival motor neuron (SMN) protein as a consequence of the deletion of the SMN1 gene. Clinically, SMA is characterized by progressive loss of muscle strength and motor function ranging from the extremely severe, the neonatal onset type 1, to the mild type 4 arising in the adult life...
2024: Acta Myologica: Myopathies and Cardiomyopathies: Official Journal of the Mediterranean Society of Myology
#40
REVIEW
Ioannis A Voutsadakis
In addition to genetic variants and copy number alterations, epigenetic deregulation of oncogenes and tumor suppressors is a major contributor in cancer development and propagation. Regulatory elements for gene transcription regulation can be found in promoters which are located in the vicinity of transcription start sites but also at a distance, in enhancer sites, brought to interact with proximal sites when occupied by enhancer protein complexes. These sites provide most of the specific regulatory sequences recognized by transcription factors...
2024: American Journal of Translational Research
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